Psyllid ID: psy16285

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------
Protein Sequence
HSSILDAYDLSANVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQNTL
Secondary Structure (PSIPRED)
cccccccccccccccccccccHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHHHHcHHHHHcccccEEEEcccHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
cccccccccccHHHHHHccccHHHHHHHHHHHHHcHEEEcccccccHHHHHHHHHHHHHHHHHHcccccccEEEEEEcHHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
HSSILDAYDLSANVQEELGLNTIQFEAYKAALTREFaiiqgppgtgkTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQNTL
Flexible Loop (DISEMBL)
HSSILDAYDLSANVQEELGLNTIQFEAYKAALTREFAiiqgppgtgKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQNTL
Low Complexity Region (SEG)
HSSILDAYDLSANVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQNTL
Disordered region (IsUnstruct)
******AYDLSANVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY*****
Disordered Region (DISOPRED)
****LDAYDLSANVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQNTL
Disordered Region (DISEMBL)
HSSILDAYDLSANVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQNTL
Disordered Region (DISPRO)
***ILDAYDLSANVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQNT*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
HSSILDAYDLSANVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQNTL
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	97	2.2.26 [Sep-21-2011]
Q8R151	1909	NFX1-type zinc finger-con	yes	N/A	0.773	0.039	0.597	3e-20
Q9P2E3	1918	NFX1-type zinc finger-con	yes	N/A	0.773	0.039	0.597	4e-20
O74465	999	Helicase required for RNA	yes	N/A	0.659	0.064	0.462	4e-12
Q09820	925	ATP-dependent helicase up	no	N/A	0.721	0.075	0.371	1e-07
Q9EPU0	1124	Regulator of nonsense tra	no	N/A	0.659	0.056	0.428	1e-07
Q92900	1129	Regulator of nonsense tra	no	N/A	0.659	0.056	0.428	1e-07
Q98TR3	1097	Putative regulator of non	N/A	N/A	0.680	0.060	0.416	2e-07
O76512	1069	Regulator of nonsense tra	no	N/A	0.680	0.061	0.402	2e-07
Q9VYS3	1180	Regulator of nonsense tra	no	N/A	0.659	0.054	0.4	2e-06
O60306	1485	Intron-binding protein aq	no	N/A	0.670	0.043	0.386	7e-06

>sp|Q8R151|ZNFX1_MOUSE NFX1-type zinc finger-containing protein 1 OS=Mus musculus GN=Znfx1 PE=2 SV=3

 Score = 97.1 bits (240), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 46/77 (59%), Positives = 58/77 (75%), Gaps = 2/77 (2%)

Query: 15  QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARY--MSGPI 72
           +E L L+  Q EA + ALT+E AIIQGPPGTGKTYV L+IV+  L NK + +    + PI
Sbjct: 586 KEALKLDDSQMEALQFALTKELAIIQGPPGTGKTYVGLKIVQALLTNKSVWQINTQTFPI 645

Query: 73  LIVCYTNHALDQFVEGV 89
           L+VCYTNHALDQF+EG+
Sbjct: 646 LVVCYTNHALDQFLEGI 662

Mus musculus (taxid: 10090)

>sp|Q9P2E3|ZNFX1_HUMAN NFX1-type zinc finger-containing protein 1 OS=Homo sapiens GN=ZNFX1 PE=1 SV=2

 Score = 96.3 bits (238), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 46/77 (59%), Positives = 57/77 (74%), Gaps = 2/77 (2%)

Query: 15  QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELAR--YMSGPI 72
           +E L L+  Q EA + ALTRE AIIQGPPGTGKTYV L+IV+  L N+ + +      PI
Sbjct: 593 KEALKLDDSQMEALQFALTRELAIIQGPPGTGKTYVGLKIVQALLTNESVWQISLQKFPI 652

Query: 73  LIVCYTNHALDQFVEGV 89
           L+VCYTNHALDQF+EG+
Sbjct: 653 LVVCYTNHALDQFLEGI 669

Homo sapiens (taxid: 9606)

>sp|O74465|HRR1_SCHPO Helicase required for RNAi-mediated heterochromatin assembly 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=hrr1 PE=1 SV=2

 Score = 70.1 bits (170), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 31/67 (46%), Positives = 46/67 (68%), Gaps = 3/67 (4%)

Query: 20  LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
           L++ Q +AY++ LT+  +IIQGPPGTGK++V L+ +E  L+N         PIL+ C TN
Sbjct: 372 LDSSQLKAYQSMLTKRLSIIQGPPGTGKSFVTLKAIETLLEN---THSHVLPILVACQTN 428

Query: 80  HALDQFV 86
           HA+DQ +
Sbjct: 429 HAVDQIL 435

Has a role in the RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation. A member of the RNA-directed RNA polymerase complex (RDRC) which is involved in the generation of small interfering RNAs (siRNAs) and mediate their association with the RNA-induced transcriptional silencing (RITS) complex. RITS acts as a priming complex for dsRNA synthesis at the site of non-coding centromeric RNA.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q09820|RENT1_SCHPO ATP-dependent helicase upf1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=upf1 PE=3 SV=2

 Score = 55.1 bits (131), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 39/70 (55%)

Query: 20  LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
           LN  Q EA +A L++  ++IQGPPGTGKT  +  +V      +   R    P+L+   +N
Sbjct: 393 LNASQSEAVRAVLSKPLSLIQGPPGTGKTVTSASVVYHLATMQSRKRKSHSPVLVCAPSN 452

Query: 80  HALDQFVEGV 89
            A+DQ  E +
Sbjct: 453 VAVDQLAEKI 462

Eliminates the production of nonsense-containing RNAs.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|Q9EPU0|RENT1_MOUSE Regulator of nonsense transcripts 1 OS=Mus musculus GN=Upf1 PE=1 SV=2

 Score = 55.1 bits (131), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 39/70 (55%), Gaps = 6/70 (8%)

Query: 20  LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
           LN  Q  A K  L R  ++IQGPPGTGKT  +  IV        LAR  +GP+L+   +N
Sbjct: 477 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIV------YHLARQGNGPVLVCAPSN 530

Query: 80  HALDQFVEGV 89
            A+DQ  E +
Sbjct: 531 IAVDQLTEKI 540

RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) (located 50-55 or more nucleotides downstream from the termination codon) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Phosphorylated UPF1 is recognized by EST1B/SMG5, SMG6 and SMG7 which are thought to provide a link to the mRNA degradation machinery involving exonucleolytic and endonucleolytic pathways, and to serve as adapters to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation. UPF1 can also activate NMD without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJC indicative for alternative NMD pathways. Plays a role in replication-dependent histone mRNA degradation at the end of phase S; the function is independent of UPF2. For the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. The ATPase activity of UPF1 is required for disassembly of mRNPs undergoing NMD (By similarity). Essential for embryonic viability.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|Q92900|RENT1_HUMAN Regulator of nonsense transcripts 1 OS=Homo sapiens GN=UPF1 PE=1 SV=2

 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 39/70 (55%), Gaps = 6/70 (8%)

Query: 20  LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
           LN  Q  A K  L R  ++IQGPPGTGKT  +  IV        LAR  +GP+L+   +N
Sbjct: 482 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIV------YHLARQGNGPVLVCAPSN 535

Query: 80  HALDQFVEGV 89
            A+DQ  E +
Sbjct: 536 IAVDQLTEKI 545

RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) (located 50-55 or more nucleotides downstream from the termination codon) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Phosphorylated UPF1 is recognized by EST1B/SMG5, SMG6 and SMG7 which are thought to provide a link to the mRNA degradation machinery involving exonucleolytic and endonucleolytic pathways, and to serve as adapters to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation and allowing the recycling of NMD factors. UPF1 can also activate NMD without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJC indicative for alternative NMD pathways. Plays a role in replication-dependent histone mRNA degradation at the end of phase S; the function is independent of UPF2. For the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. The ATPase activity of UPF1 is required for disassembly of mRNPs undergoing NMD. Essential for embryonic viability.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|Q98TR3|RENT1_TAKRU Putative regulator of nonsense transcripts 1 OS=Takifugu rubripes GN=rent1 PE=3 SV=1

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/72 (41%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 20  LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
           LN  Q  A K  L R  ++IQGPPGTGKT  +  IV        L+R  +GP+L+   +N
Sbjct: 453 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIV------YHLSRQGNGPVLVCAPSN 506

Query: 80  HALDQFVEGVLK 91
            A+DQ  E + K
Sbjct: 507 IAVDQLTEKIDK 518

RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. The formation of an rent1-rent2-rent3 surveillance complex is believed to activate NMD.

Takifugu rubripes (taxid: 31033)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|O76512|RENT1_CAEEL Regulator of nonsense transcripts 1 OS=Caenorhabditis elegans GN=smg-2 PE=1 SV=1

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/72 (40%), Positives = 41/72 (56%), Gaps = 6/72 (8%)

Query: 20  LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
           LN+ Q +A K  LTR  ++IQGPPGTGKT V+  IV   ++  E      G +L+   +N
Sbjct: 446 LNSSQMQAVKQVLTRPLSLIQGPPGTGKTVVSATIVYHLVQKTE------GNVLVCSPSN 499

Query: 80  HALDQFVEGVLK 91
            A+D   E + K
Sbjct: 500 IAVDHLAEKIHK 511

RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. The formation of an smg-2-3-4 surveillance complex is believed to activate NMD.

Caenorhabditis elegans (taxid: 6239)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|Q9VYS3|RENT1_DROME Regulator of nonsense transcripts 1 homolog OS=Drosophila melanogaster GN=Upf1 PE=1 SV=2

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 6/70 (8%)

Query: 20  LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
           LN  Q  A K AL R  ++IQGPPGTGKT  +  IV       +L +   G +L+   +N
Sbjct: 452 LNRSQVYAVKHALQRPLSLIQGPPGTGKTVTSATIV------YQLVKLHGGTVLVCAPSN 505

Query: 80  HALDQFVEGV 89
            A+DQ  E +
Sbjct: 506 TAVDQLTEKI 515

RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. The formation of an Upf1-Upf2-Upf3 surveillance complex is believed to activate NMD.

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|O60306|AQR_HUMAN Intron-binding protein aquarius OS=Homo sapiens GN=AQR PE=1 SV=4

 Score = 49.3 bits (116), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 41/75 (54%), Gaps = 10/75 (13%)

Query: 21  NTIQF-----EAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIV 75
           NTIQF     EA +A +     ++ GPPGTGKT VA++I+     N    R      LIV
Sbjct: 798 NTIQFTHTQIEAIRAGMQPGLTMVVGPPGTGKTDVAVQIISNIYHNFPEQR-----TLIV 852

Query: 76  CYTNHALDQFVEGVL 90
            ++N AL+Q  E ++
Sbjct: 853 THSNQALNQLFEKIM 867

Intron-binding spliceosomal protein required to link pre-mRNA splicing and snoRNP (small nucleolar ribonucleoprotein) biogenesis. Plays a key role in position-dependent assembly of intron-encoded box C/D small snoRNP, splicing being required for snoRNP assembly. May act by helping the folding of the snoRNA sequence. Binds to intron of pre-mRNAs in a sequence-independent manner, contacting the region between snoRNA and the branchpoint of introns (40 nucleotides upstream of the branchpoint) during the late stages of splicing.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	97
301617896	2091	PREDICTED: NFX1-type zinc finger-contain	0.804	0.037	0.653	9e-24
328716888	1820	PREDICTED: NFX1-type zinc finger-contain	0.855	0.045	0.554	1e-23
328716878	1999	PREDICTED: NFX1-type zinc finger-contain	0.855	0.041	0.542	7e-23
328716886	1870	PREDICTED: NFX1-type zinc finger-contain	0.855	0.044	0.554	1e-22
328721154	1744	PREDICTED: NFX1-type zinc finger-contain	0.855	0.047	0.534	2e-22
328716874	2065	PREDICTED: NFX1-type zinc finger-contain	0.855	0.040	0.530	6e-22
47222854	1452	unnamed protein product [Tetraodon nigro	0.855	0.057	0.554	6e-22
328721752	2052	PREDICTED: NFX1-type zinc finger-contain	0.948	0.044	0.5	1e-21
327288951	1876	PREDICTED: NFX1-type zinc finger-contain	0.835	0.043	0.580	2e-21
317418761	1990	NFX1-type zinc finger-containing protein	0.824	0.040	0.585	3e-21

>gi|301617896|ref|XP_002938366.1| PREDICTED: NFX1-type zinc finger-containing protein 1-like, partial [Xenopus (Silurana) tropicalis]

 Score =  114 bits (284), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 51/78 (65%), Positives = 62/78 (79%)

Query: 15  QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILI 74
           +EELGL+  QFEA K +LTRE +I+QGPPGTGKTYV L+IV   L N +L +    PILI
Sbjct: 846 KEELGLDESQFEAIKMSLTRELSIVQGPPGTGKTYVGLKIVHTLLANSDLWKTGKNPILI 905

Query: 75  VCYTNHALDQFVEGVLKY 92
           VC+TNHALDQF+EG+LKY
Sbjct: 906 VCFTNHALDQFLEGILKY 923

Source: Xenopus (Silurana) tropicalis

Species: Xenopus (Silurana) tropicalis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|328716888|ref|XP_001949997.2| PREDICTED: NFX1-type zinc finger-containing protein 1-like [Acyrthosiphon pisum]

 Score =  113 bits (283), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 46/83 (55%), Positives = 68/83 (81%)

Query: 15  QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILI 74
           +E+LGL+ +QF A+KAALT+EF +IQGPPGTGKT++ L+I++  + N    R+++ PIL+
Sbjct: 447 KEQLGLDEMQFGAFKAALTQEFTVIQGPPGTGKTFIGLKIMKTIINNLYHKRFLTKPILV 506

Query: 75  VCYTNHALDQFVEGVLKYTQNTL 97
           VCYTNHALDQF+EG+L +T+  +
Sbjct: 507 VCYTNHALDQFMEGILSFTKKVV 529

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328716878|ref|XP_001950343.2| PREDICTED: NFX1-type zinc finger-containing protein 1-like [Acyrthosiphon pisum]

 Score =  111 bits (277), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 45/83 (54%), Positives = 68/83 (81%)

Query: 15  QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILI 74
           +E+LGL+ +QF A+KAALT+EF +IQGPPGTGKT++ L+I++  + N    ++++ PIL+
Sbjct: 529 KEQLGLDEMQFGAFKAALTQEFTVIQGPPGTGKTFIGLKIMKTIINNLYDKQFLTKPILV 588

Query: 75  VCYTNHALDQFVEGVLKYTQNTL 97
           VCYTNHALDQF+EG+L +T+  +
Sbjct: 589 VCYTNHALDQFMEGILSFTKKVV 611

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328716886|ref|XP_001950310.2| PREDICTED: NFX1-type zinc finger-containing protein 1-like [Acyrthosiphon pisum]

 Score =  110 bits (274), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 46/83 (55%), Positives = 66/83 (79%)

Query: 15  QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILI 74
           +EELGL+ +Q+ A+KAALT+EF IIQGPPGTGKT++ L+I++  + N     +++ PIL+
Sbjct: 376 KEELGLDEMQYGAFKAALTQEFTIIQGPPGTGKTFIGLKIMKTIISNLYEEPFLTKPILV 435

Query: 75  VCYTNHALDQFVEGVLKYTQNTL 97
           VCYTNHALDQF+EG+L +T   +
Sbjct: 436 VCYTNHALDQFMEGILSFTNQVV 458

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328721154|ref|XP_001947220.2| PREDICTED: NFX1-type zinc finger-containing protein 1-like [Acyrthosiphon pisum]

 Score =  109 bits (272), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 46/86 (53%), Positives = 67/86 (77%), Gaps = 3/86 (3%)

Query: 15  QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNK---ELARYMSGP 71
           QE+ GL+ +Q++A+KAALT E A+IQGPPGTGKT++ L I+E  +KN     +   +  P
Sbjct: 211 QEKFGLDEMQYKAFKAALTNELAVIQGPPGTGKTFIGLMIIESIIKNVYQWNVPNRLKNP 270

Query: 72  ILIVCYTNHALDQFVEGVLKYTQNTL 97
           IL+VCYTNHALDQF+EG++++T+N +
Sbjct: 271 ILVVCYTNHALDQFMEGIVQFTKNVV 296

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328716874|ref|XP_003246062.1| PREDICTED: NFX1-type zinc finger-containing protein 1-like isoform 2 [Acyrthosiphon pisum] gi|328716876|ref|XP_001949970.2| PREDICTED: NFX1-type zinc finger-containing protein 1-like isoform 1 [Acyrthosiphon pisum]

 Score =  108 bits (269), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 44/83 (53%), Positives = 65/83 (78%)

Query: 15  QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILI 74
           +E+LGL+ +QF A++AALT EF +IQGPPGTGKT++ L+I++  + N     +++ PIL+
Sbjct: 563 KEQLGLDEMQFGAFRAALTHEFTVIQGPPGTGKTFIGLKIMKTIINNLYDKPFLTKPILV 622

Query: 75  VCYTNHALDQFVEGVLKYTQNTL 97
           VCYTNHALDQF+EG+L +T   +
Sbjct: 623 VCYTNHALDQFMEGILSFTNKVI 645

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|47222854|emb|CAF96521.1| unnamed protein product [Tetraodon nigroviridis]

 Score =  107 bits (268), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 46/83 (55%), Positives = 65/83 (78%)

Query: 15  QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILI 74
           +E LGL+  Q EA++ ALT+E AIIQGPPGTGKTYV L+I +  L N++L +  + P+L+
Sbjct: 436 KERLGLDGSQMEAFQLALTKELAIIQGPPGTGKTYVGLKIAQALLSNQDLWKEDNAPMLV 495

Query: 75  VCYTNHALDQFVEGVLKYTQNTL 97
           VCYTNHALDQF+EG+ K+ ++ +
Sbjct: 496 VCYTNHALDQFLEGIHKFLESDI 518

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|328721752|ref|XP_001946566.2| PREDICTED: NFX1-type zinc finger-containing protein 1-like [Acyrthosiphon pisum]

 Score =  107 bits (266), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 47/94 (50%), Positives = 70/94 (74%), Gaps = 2/94 (2%)

Query: 4   ILDAYDLSANVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKE 63
           IL+ Y+     +E+L L+ +Q++A++AALT+EF +IQGPPGTGKT++ L+I+E  + N  
Sbjct: 540 ILNKYEWPT--EEQLKLDGMQYKAFRAALTQEFTVIQGPPGTGKTFIGLKIMETIINNLY 597

Query: 64  LARYMSGPILIVCYTNHALDQFVEGVLKYTQNTL 97
               +S PIL+VCYTNHALDQF+EG+L +T   +
Sbjct: 598 KNPCLSKPILVVCYTNHALDQFMEGILNFTNKVI 631

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|327288951|ref|XP_003229188.1| PREDICTED: NFX1-type zinc finger-containing protein 1-like [Anolis carolinensis]

 Score =  106 bits (265), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 47/81 (58%), Positives = 59/81 (72%)

Query: 15  QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILI 74
           +E LGL+  Q EA + ALT+E AIIQGPPGTGKTYV L+IV   L N    R  S P+L+
Sbjct: 543 KETLGLDETQLEALRLALTKELAIIQGPPGTGKTYVGLKIVRALLANGATGRVHSSPMLV 602

Query: 75  VCYTNHALDQFVEGVLKYTQN 95
           VCYTNHALDQF+EG+  + ++
Sbjct: 603 VCYTNHALDQFLEGIHTFQED 623

Source: Anolis carolinensis

Species: Anolis carolinensis

Genus: Anolis

Family: Iguanidae

Order: Squamata

Phylum: Chordata

Superkingdom: Eukaryota

>gi|317418761|emb|CBN80799.1| NFX1-type zinc finger-containing protein 1 [Dicentrarchus labrax]

 Score =  105 bits (263), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 48/82 (58%), Positives = 64/82 (78%), Gaps = 2/82 (2%)

Query: 16  EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYM--SGPIL 73
           EELGL+  Q +A++ ALT+E AIIQGPPGTGKTYV L+I +  L N+EL R    + P+L
Sbjct: 666 EELGLDESQMQAFQLALTKELAIIQGPPGTGKTYVGLKIAQALLTNQELWRSKLDTVPML 725

Query: 74  IVCYTNHALDQFVEGVLKYTQN 95
           +VCYTNHALDQF+EG+ K+ ++
Sbjct: 726 VVCYTNHALDQFLEGIHKFLKD 747

Source: Dicentrarchus labrax

Species: Dicentrarchus labrax

Genus: Dicentrarchus

Family: Moronidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	97
MGI|MGI:2138982	1909	Znfx1 "zinc finger, NFX1-type	0.773	0.039	0.597	2.4e-17
UNIPROTKB|Q9P2E3	1918	ZNFX1 "NFX1-type zinc finger-c	0.773	0.039	0.597	4e-17
POMBASE|SPCC1739.03	999	hrr1 "Helicase Required for RN	0.659	0.064	0.462	1.2e-10
ASPGD|ASPL0000069352	2310	AN7246 [Emericella nidulans (t	0.721	0.030	0.434	8.4e-10
WB|WBGene00014208	2443	ZK1067.2 [Caenorhabditis elega	0.618	0.024	0.426	1.3e-08
GENEDB_PFALCIPARUM|MAL7P1.12	2283	MAL7P1.12 "erythrocyte membran	0.845	0.035	0.397	6.1e-07
UNIPROTKB|Q8IC35	2283	MAL7P1.12 "Erythrocyte membran	0.845	0.035	0.397	6.1e-07
POMBASE|SPAC16C9.06c	925	upf1 "ATP-dependent RNA helica	0.721	0.075	0.371	9.5e-07
ZFIN|ZDB-GENE-040426-2836	1100	upf1 "upf1 regulator of nonsen	0.659	0.058	0.428	2.4e-06
UNIPROTKB|E1C0J4	1117	UPF1 "Uncharacterized protein"	0.659	0.057	0.428	2.5e-06

MGI|MGI:2138982 Znfx1 "zinc finger, NFX1-type containing 1" [Mus musculus (taxid:10090)]

 Score = 228 (85.3 bits), Expect = 2.4e-17, P = 2.4e-17
 Identities = 46/77 (59%), Positives = 58/77 (75%)

Query:    15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARY--MSGPI 72
             +E L L+  Q EA + ALT+E AIIQGPPGTGKTYV L+IV+  L NK + +    + PI
Sbjct:   586 KEALKLDDSQMEALQFALTKELAIIQGPPGTGKTYVGLKIVQALLTNKSVWQINTQTFPI 645

Query:    73 LIVCYTNHALDQFVEGV 89
             L+VCYTNHALDQF+EG+
Sbjct:   646 LVVCYTNHALDQFLEGI 662

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|Q9P2E3 ZNFX1 "NFX1-type zinc finger-containing protein 1" [Homo sapiens (taxid:9606)]

 Score = 226 (84.6 bits), Expect = 4.0e-17, P = 4.0e-17
 Identities = 46/77 (59%), Positives = 57/77 (74%)

Query:    15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARY--MSGPI 72
             +E L L+  Q EA + ALTRE AIIQGPPGTGKTYV L+IV+  L N+ + +      PI
Sbjct:   593 KEALKLDDSQMEALQFALTRELAIIQGPPGTGKTYVGLKIVQALLTNESVWQISLQKFPI 652

Query:    73 LIVCYTNHALDQFVEGV 89
             L+VCYTNHALDQF+EG+
Sbjct:   653 LVVCYTNHALDQFLEGI 669

GO:0046872 "metal ion binding" evidence=IEA

POMBASE|SPCC1739.03 hrr1 "Helicase Required for RNAi-mediated heterochromatin assembly Hrr1" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 162 (62.1 bits), Expect = 1.2e-10, P = 1.2e-10
 Identities = 31/67 (46%), Positives = 48/67 (71%)

Query:    20 LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
             L++ Q +AY++ LT+  +IIQGPPGTGK++V L+ +E  L+N   +  +  PIL+ C TN
Sbjct:   372 LDSSQLKAYQSMLTKRLSIIQGPPGTGKSFVTLKAIETLLENTH-SHVL--PILVACQTN 428

Query:    80 HALDQFV 86
             HA+DQ +
Sbjct:   429 HAVDQIL 435

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0006338 "chromatin remodeling" evidence=NAS

GO:0030702 "chromatin silencing at centromere" evidence=IMP

GO:0031048 "chromatin silencing by small RNA" evidence=IMP

GO:0031379 "RNA-directed RNA polymerase complex" evidence=IDA

GO:0031380 "nuclear RNA-directed RNA polymerase complex" evidence=IDA

ASPGD|ASPL0000069352 AN7246 [Emericella nidulans (taxid:162425)]

 Score = 158 (60.7 bits), Expect = 8.4e-10, P = 8.4e-10
 Identities = 33/76 (43%), Positives = 50/76 (65%)

Query:    15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILI 74
             ++ L L+  Q E+  + LT+  ++IQGPPGTGK++V      G L  K L ++    IL+
Sbjct:   457 EKPLSLDPSQMESLLSGLTQRVSLIQGPPGTGKSFV------GALIAKALYKHSKETILV 510

Query:    75 VCYTNHALDQFVEGVL 90
             +CYTNHALDQF+E ++
Sbjct:   511 MCYTNHALDQFLEDLM 526

GO:0005575 "cellular_component" evidence=ND

GO:0005525 "GTP binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0006614 "SRP-dependent cotranslational protein targeting to membrane" evidence=IEA

WB|WBGene00014208 ZK1067.2 [Caenorhabditis elegans (taxid:6239)]

 Score = 147 (56.8 bits), Expect = 1.3e-08, P = 1.3e-08
 Identities = 26/61 (42%), Positives = 44/61 (72%)

Query:    35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ 94
             E ++IQGPPGTGKT++ ++IV+  L+N+   + ++ PIL+VC+TN  LD  +E + +  +
Sbjct:  1055 ELSLIQGPPGTGKTHIGVQIVKTILQNRSYWK-ITEPILVVCFTNSGLDNLLERIYQMIE 1113

Query:    95 N 95
             N
Sbjct:  1114 N 1114

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GENEDB_PFALCIPARUM|MAL7P1.12 MAL7P1.12 "erythrocyte membrane-associated antigen" [Plasmodium falciparum (taxid:5833)]

 Score = 131 (51.2 bits), Expect = 6.1e-07, P = 6.1e-07
 Identities = 35/88 (39%), Positives = 49/88 (55%)

Query:     5 LDAYDL-SANVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKE 63
             +D Y + S N+   L LN  Q  A  +ALTR   ++QGPPGTGKT+VA  I++ + K   
Sbjct:  1761 IDKYLIESINLPTNLPLNDSQKLACLSALTRRLTLVQGPPGTGKTHVACAIIDSWHKQNS 1820

Query:    64 LARYMSGPILIVCYTNHALDQFVEGVLK 91
               +     IL V  +N A +  VEG+ K
Sbjct:  1821 NKK-----ILAVADSNVAANNLVEGLKK 1843

GO:0016020 "membrane" evidence=ISS

UNIPROTKB|Q8IC35 MAL7P1.12 "Erythrocyte membrane-associated antigen" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 131 (51.2 bits), Expect = 6.1e-07, P = 6.1e-07
 Identities = 35/88 (39%), Positives = 49/88 (55%)

Query:     5 LDAYDL-SANVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKE 63
             +D Y + S N+   L LN  Q  A  +ALTR   ++QGPPGTGKT+VA  I++ + K   
Sbjct:  1761 IDKYLIESINLPTNLPLNDSQKLACLSALTRRLTLVQGPPGTGKTHVACAIIDSWHKQNS 1820

Query:    64 LARYMSGPILIVCYTNHALDQFVEGVLK 91
               +     IL V  +N A +  VEG+ K
Sbjct:  1821 NKK-----ILAVADSNVAANNLVEGLKK 1843

GO:0016020 "membrane" evidence=ISS

POMBASE|SPAC16C9.06c upf1 "ATP-dependent RNA helicase Upf1" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 125 (49.1 bits), Expect = 9.5e-07, P = 9.5e-07
 Identities = 26/70 (37%), Positives = 39/70 (55%)

Query:    20 LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
             LN  Q EA +A L++  ++IQGPPGTGKT  +  +V      +   R    P+L+   +N
Sbjct:   393 LNASQSEAVRAVLSKPLSLIQGPPGTGKTVTSASVVYHLATMQSRKRKSHSPVLVCAPSN 452

Query:    80 HALDQFVEGV 89
              A+DQ  E +
Sbjct:   453 VAVDQLAEKI 462

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=ISO

GO:0002184 "cytoplasmic translational termination" evidence=NAS

GO:0003677 "DNA binding" evidence=IEA

GO:0004004 "ATP-dependent RNA helicase activity" evidence=ISO

GO:0005524 "ATP binding" evidence=IC

GO:0005737 "cytoplasm" evidence=ISO

GO:0005829 "cytosol" evidence=IDA

GO:0006415 "translational termination" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

ZFIN|ZDB-GENE-040426-2836 upf1 "upf1 regulator of nonsense transcripts homolog (yeast)" [Danio rerio (taxid:7955)]

 Score = 122 (48.0 bits), Expect = 2.4e-06, P = 2.4e-06
 Identities = 30/70 (42%), Positives = 39/70 (55%)

Query:    20 LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
             LN  Q  A K  L R  ++IQGPPGTGKT  +  IV        LAR  +GP+L+   +N
Sbjct:   451 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVY------HLARQGNGPVLVCAPSN 504

Query:    80 HALDQFVEGV 89
              A+DQ  E +
Sbjct:   505 IAVDQLTEKI 514

GO:0003677 "DNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA;IMP

GO:0005524 "ATP binding" evidence=IEA

GO:0009790 "embryo development" evidence=IMP

UNIPROTKB|E1C0J4 UPF1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 122 (48.0 bits), Expect = 2.5e-06, P = 2.5e-06
 Identities = 30/70 (42%), Positives = 39/70 (55%)

Query:    20 LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
             LN  Q  A K  L R  ++IQGPPGTGKT  +  IV        LAR  +GP+L+   +N
Sbjct:   470 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVY------HLARQGNGPVLVCAPSN 523

Query:    80 HALDQFVEGV 89
              A+DQ  E +
Sbjct:   524 IAVDQLTEKI 533

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8R151	ZNFX1_MOUSE	No assigned EC number	0.5974	0.7731	0.0392	yes	N/A
Q9P2E3	ZNFX1_HUMAN	No assigned EC number	0.5974	0.7731	0.0391	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	97
pfam13086	220	pfam13086, AAA_11, AAA domain	1e-10
pfam13245	73	pfam13245, AAA_19, Part of AAA domain	8e-08
TIGR00376	637	TIGR00376, TIGR00376, DNA helicase, putative	1e-07
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	9e-06
pfam04851	100	pfam04851, ResIII, Type III restriction enzyme, re	4e-05
pfam09848	348	pfam09848, DUF2075, Uncharacterized conserved prot	3e-04
pfam13604	195	pfam13604, AAA_30, AAA domain	6e-04
COG1199	654	COG1199, DinG, Rad3-related DNA helicases [Transcr	7e-04
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	0.001
TIGR01448	720	TIGR01448, recD_rel, helicase, putative, RecD/TraA	0.002
PRK10875	615	PRK10875, recD, exonuclease V subunit alpha; Provi	0.003
TIGR01447	586	TIGR01447, recD, exodeoxyribonuclease V, alpha sub	0.004

>gnl|CDD|221912 pfam13086, AAA_11, AAA domain

 Score = 55.1 bits (133), Expect = 1e-10
 Identities = 30/74 (40%), Positives = 40/74 (54%), Gaps = 8/74 (10%)

Query: 20 LNTIQFEAYKAALTRE-FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSG-PILIVCY 77
          LN  Q EA K AL+     +IQGPPGTGKT     IVE     K+L     G  +L+   
Sbjct: 2  LNDSQREAIKKALSSSDITLIQGPPGTGKTTT---IVEII---KQLLSNAPGKKVLVCAP 55

Query: 78 TNHALDQFVEGVLK 91
          +N A+D  +E +L+
Sbjct: 56 SNSAVDNILERLLE 69

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. Length = 220

>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain

 Score = 45.0 bits (107), Expect = 8e-08
 Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 8/63 (12%)

Query: 26 EAYKAALTRE-FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQ 84
          EA +AA +     ++ G PGTGKT  A  I+   L            +L+V  T  A  +
Sbjct: 1  EAVEAAASGRSLFVVDGGPGTGKTATAAAIIARLLAAGR-------SVLVVAPTGRAARR 53

Query: 85 FVE 87
            E
Sbjct: 54 LRE 56

Length = 73

>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative

 Score = 47.1 bits (112), Expect = 1e-07
 Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 8/79 (10%)

Query: 20  LNTIQFEAYKAAL-TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT 78
           LN  Q EA   AL +++  +I GPPGTGKT   + ++   +K           +L+   +
Sbjct: 158 LNESQKEAVLFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKRGL-------RVLVTAPS 210

Query: 79  NHALDQFVEGVLKYTQNTL 97
           N A+D  +E +    Q  +
Sbjct: 211 NIAVDNLLERLALCDQKIV 229

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases [DNA metabolism, DNA replication, recombination, and repair]. Length = 637

>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]

 Score = 42.0 bits (99), Expect = 9e-06
 Identities = 18/71 (25%), Positives = 23/71 (32%), Gaps = 17/71 (23%)

Query: 15 QEELGLNTIQFEAYKAALTRE-FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPIL 73
          QEE        +A       E   +I  P G GKT VA                +    L
Sbjct: 41 QEE------ALDALVKNRRTERRGVIVLPTGAGKTVVAAEA----------IAELKRSTL 84

Query: 74 IVCYTNHALDQ 84
          ++  T   LDQ
Sbjct: 85 VLVPTKELLDQ 95

Length = 442

>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit

 Score = 38.7 bits (91), Expect = 4e-05
 Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 7/68 (10%)

Query: 17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC 76
          +L L   Q EA +  L ++  +I    G+GKT  A  ++    K K+        +L V 
Sbjct: 1  KLELRPYQEEAIERLLEKKRGLIVMATGSGKTLTAAALIARLAKGKK-------KVLFVV 53

Query: 77 YTNHALDQ 84
               L+Q
Sbjct: 54 PRKDLLEQ 61

Length = 100

>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075)

 Score = 37.6 bits (88), Expect = 3e-04
 Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 10/58 (17%)

Query: 38 IIQGPPGTGKTYVALRIVE--GFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT 93
          ++ G PGTGKT VAL +            A ++SG        NH L   +   L   
Sbjct: 5  LVTGGPGTGKTVVALNLFAELSDSDLGRTAVFLSG--------NHPLVLVLYEALAGD 54

This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function. Length = 348

>gnl|CDD|222258 pfam13604, AAA_30, AAA domain

 Score = 36.4 bits (85), Expect = 6e-04
 Identities = 17/41 (41%), Positives = 21/41 (51%), Gaps = 4/41 (9%)

Query: 19 GLNTIQFEAYKAALT--REFAIIQGPPGTGKTYV--ALRIV 55
           L+  Q EA +  LT     A++QGP GTGKT    A R  
Sbjct: 1  TLSAEQREAVRHVLTSGDRVAVVQGPAGTGKTTSLKAAREA 41

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B. Length = 195

>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

 Score = 36.7 bits (85), Expect = 7e-04
 Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 6/63 (9%)

Query: 25 FEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQ 84
              +A    E  +I+ P GTGKT   L     +      AR     ++I   T    +Q
Sbjct: 25 EAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAY------AREEGKKVIISTRTKALQEQ 78

Query: 85 FVE 87
           +E
Sbjct: 79 LLE 81

Length = 654

>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 20 LNTIQFEAYKAALTREF-AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT 78
          L   Q EA +A L+     I+  P G+GKT  AL         + L R   G +L++  T
Sbjct: 9  LRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPAL-----EALKRGKGGRVLVLVPT 63

Query: 79 NHALDQFVEGVLKYTQNT 96
              +Q+ E + K   + 
Sbjct: 64 RELAEQWAEELKKLGPSL 81

Length = 201

>gnl|CDD|233418 TIGR01448, recD_rel, helicase, putative, RecD/TraA family

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 16/47 (34%), Positives = 24/47 (51%)

Query: 18  LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKEL 64
            GL+  Q +A   A+  +  I+ G PGTGKT +   I+E   +   L
Sbjct: 322 KGLSEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGGL 368

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD [Unknown function, Enzymes of unknown specificity]. Length = 720

>gnl|CDD|236783 PRK10875, recD, exonuclease V subunit alpha; Provisional

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 12/18 (66%), Positives = 14/18 (77%)

Query: 31  ALTREFAIIQGPPGTGKT 48
           ALTR  ++I G PGTGKT
Sbjct: 164 ALTRRISVISGGPGTGKT 181

Length = 615

>gnl|CDD|233417 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit

 Score = 34.7 bits (80), Expect = 0.004
 Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 4/47 (8%)

Query: 9   DLSANVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIV 55
           +L   + E+      Q  A   AL   F++I G PGTGKT    R++
Sbjct: 139 NLFPLLNEQ----NWQKVAVALALKSNFSLITGGPGTGKTTTVARLL 181

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model [DNA metabolism, DNA replication, recombination, and repair]. Length = 586

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	97
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	99.72
KOG1803|consensus	649		99.66
TIGR00376	637	DNA helicase, putative. The gene product may repre	99.63
KOG1802|consensus	935		99.62
PF13245	76	AAA_19: Part of AAA domain	99.61
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	99.5
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	99.47
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.38
PHA02558	501	uvsW UvsW helicase; Provisional	99.34
KOG1805|consensus	1100		99.34
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.34
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.34
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	99.31
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.31
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	99.29
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	99.28
PRK11054	684	helD DNA helicase IV; Provisional	99.28
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	99.28
PRK10875	615	recD exonuclease V subunit alpha; Provisional	99.27
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	99.27
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.23
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	99.21
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.2
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	99.2
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.17
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	99.17
PRK08181	269	transposase; Validated	99.17
PTZ00424	401	helicase 45; Provisional	99.16
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.15
KOG1807|consensus	1025		99.14
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.14
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.14
PRK01172	674	ski2-like helicase; Provisional	99.12
PRK09401	1176	reverse gyrase; Reviewed	99.11
KOG0354|consensus	746		99.11
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	99.09
PRK05580	679	primosome assembly protein PriA; Validated	99.09
PRK06526	254	transposase; Provisional	99.09
COG1484	254	DnaC DNA replication protein [DNA replication, rec	99.09
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.08
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.08
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	99.07
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.06
PRK13889	988	conjugal transfer relaxase TraA; Provisional	99.06
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.05
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.05
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.05
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.05
PRK02362	737	ski2-like helicase; Provisional	99.01
PTZ00110	545	helicase; Provisional	99.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	98.99
PRK13766	773	Hef nuclease; Provisional	98.99
PRK10689	1147	transcription-repair coupling factor; Provisional	98.99
PRK00254	720	ski2-like helicase; Provisional	98.97
COG4096	875	HsdR Type I site-specific restriction-modification	98.96
PRK12377	248	putative replication protein; Provisional	98.95
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	98.94
PRK13826	1102	Dtr system oriT relaxase; Provisional	98.94
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	98.93
PRK09183	259	transposase/IS protein; Provisional	98.93
PRK06835	329	DNA replication protein DnaC; Validated	98.93
PRK14701	1638	reverse gyrase; Provisional	98.93
PRK07952	244	DNA replication protein DnaC; Validated	98.92
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.92
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	98.92
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	98.89
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	98.88
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	98.87
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	98.85
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	98.84
PRK10536	262	hypothetical protein; Provisional	98.84
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	98.82
PRK13767	876	ATP-dependent helicase; Provisional	98.8
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	98.79
COG3973	747	Superfamily I DNA and RNA helicases [General funct	98.78
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.77
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	98.77
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	98.75
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.74
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.74
PRK08116	268	hypothetical protein; Validated	98.74
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	98.73
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	98.72
PRK08939	306	primosomal protein DnaI; Reviewed	98.71
KOG1806|consensus	1320		98.71
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	98.7
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	98.7
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.7
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.69
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.69
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	98.68
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	98.67
PRK06921	266	hypothetical protein; Provisional	98.67
PRK09694	878	helicase Cas3; Provisional	98.67
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	98.66
COG1204	766	Superfamily II helicase [General function predicti	98.65
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	98.64
PHA00729	226	NTP-binding motif containing protein	98.64
KOG0330|consensus	476		98.64
PHA02653	675	RNA helicase NPH-II; Provisional	98.64
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.63
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	98.62
PRK08533	230	flagellar accessory protein FlaH; Reviewed	98.62
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.62
PRK08084	235	DNA replication initiation factor; Provisional	98.62
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	98.6
TIGR00595	505	priA primosomal protein N'. All proteins in this f	98.6
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.59
PRK06893	229	DNA replication initiation factor; Validated	98.59
COG1201	814	Lhr Lhr-like helicases [General function predictio	98.59
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.58
PRK08727	233	hypothetical protein; Validated	98.58
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	98.57
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.57
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	98.56
smart00382	148	AAA ATPases associated with a variety of cellular	98.55
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.55
PRK05642	234	DNA replication initiation factor; Validated	98.54
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.53
PRK06067	234	flagellar accessory protein FlaH; Validated	98.53
PRK04328	249	hypothetical protein; Provisional	98.52
PRK05973	237	replicative DNA helicase; Provisional	98.5
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	98.49
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.48
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	98.47
PF00004	132	AAA: ATPase family associated with various cellula	98.46
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.46
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	98.46
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.46
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	98.45
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	98.44
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	98.44
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	98.44
KOG0952|consensus	1230		98.43
COG4889	1518	Predicted helicase [General function prediction on	98.43
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	98.42
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.42
PRK13833	323	conjugal transfer protein TrbB; Provisional	98.42
TIGR00609	1087	recB exodeoxyribonuclease V, beta subunit. All pro	98.42
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	98.41
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	98.4
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	98.4
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.4
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.4
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.4
COG1205	851	Distinct helicase family with a unique C-terminal	98.4
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.39
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.38
KOG0331|consensus	519		98.38
KOG1123|consensus	776		98.38
PLN03025	319	replication factor C subunit; Provisional	98.36
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	98.35
KOG0744|consensus	423		98.35
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	98.35
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	98.35
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	98.34
PRK00149	450	dnaA chromosomal replication initiation protein; R	98.34
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	98.33
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	98.33
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.33
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	98.32
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	98.32
TIGR02237	209	recomb_radB DNA repair and recombination protein R	98.31
PRK14974	336	cell division protein FtsY; Provisional	98.31
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.31
KOG0335|consensus	482		98.31
PRK12422	445	chromosomal replication initiation protein; Provis	98.3
KOG0991|consensus	333		98.29
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.29
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	98.29
PRK04195	482	replication factor C large subunit; Provisional	98.27
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	98.27
PRK05298	652	excinuclease ABC subunit B; Provisional	98.27
KOG0345|consensus	567		98.26
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	98.26
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	98.26
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.26
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	98.26
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.25
CHL00181	287	cbbX CbbX; Provisional	98.25
PRK11823	446	DNA repair protein RadA; Provisional	98.24
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	98.24
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.24
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	98.23
PRK09302	509	circadian clock protein KaiC; Reviewed	98.23
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.23
TIGR00064	272	ftsY signal recognition particle-docking protein F	98.23
KOG0989|consensus	346		98.23
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	98.23
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	98.22
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.22
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.21
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	98.2
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.2
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.2
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	98.2
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	98.19
PRK04296	190	thymidine kinase; Provisional	98.19
PRK10416	318	signal recognition particle-docking protein FtsY;	98.19
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	98.18
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	98.18
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	98.18
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	98.18
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	98.17
PHA02544	316	44 clamp loader, small subunit; Provisional	98.17
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	98.17
PHA02244	383	ATPase-like protein	98.17
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	98.17
PRK10436	462	hypothetical protein; Provisional	98.17
cd01394	218	radB RadB. The archaeal protein radB shares simila	98.16
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	98.16
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	98.16
PRK12402	337	replication factor C small subunit 2; Reviewed	98.15
TIGR02533	486	type_II_gspE general secretory pathway protein E.	98.15
KOG0328|consensus	400		98.15
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	98.15
PRK08118	167	topology modulation protein; Reviewed	98.14
PRK09302	509	circadian clock protein KaiC; Reviewed	98.14
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	98.14
KOG2028|consensus	554		98.14
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	98.13
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.13
KOG0922|consensus	674		98.12
PRK13342	413	recombination factor protein RarA; Reviewed	98.12
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	98.12
cd03115	173	SRP The signal recognition particle (SRP) mediates	98.12
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	98.12
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	98.12
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	98.12
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	98.12
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	98.1
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	98.1
KOG0731|consensus	774		98.1
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	98.1
KOG0948|consensus	1041		98.09
PF05729	166	NACHT: NACHT domain	98.09
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	98.09
PRK06620	214	hypothetical protein; Validated	98.08
PRK10876	1181	recB exonuclease V subunit beta; Provisional	98.08
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	98.08
PRK13909	910	putative recombination protein RecB; Provisional	98.07
KOG0743|consensus	457		98.07
PRK14086	617	dnaA chromosomal replication initiation protein; P	98.07
KOG0342|consensus	543		98.07
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.07
PF13173	128	AAA_14: AAA domain	98.05
cd00983	325	recA RecA is a bacterial enzyme which has roles in	98.05
KOG0920|consensus	924		98.05
PF12846	304	AAA_10: AAA-like domain	98.04
PRK13531	498	regulatory ATPase RavA; Provisional	98.04
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	98.04
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	98.04
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	98.04
PRK14530	215	adenylate kinase; Provisional	98.04
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	98.03
KOG0348|consensus	708		98.03
PRK03992	389	proteasome-activating nucleotidase; Provisional	98.03
COG0593	408	DnaA ATPase involved in DNA replication initiation	98.03
PRK00771	437	signal recognition particle protein Srp54; Provisi	98.02
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	98.01
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	98.01
PRK10867	433	signal recognition particle protein; Provisional	98.01
PRK03839	180	putative kinase; Provisional	98.01
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	98.01
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	98.0
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	98.0
CHL00195	489	ycf46 Ycf46; Provisional	98.0
KOG0947|consensus	1248		98.0
PRK00131	175	aroK shikimate kinase; Reviewed	97.99
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.99
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	97.99
PRK05541	176	adenylylsulfate kinase; Provisional	97.99
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	97.99
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.99
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	97.99
PRK06762	166	hypothetical protein; Provisional	97.98
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	97.98
PRK00889	175	adenylylsulfate kinase; Provisional	97.98
KOG0340|consensus	442		97.97
PRK13851	344	type IV secretion system protein VirB11; Provision	97.97
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	97.97
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	97.97
PRK07261	171	topology modulation protein; Provisional	97.97
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.96
PRK14532	188	adenylate kinase; Provisional	97.96
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	97.95
TIGR00959	428	ffh signal recognition particle protein. This mode	97.95
PRK14531	183	adenylate kinase; Provisional	97.95
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	97.95
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	97.95
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	97.94
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	97.94
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.94
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	97.94
PRK06851	367	hypothetical protein; Provisional	97.93
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	97.92
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	97.92
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	97.92
PRK09354	349	recA recombinase A; Provisional	97.92
PRK08233	182	hypothetical protein; Provisional	97.92
COG0714	329	MoxR-like ATPases [General function prediction onl	97.92
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	97.92
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.92
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	97.91
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	97.91
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	97.91
CHL00095	821	clpC Clp protease ATP binding subunit	97.91
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	97.91
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	97.91
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	97.91
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.9
PRK09200	790	preprotein translocase subunit SecA; Reviewed	97.9
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.9
PRK13947	171	shikimate kinase; Provisional	97.9
PRK13341	725	recombination factor protein RarA/unknown domain f	97.89
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	97.89
KOG0338|consensus	691		97.89
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.89
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	97.88
TIGR00665	434	DnaB replicative DNA helicase. This model describe	97.88
PRK13764	602	ATPase; Provisional	97.88
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	97.88
KOG3347|consensus	176		97.88
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	97.88
PTZ00301	210	uridine kinase; Provisional	97.88
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.88
PRK06851	367	hypothetical protein; Provisional	97.88
PRK12608	380	transcription termination factor Rho; Provisional	97.87
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	97.86
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	97.86
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	97.86
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.85
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	97.85
KOG0739|consensus	439		97.85
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.85
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	97.84
PRK02496	184	adk adenylate kinase; Provisional	97.84
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	97.84
PRK13768	253	GTPase; Provisional	97.84
PRK06217	183	hypothetical protein; Validated	97.83
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	97.83
KOG0350|consensus	620		97.83
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	97.83
PRK14528	186	adenylate kinase; Provisional	97.83
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	97.83
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	97.82
KOG0343|consensus	758		97.82
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	97.82
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	97.82
COG3842	352	PotA ABC-type spermidine/putrescine transport syst	97.82
PRK14527	191	adenylate kinase; Provisional	97.82
KOG0327|consensus	397		97.82
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	97.82
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	97.82
PRK05480	209	uridine/cytidine kinase; Provisional	97.82
PHA02624	647	large T antigen; Provisional	97.82
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	97.81
PRK06696	223	uridine kinase; Validated	97.81
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	97.81
PF13555	62	AAA_29: P-loop containing region of AAA domain	97.81
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.81
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	97.8
PRK07667	193	uridine kinase; Provisional	97.8
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	97.8
COG1702	348	PhoH Phosphate starvation-inducible protein PhoH,	97.8
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	97.8
PRK13949	169	shikimate kinase; Provisional	97.8
PRK04914	956	ATP-dependent helicase HepA; Validated	97.8
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	97.8
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	97.79
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	97.79
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.79
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	97.79
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	97.78
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	97.78
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	97.78
KOG0923|consensus	902		97.78
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	97.78
PLN02200	234	adenylate kinase family protein	97.78
KOG0334|consensus	997		97.78
PLN02165	334	adenylate isopentenyltransferase	97.78
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	97.77
KOG0344|consensus	593		97.77
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	97.77
PRK09087	226	hypothetical protein; Validated	97.77
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	97.77
PRK04040	188	adenylate kinase; Provisional	97.77
KOG0346|consensus	569		97.76
KOG0733|consensus	802		97.76
PRK00279	215	adk adenylate kinase; Reviewed	97.76
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	97.76
PTZ00088	229	adenylate kinase 1; Provisional	97.75
PRK05748	448	replicative DNA helicase; Provisional	97.75
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	97.75
PRK10865	857	protein disaggregation chaperone; Provisional	97.75
PRK00625	173	shikimate kinase; Provisional	97.74
cd03114	148	ArgK-like The function of this protein family is u	97.74
PRK06547	172	hypothetical protein; Provisional	97.74
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.74
PRK00300	205	gmk guanylate kinase; Provisional	97.74
COG0606	490	Predicted ATPase with chaperone activity [Posttran	97.74
PRK09435	332	membrane ATPase/protein kinase; Provisional	97.74
KOG0727|consensus	408		97.74
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	97.74
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	97.73
TIGR00235	207	udk uridine kinase. Model contains a number of lon	97.73
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.73
KOG1970|consensus	634		97.72
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	97.72
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	97.72
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	97.72
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	97.7
PRK08506	472	replicative DNA helicase; Provisional	97.7
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	97.7
KOG0738|consensus	491		97.7
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	97.7
PRK13765	637	ATP-dependent protease Lon; Provisional	97.7
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	97.7
PRK04301	317	radA DNA repair and recombination protein RadA; Va	97.69
cd01128	249	rho_factor Transcription termination factor rho is	97.69
PRK09825	176	idnK D-gluconate kinase; Provisional	97.69
PRK08760	476	replicative DNA helicase; Provisional	97.69
PRK03846	198	adenylylsulfate kinase; Provisional	97.69
PRK05057	172	aroK shikimate kinase I; Reviewed	97.68
cd02034	116	CooC The accessory protein CooC, which contains a	97.68
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	97.68
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	97.68
PF02492	178	cobW: CobW/HypB/UreG, nucleotide-binding domain; I	97.68
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	97.68
KOG1533|consensus	290		97.68
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.68
PHA02530	300	pseT polynucleotide kinase; Provisional	97.67
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.67
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	97.66
KOG0733|consensus	802		97.66
KOG0741|consensus	744		97.66
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	97.66
CHL00176	638	ftsH cell division protein; Validated	97.66
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	97.65
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	97.65
PF07726	131	AAA_3: ATPase family associated with various cellu	97.65
PRK09376	416	rho transcription termination factor Rho; Provisio	97.64
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.64
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.64
KOG0329|consensus	387		97.63
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	97.63
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	97.63
PRK15453	290	phosphoribulokinase; Provisional	97.63
TIGR02236	310	recomb_radA DNA repair and recombination protein R	97.63
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	97.63
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	97.62
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.62
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	97.62
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	97.62
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	97.62
PHA02774	613	E1; Provisional	97.62
PRK14526	211	adenylate kinase; Provisional	97.61
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	97.61
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	97.61
PRK05595	444	replicative DNA helicase; Provisional	97.61
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.61
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.61
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.61
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	97.6
PRK14529	223	adenylate kinase; Provisional	97.6
KOG0951|consensus	1674		97.6
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	97.6
PLN02674	244	adenylate kinase	97.59
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	97.59
PHA02542	473	41 41 helicase; Provisional	97.59
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	97.59
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	97.58
PF00005	137	ABC_tran: ABC transporter This structure is on hol	97.58
PRK00698	205	tmk thymidylate kinase; Validated	97.58
KOG0730|consensus	693		97.58
KOG0736|consensus	953		97.58
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	97.58
PRK14738	206	gmk guanylate kinase; Provisional	97.57
TIGR00767	415	rho transcription termination factor Rho. Members	97.57
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	97.57
KOG0734|consensus	752		97.57
PRK10865	857	protein disaggregation chaperone; Provisional	97.57
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.57
PRK01184	184	hypothetical protein; Provisional	97.56
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	97.56
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.56
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	97.56
COG3911	183	Predicted ATPase [General function prediction only	97.56
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	97.55
PTZ00202	550	tuzin; Provisional	97.55
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	97.55
PRK03731	171	aroL shikimate kinase II; Reviewed	97.55
PRK13946	184	shikimate kinase; Provisional	97.54
PRK14737	186	gmk guanylate kinase; Provisional	97.54
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	97.54
KOG0949|consensus	1330		97.54
PRK15455	644	PrkA family serine protein kinase; Provisional	97.54
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	97.53
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	97.53
PRK13975	196	thymidylate kinase; Provisional	97.53

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=99.72  E-value=2.3e-17  Score=106.52  Aligned_cols=73  Identities=37%  Similarity=0.465  Sum_probs=55.8

Q ss_pred             CCCHHHHHHHHHHhcCCc-eEEeCCCCCchHHHHHHHHHHHHhch-hhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         19 GLNTIQFEAYKAALTREF-AIIQGPPGTGKTYVALRIVEGFLKNK-ELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~-~~v~Gp~GtGKT~~~~~~~~~~~~~~-~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      .||+.|++|+..+..... .+|+||||||||+++..++..+.+.. ......+.++|+++++|.+++++.+++.+
T Consensus         1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            378999999999998876 99999999999999999998884210 00011588999999999999999999988

>KOG1803|consensus

Probab=99.66  E-value=2.6e-16  Score=113.18  Aligned_cols=74  Identities=32%  Similarity=0.464  Sum_probs=65.4

Q ss_pred             ccCCCCCHHHHHHHHHHhcC-CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         15 QEELGLNTIQFEAYKAALTR-EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~-~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .-...++..|.+|+..+... ...+|.||||||||+++..++.+++.+       +++||+|+|||.+++++.+++.-.+
T Consensus       181 ~~~~~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~-------~k~VLVcaPSn~AVdNiverl~~~~  253 (649)
T KOG1803|consen  181 FFNKNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQ-------KKRVLVCAPSNVAVDNIVERLTHLK  253 (649)
T ss_pred             cCCccccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHc-------CCeEEEEcCchHHHHHHHHHhcccc
Confidence            34567899999999998866 788999999999999999999999998       7999999999999999999977544


Q ss_pred             cC
Q psy16285         94 QN   95 (97)
Q Consensus        94 ~~   95 (97)
                      .+
T Consensus       254 ~~  255 (649)
T KOG1803|consen  254 LN  255 (649)
T ss_pred             cc
Confidence            33

>TIGR00376 DNA helicase, putative

Probab=99.63  E-value=1.9e-15  Score=111.13  Aligned_cols=69  Identities=32%  Similarity=0.479  Sum_probs=62.8

Q ss_pred             CCCCHHHHHHHHHHhcC-CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         18 LGLNTIQFEAYKAALTR-EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~-~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..+++.|.+++..+... +.++|.||||||||+++..++.++++.       +.+||+++|||.|++++.+++.+.+
T Consensus       156 ~~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~~-------g~~VLv~a~sn~Avd~l~e~l~~~~  225 (637)
T TIGR00376       156 PNLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKR-------GLRVLVTAPSNIAVDNLLERLALCD  225 (637)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHHc-------CCCEEEEcCcHHHHHHHHHHHHhCC
Confidence            57899999999998876 789999999999999999999998876       6699999999999999999998753

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

>KOG1802|consensus

Probab=99.62  E-value=1.3e-15  Score=110.92  Aligned_cols=79  Identities=37%  Similarity=0.504  Sum_probs=71.2

Q ss_pred             cccccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         12 ANVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        12 ~~~~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      +....-..||..|..|++.+++++..+|+||||||||.+...|+.++.+.      ...+||+++|+|.|+|++.+++.+
T Consensus       403 ~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~------~~~~VLvcApSNiAVDqLaeKIh~  476 (935)
T KOG1802|consen  403 FSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ------HAGPVLVCAPSNIAVDQLAEKIHK  476 (935)
T ss_pred             hcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHh------cCCceEEEcccchhHHHHHHHHHh
Confidence            34456677899999999999999999999999999999999999999988      588999999999999999999988


Q ss_pred             hccCC
Q psy16285         92 YTQNT   96 (97)
Q Consensus        92 ~~~~~   96 (97)
                      .+..+
T Consensus       477 tgLKV  481 (935)
T KOG1802|consen  477 TGLKV  481 (935)
T ss_pred             cCceE
Confidence            77554

>PF13245 AAA_19: Part of AAA domain

Probab=99.61  E-value=4.3e-15  Score=82.49  Aligned_cols=60  Identities=30%  Similarity=0.445  Sum_probs=47.9

Q ss_pred             HHHHHhc-CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         27 AYKAALT-REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        27 ~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      ++..+.. ++.++|.||||||||+++..++..+......   .+++|++++|++.+++++.+++
T Consensus         2 av~~al~~~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~---~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen    2 AVRRALAGSPLFVVQGPPGTGKTTTLAARIAELLAARAD---PGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             HHHHHHhhCCeEEEECCCCCCHHHHHHHHHHHHHHHhcC---CCCeEEEECCCHHHHHHHHHHH
Confidence            4454444 6677789999999999988888888753211   3679999999999999999998

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=99.50  E-value=2.3e-13  Score=87.51  Aligned_cols=64  Identities=33%  Similarity=0.409  Sum_probs=52.1

Q ss_pred             CCCHHHHHHHHHHhcC--CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         19 GLNTIQFEAYKAALTR--EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~--~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      +|++.|.+++..+..+  +..+|+||||||||+++..+...+...       +.++++++||+.++.++.++.
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~-------g~~v~~~apT~~Aa~~L~~~~   66 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLLKALAEALEAA-------GKRVIGLAPTNKAAKELREKT   66 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHHHHT-------T--EEEEESSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHHHhC-------CCeEEEECCcHHHHHHHHHhh
Confidence            4789999999998754  478889999999999988877777665       789999999999999988874

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=99.47  E-value=2e-13  Score=91.73  Aligned_cols=69  Identities=22%  Similarity=0.273  Sum_probs=57.5

Q ss_pred             CCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         20 LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        20 l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      |+++|.+++..  ..+.++|.|+||||||+++...+..++...+.   ++.+||++++|+.++.++.+++.+..
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~---~~~~Il~lTft~~aa~e~~~ri~~~l   69 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGV---PPERILVLTFTNAAAQEMRERIRELL   69 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSS---TGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccC---ChHHheecccCHHHHHHHHHHHHHhc
Confidence            57889999886  67889999999999999998888888877532   57899999999999999999998864

THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=99.38  E-value=4e-12  Score=79.46  Aligned_cols=67  Identities=24%  Similarity=0.391  Sum_probs=56.5

Q ss_pred             CCCCHHHHHHHHHHhc-------CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         18 LGLNTIQFEAYKAALT-------REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~-------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      +.|+++|.+++..+.+       .+.+++.+|+|+|||.++..++..+..          ++++++|+...++|+.+.+.
T Consensus         2 ~~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~----------~~l~~~p~~~l~~Q~~~~~~   71 (184)
T PF04851_consen    2 YKLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR----------KVLIVAPNISLLEQWYDEFD   71 (184)
T ss_dssp             -EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC----------EEEEEESSHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc----------ceeEecCHHHHHHHHHHHHH
Confidence            5689999999999884       578999999999999999987777744          69999999999999999996


Q ss_pred             hhcc
Q psy16285         91 KYTQ   94 (97)
Q Consensus        91 ~~~~   94 (97)
                      .+..
T Consensus        72 ~~~~   75 (184)
T PF04851_consen   72 DFGS   75 (184)
T ss_dssp             HHST
T ss_pred             Hhhh
Confidence            5553

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.34  E-value=1.1e-11  Score=89.34  Aligned_cols=71  Identities=20%  Similarity=0.401  Sum_probs=62.3

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...++++|.+++..+..+...++.+|+|+|||.++..++..+...      ...++||++|+.+++.|+.+++.++.
T Consensus       112 ~~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~------~~~~vLilvpt~eL~~Q~~~~l~~~~  182 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLEN------YEGKVLIIVPTTSLVTQMIDDFVDYR  182 (501)
T ss_pred             cCCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhc------CCCeEEEEECcHHHHHHHHHHHHHhc
Confidence            468999999999999988889999999999999987777666555      24489999999999999999999876

>KOG1805|consensus

Probab=99.34  E-value=3.7e-12  Score=95.81  Aligned_cols=73  Identities=29%  Similarity=0.385  Sum_probs=65.7

Q ss_pred             CCCCCHHHHHHHHHHhcC-CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         17 ELGLNTIQFEAYKAALTR-EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~-~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      ...||..|++|+..+... ...+|.|-|||||||++..++..+...       +++||+.++|+.|+++++.+|+.++..
T Consensus       667 ~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~LIkiL~~~-------gkkVLLtsyThsAVDNILiKL~~~~i~  739 (1100)
T KOG1805|consen  667 LLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVAL-------GKKVLLTSYTHSAVDNILIKLKGFGIY  739 (1100)
T ss_pred             HhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHHHHHHHHHc-------CCeEEEEehhhHHHHHHHHHHhccCcc
Confidence            447899999999998864 578999999999999999999999887       899999999999999999999988754


Q ss_pred             C
Q psy16285         96 T   96 (97)
Q Consensus        96 ~   96 (97)
                      +
T Consensus       740 ~  740 (1100)
T KOG1805|consen  740 I  740 (1100)
T ss_pred             e
Confidence            3

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=99.34  E-value=1.8e-11  Score=75.87  Aligned_cols=70  Identities=26%  Similarity=0.330  Sum_probs=58.4

Q ss_pred             CHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         21 NTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        21 ~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      ++.|.+++..+.+++++++.||+|+|||+.+...+...+.+.     ...++++++|+..++.+..+++.+++..
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~-----~~~~~lii~P~~~l~~q~~~~~~~~~~~   70 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG-----KDARVLIIVPTRALAEQQFERLRKFFSN   70 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT-----SSSEEEEEESSHHHHHHHHHHHHHHTTT
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC-----CCceEEEEeecccccccccccccccccc
Confidence            378999999999888999999999999998776655555441     2459999999999999999999998754

Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]

Probab=99.34  E-value=1.1e-11  Score=88.20  Aligned_cols=71  Identities=31%  Similarity=0.384  Sum_probs=63.2

Q ss_pred             cccCCCCCHHHHHHHHHHhc----CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         14 VQEELGLNTIQFEAYKAALT----REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        14 ~~~~~~l~~~Q~~~i~~~~~----~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      ....+.++++|.++++.+.+    .+..+|..|||+|||.+++.++..+          ..++||++|+.++++||.+++
T Consensus        31 ~~~~~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~----------~~~~Lvlv~~~~L~~Qw~~~~  100 (442)
T COG1061          31 VAFEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAEL----------KRSTLVLVPTKELLDQWAEAL  100 (442)
T ss_pred             cccCCCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHh----------cCCEEEEECcHHHHHHHHHHH
Confidence            45677899999999999998    7899999999999999999998887          555999999999999999888


Q ss_pred             Hhhcc
Q psy16285         90 LKYTQ   94 (97)
Q Consensus        90 ~~~~~   94 (97)
                      ..+..
T Consensus       101 ~~~~~  105 (442)
T COG1061         101 KKFLL  105 (442)
T ss_pred             HHhcC
Confidence            87764

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=99.31  E-value=8.4e-12  Score=92.59  Aligned_cols=70  Identities=23%  Similarity=0.231  Sum_probs=59.8

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .|++.|++++..  ..+.++|.|+||||||+++...+.+++.....   ++.+||++++|+.|+.++.+++.+..
T Consensus         2 ~Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v---~p~~IL~lTFT~kAA~em~~Rl~~~l   71 (672)
T PRK10919          2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGY---QARHIAAVTFTNKAAREMKERVAQTL   71 (672)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCC---CHHHeeeEechHHHHHHHHHHHHHHh
Confidence            589999999875  35678899999999999999999999875322   47899999999999999999998764

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.31  E-value=4.5e-11  Score=74.71  Aligned_cols=74  Identities=28%  Similarity=0.271  Sum_probs=62.3

Q ss_pred             cCCCCCHHHHHHHHHHhcC-CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTR-EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~-~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ....+++.|.+++..+... ...++.||+|||||+++...+.......     ...++++++|+..++.++.+.+.++..
T Consensus         5 ~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~-----~~~~~l~~~p~~~~~~~~~~~~~~~~~   79 (201)
T smart00487        5 GFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRG-----KGKRVLVLVPTRELAEQWAEELKKLGP   79 (201)
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhccc-----CCCcEEEEeCCHHHHHHHHHHHHHHhc
Confidence            4567899999999998888 8999999999999997666666665552     257899999999999999999987763

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=99.29  E-value=1.4e-11  Score=92.01  Aligned_cols=71  Identities=23%  Similarity=0.244  Sum_probs=60.8

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .|++.|++++..  ..+.++|.|+||||||+++...+.+++.....   ++.+||++++||.|+.++.+++.+...
T Consensus         9 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v---~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773          9 SLNDKQREAVAA--PLGNMLVLAGAGSGKTRVLVHRIAWLMQVENA---SPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             hcCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCC---ChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            489999999874  35678999999999999999999999875333   578999999999999999999988653

>TIGR01075 uvrD DNA helicase II

Probab=99.28  E-value=1.1e-11  Score=92.38  Aligned_cols=71  Identities=25%  Similarity=0.257  Sum_probs=61.0

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .|++.|++++..  ..+.++|.|+||||||+++...+.+++.....   ++.+||++++||.|+.++.+++.+...
T Consensus         4 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v---~p~~IL~lTFTnkAA~em~~Rl~~~~~   74 (715)
T TIGR01075         4 GLNDKQREAVAA--PPGNLLVLAGAGSGKTRVLTHRIAWLLSVENA---SPHSIMAVTFTNKAAAEMRHRIGALLG   74 (715)
T ss_pred             ccCHHHHHHHcC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCC---CHHHeEeeeccHHHHHHHHHHHHHHhc
Confidence            489999999874  35678999999999999999999999875333   578999999999999999999988753

Designed to identify uvrD members of the uvrD/rep subfamily.

>PRK11054 helD DNA helicase IV; Provisional

Probab=99.28  E-value=7.3e-12  Score=93.00  Aligned_cols=75  Identities=20%  Similarity=0.214  Sum_probs=62.7

Q ss_pred             cccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         14 VQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        14 ~~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..+..+|++.|++++..  ..+.++|.|+||||||+++...+.+++.....   .+.+||++++++.++.++.+++.+..
T Consensus       191 ~~e~~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~---~~~~IL~ltft~~AA~em~eRL~~~l  265 (684)
T PRK11054        191 QVESSPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQA---QPEQILLLAFGRQAAEEMDERIRERL  265 (684)
T ss_pred             hccCCCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCC---CHHHeEEEeccHHHHHHHHHHHHHhc
Confidence            34557899999999874  34568999999999999999999988876432   46799999999999999999998754

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=99.28  E-value=3.2e-11  Score=88.30  Aligned_cols=69  Identities=29%  Similarity=0.330  Sum_probs=58.1

Q ss_pred             HHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         22 TIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        22 ~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ++|+.++..+..+...+|+|+|||||||++..++..+.+.....  ...+|++++||..|+.++.+.+...
T Consensus       148 ~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~--~~~~I~l~APTGkAA~rL~e~~~~~  216 (586)
T TIGR01447       148 NWQKVAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQ--GKLRIALAAPTGKAAARLAESLRKA  216 (586)
T ss_pred             HHHHHHHHHHhhCCeEEEEcCCCCCHHHHHHHHHHHHHHhcccc--CCCcEEEECCcHHHHHHHHHHHHhh
Confidence            78999999999999999999999999999999998887642100  1257999999999999999987653

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=99.27  E-value=2.7e-11  Score=89.08  Aligned_cols=69  Identities=28%  Similarity=0.308  Sum_probs=58.6

Q ss_pred             CCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         20 LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        20 l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      ..++|+.|+..+..++..+|+|+|||||||++..++..+.+....   +..+|++++||+.|+.++.+.+..
T Consensus       153 ~~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~---~~~~i~l~APTgkAA~rL~e~~~~  221 (615)
T PRK10875        153 EVDWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLADG---ERCRIRLAAPTGKAAARLTESLGK  221 (615)
T ss_pred             CCHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCC---CCcEEEEECCcHHHHHHHHHHHHh
Confidence            348999999999999999999999999999999999888664110   246799999999999999998764

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=99.27  E-value=2.9e-11  Score=90.28  Aligned_cols=68  Identities=28%  Similarity=0.278  Sum_probs=58.6

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      ..+.+++.|++++..+..++..+|+|+||||||+++..++..+...+     +..++++++||..++.++.+.
T Consensus       320 ~~~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l~~i~~~~~~~~-----~~~~v~l~ApTg~AA~~L~e~  387 (720)
T TIGR01448       320 LRKGLSEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELG-----GLLPVGLAAPTGRAAKRLGEV  387 (720)
T ss_pred             cCCCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHHHHHHHHHHHcC-----CCceEEEEeCchHHHHHHHHh
Confidence            45789999999999999889999999999999999999988776651     126899999999999988764

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.23  E-value=9.9e-11  Score=87.23  Aligned_cols=68  Identities=16%  Similarity=0.266  Sum_probs=58.8

Q ss_pred             cCCCCCHHHHHHHHHHhcC---CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         16 EELGLNTIQFEAYKAALTR---EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ....++++|.+++..+...   ++.+|..|+|+|||.++..++..+          .+++||+||+..+++||.+++.+|
T Consensus       252 ~~~~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~l----------~k~tLILvps~~Lv~QW~~ef~~~  321 (732)
T TIGR00603       252 PTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTV----------KKSCLVLCTSAVSVEQWKQQFKMW  321 (732)
T ss_pred             cCCCcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHHh----------CCCEEEEeCcHHHHHHHHHHHHHh
Confidence            4577999999999998853   378999999999999988776654          567999999999999999999988


Q ss_pred             c
Q psy16285         93 T   93 (97)
Q Consensus        93 ~   93 (97)
                      .
T Consensus       322 ~  322 (732)
T TIGR00603       322 S  322 (732)
T ss_pred             c
Confidence            5

All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=99.21  E-value=4.6e-11  Score=89.23  Aligned_cols=70  Identities=31%  Similarity=0.329  Sum_probs=60.3

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .|++.|++++..  ..+.++|.|+||||||+++...+.+++.....   .+.+||++++||.|+.++.+++.+..
T Consensus         4 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i---~P~~IL~lTFT~kAA~em~~Rl~~~~   73 (726)
T TIGR01073         4 HLNPEQREAVKT--TEGPLLIMAGAGSGKTRVLTHRIAHLIAEKNV---APWNILAITFTNKAAREMKERVEKLL   73 (726)
T ss_pred             ccCHHHHHHHhC--CCCCEEEEeCCCCCHHHHHHHHHHHHHHcCCC---CHHHeeeeeccHHHHHHHHHHHHHHh
Confidence            489999999874  35679999999999999999999999875332   46899999999999999999998764

Designed to identify pcrA members of the uvrD/rep subfamily.

>cd00268 DEADc DEAD-box helicases

Probab=99.20  E-value=2.7e-10  Score=72.85  Aligned_cols=74  Identities=24%  Similarity=0.137  Sum_probs=58.8

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHH-HHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         18 LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVA-LRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~-~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ..+++.|.+++..+.+++++++.+|+|+|||.+. ..++..+.....   ..+.++++++|+..++.|+.+.++++..
T Consensus        20 ~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~---~~~~~viii~p~~~L~~q~~~~~~~~~~   94 (203)
T cd00268          20 EKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPK---KDGPQALILAPTRELALQIAEVARKLGK   94 (203)
T ss_pred             CCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcc---cCCceEEEEcCCHHHHHHHHHHHHHHhc
Confidence            3578999999999999999999999999999873 444444443310   0356899999999999999999888753

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=99.20  E-value=8.2e-11  Score=87.05  Aligned_cols=69  Identities=28%  Similarity=0.267  Sum_probs=58.7

Q ss_pred             CCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         20 LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        20 l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      |++.|++++..  ..+.++|.|+||||||+++...+..++.....   ++.+||++++|+.++.++.+++.+..
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~---~p~~IL~vTFt~~Aa~em~~Rl~~~l   70 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGY---KARNIAAVTFTNKAAREMKERVAKTL   70 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCC---CHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            78999999874  35789999999999999999999888864222   47899999999999999999998754

Designed to identify rep members of the uvrD/rep subfamily.

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.17  E-value=3.3e-10  Score=80.14  Aligned_cols=78  Identities=24%  Similarity=0.168  Sum_probs=59.2

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHH-HHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRI-VEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~-~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +...+++.|.+++..+.++..+++.+|||+|||..+... +..+...... .....++++++|+.+++.|+.+.+..+..
T Consensus        20 g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~-~~~~~~~lil~Pt~eLa~Q~~~~~~~l~~   98 (434)
T PRK11192         20 GYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRR-KSGPPRILILTPTRELAMQVADQARELAK   98 (434)
T ss_pred             CCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhcccc-CCCCceEEEECCcHHHHHHHHHHHHHHHc
Confidence            445678999999999999999999999999999865433 3333322100 01246899999999999999998888753

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=99.17  E-value=1.7e-10  Score=86.50  Aligned_cols=66  Identities=18%  Similarity=0.262  Sum_probs=56.6

Q ss_pred             cCCCCCHHHHHHHHHHhc-CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      ..+.|++.|++++..+.. ++.++|+|+||||||+++..+...+...       +.++++++||..++..+.+.
T Consensus       349 ~~~~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll~~i~~~~~~~-------g~~V~~~ApTg~Aa~~L~~~  415 (744)
T TIGR02768       349 QHYRLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTMLKAAREAWEAA-------GYRVIGAALSGKAAEGLQAE  415 (744)
T ss_pred             ccCCCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHHHHHHHHHHhC-------CCeEEEEeCcHHHHHHHHhc
Confidence            357899999999999886 4688999999999999999887766554       78899999999999988753

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PRK08181 transposase; Validated

Probab=99.17  E-value=2.8e-10  Score=76.52  Aligned_cols=51  Identities=25%  Similarity=0.318  Sum_probs=41.4

Q ss_pred             CCCHHHHHHHHHH----hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         19 GLNTIQFEAYKAA----LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        19 ~l~~~Q~~~i~~~----~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      .++..|..++..+    ..+.++++.|||||||||++.+++..+++.       +.+++++.
T Consensus        87 ~~~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~Aia~~a~~~-------g~~v~f~~  141 (269)
T PRK08181         87 MVSKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAAAIGLALIEN-------GWRVLFTR  141 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHHHHHHHHHHc-------CCceeeee
Confidence            4567777777543    356789999999999999999999999877       67787776

>PTZ00424 helicase 45; Provisional

Probab=99.16  E-value=3.5e-10  Score=78.97  Aligned_cols=73  Identities=23%  Similarity=0.102  Sum_probs=58.7

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...+++.|.+++..+.++...++.+|||+|||.++...+...+....    ...++++++|+.+++.|+.+.+..++
T Consensus        48 ~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~----~~~~~lil~Pt~~L~~Q~~~~~~~~~  120 (401)
T PTZ00424         48 FEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDL----NACQALILAPTRELAQQIQKVVLALG  120 (401)
T ss_pred             CCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCC----CCceEEEECCCHHHHHHHHHHHHHHh
Confidence            34589999999999999999999999999999876544444433211    35689999999999999998887775

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.15  E-value=3.6e-10  Score=84.13  Aligned_cols=73  Identities=21%  Similarity=0.165  Sum_probs=61.8

Q ss_pred             ccCCCCCHHHHHHHHHHhcC------CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALTR------EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~------~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      .-.+.+++.|.+++..+..+      .+.+++||+|||||.++...+...+..       +.++++++||.+++.|..+.
T Consensus       257 ~l~f~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~-------g~q~lilaPT~~LA~Q~~~~  329 (681)
T PRK10917        257 SLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA-------GYQAALMAPTEILAEQHYEN  329 (681)
T ss_pred             hCCCCCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc-------CCeEEEEeccHHHHHHHHHH
Confidence            35678999999999998764      378999999999999877666655554       77899999999999999999


Q ss_pred             HHhhcc
Q psy16285         89 VLKYTQ   94 (97)
Q Consensus        89 l~~~~~   94 (97)
                      +.++..
T Consensus       330 l~~l~~  335 (681)
T PRK10917        330 LKKLLE  335 (681)
T ss_pred             HHHHHh
Confidence            998764

>KOG1807|consensus

Probab=99.14  E-value=1.2e-10  Score=86.46  Aligned_cols=76  Identities=43%  Similarity=0.630  Sum_probs=65.2

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      .+...++..|+.|.......+..+++||||||||++...++..++.+.-.+ ....++++.|.||.+++|+..++..
T Consensus       374 ~g~~ildsSq~~A~qs~ltyelsliqgppGTgkt~vtlkav~tLL~n~s~~-~~~epIlvvC~Tnhavdq~ligiy~  449 (1025)
T KOG1807|consen  374 PGLVILDSSQQFAKQSKLTYELSLIQGPPGTGKTLVTLKAVDTLLLNSSGY-TEPEPILVVCLTNHAVDQYLIGIYY  449 (1025)
T ss_pred             CCceeecHHHHHHHHHHhhhhhheeecCCCCCceeehHHHHHHHHhccccc-ccccceeeeehhhHHHHHHHHHHHh
Confidence            355667889999999999999999999999999999999999998874111 1468999999999999999999875

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.14  E-value=5.7e-10  Score=79.54  Aligned_cols=73  Identities=21%  Similarity=0.254  Sum_probs=57.6

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHH-HHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVAL-RIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~-~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +...+++.|.+++..+.++..+++.+|||||||.... .++..+....     ...++++++||.+++.|+.+.++.+.
T Consensus        23 g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~-----~~~~~lil~PtreLa~Q~~~~~~~~~   96 (460)
T PRK11776         23 GYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKR-----FRVQALVLCPTRELADQVAKEIRRLA   96 (460)
T ss_pred             CCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhcc-----CCceEEEEeCCHHHHHHHHHHHHHHH
Confidence            3445889999999999999999999999999997643 3334332221     24579999999999999999988765

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.14  E-value=4.2e-10  Score=83.11  Aligned_cols=73  Identities=19%  Similarity=0.179  Sum_probs=60.6

Q ss_pred             ccCCCCCHHHHHHHHHHhcC------CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALTR------EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~------~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      .-.+.+++.|++++..+..+      .+.+++||+|||||.++...+...+..       +.++++++||.+++.|+.+.
T Consensus       231 ~lpf~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~-------g~qvlilaPT~~LA~Q~~~~  303 (630)
T TIGR00643       231 SLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA-------GYQVALMAPTEILAEQHYNS  303 (630)
T ss_pred             hCCCCCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc-------CCcEEEECCHHHHHHHHHHH
Confidence            34678999999999988753      257999999999999876655555554       67899999999999999999


Q ss_pred             HHhhcc
Q psy16285         89 VLKYTQ   94 (97)
Q Consensus        89 l~~~~~   94 (97)
                      +++++.
T Consensus       304 ~~~l~~  309 (630)
T TIGR00643       304 LRNLLA  309 (630)
T ss_pred             HHHHhc
Confidence            998764

>PRK01172 ski2-like helicase; Provisional

Probab=99.12  E-value=6.6e-10  Score=82.51  Aligned_cols=70  Identities=16%  Similarity=0.097  Sum_probs=59.2

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ..+.+++.|.+++..+.+++++++.+|||+|||.++...+...+..       +.++++++|+++++.+..+++.++
T Consensus        19 ~~~~l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~-------~~k~v~i~P~raLa~q~~~~~~~l   88 (674)
T PRK01172         19 NDFELYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA-------GLKSIYIVPLRSLAMEKYEELSRL   88 (674)
T ss_pred             CCCCCCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh-------CCcEEEEechHHHHHHHHHHHHHH
Confidence            4567899999999999889999999999999999866555444443       568999999999999999998865

>PRK09401 reverse gyrase; Reviewed

Probab=99.11  E-value=6.5e-10  Score=86.61  Aligned_cols=71  Identities=25%  Similarity=0.175  Sum_probs=60.5

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ++.+.+.|+.++..+..+.++++.+|||+|||+.+..++..+..       .+.++++++||++++.|+.+++.+++.
T Consensus        78 G~~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~f~l~~~~~l~~-------~g~~alIL~PTreLa~Qi~~~l~~l~~  148 (1176)
T PRK09401         78 GSKPWSLQRTWAKRLLLGESFAIIAPTGVGKTTFGLVMSLYLAK-------KGKKSYIIFPTRLLVEQVVEKLEKFGE  148 (1176)
T ss_pred             CCCCcHHHHHHHHHHHCCCcEEEEcCCCCCHHHHHHHHHHHHHh-------cCCeEEEEeccHHHHHHHHHHHHHHhh
Confidence            45789999999999999999999999999999865555444432       378899999999999999999998874

>KOG0354|consensus

Probab=99.11  E-value=3.7e-10  Score=83.78  Aligned_cols=77  Identities=25%  Similarity=0.311  Sum_probs=68.5

Q ss_pred             CcccccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         11 SANVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        11 ~~~~~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      .|..+..+.++++|.+.+..++ +.+++|..|+|+|||.+|..++...++..     +..+|+|++|+..++.|-...+.
T Consensus        54 ~~~~p~~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~-----p~~KiVF~aP~~pLv~QQ~a~~~  127 (746)
T KOG0354|consen   54 RWIYPTNLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWR-----PKGKVVFLAPTRPLVNQQIACFS  127 (746)
T ss_pred             cccccCcccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcC-----CcceEEEeeCCchHHHHHHHHHh
Confidence            3455678999999999999999 99999999999999999999998888874     56899999999999999887777


Q ss_pred             hhc
Q psy16285         91 KYT   93 (97)
Q Consensus        91 ~~~   93 (97)
                      .++
T Consensus       128 ~~~  130 (746)
T KOG0354|consen  128 IYL  130 (746)
T ss_pred             hcc
Confidence            766

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=99.09  E-value=3.3e-10  Score=78.94  Aligned_cols=60  Identities=22%  Similarity=0.290  Sum_probs=51.9

Q ss_pred             CCCHHHHHHHHHH------hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHH
Q psy16285         19 GLNTIQFEAYKAA------LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQF   85 (97)
Q Consensus        19 ~l~~~Q~~~i~~~------~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~   85 (97)
                      .|+++|+.+++.+      .++.+++|.||.|||||+++.++...+...       +..+++++||..|+..+
T Consensus         1 ~Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~~~~~-------~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    1 KLNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDYLRSR-------GKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHHHHHHHhccc-------cceEEEecchHHHHHhc
Confidence            4789999999888      456789999999999999999988877443       67899999999998877

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.09  E-value=1.1e-09  Score=81.49  Aligned_cols=71  Identities=23%  Similarity=0.184  Sum_probs=62.0

Q ss_pred             cCCCCCHHHHHHHHHHhcC---CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         16 EELGLNTIQFEAYKAALTR---EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ....+++.|+++++.+..+   ..+++.||||+|||.+...++...+..       ++++++++|+.+++.|+.++++++
T Consensus       141 ~~~~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~-------g~~vLvLvPt~~L~~Q~~~~l~~~  213 (679)
T PRK05580        141 EPPTLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ-------GKQALVLVPEIALTPQMLARFRAR  213 (679)
T ss_pred             CCCCCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHc-------CCeEEEEeCcHHHHHHHHHHHHHH
Confidence            4567999999999998863   679999999999999988777777665       678999999999999999999886


Q ss_pred             c
Q psy16285         93 T   93 (97)
Q Consensus        93 ~   93 (97)
                      +
T Consensus       214 f  214 (679)
T PRK05580        214 F  214 (679)
T ss_pred             h
Confidence            5

>PRK06526 transposase; Provisional

Probab=99.09  E-value=2e-10  Score=76.68  Aligned_cols=51  Identities=24%  Similarity=0.322  Sum_probs=38.3

Q ss_pred             CCCHHHHHHH---HHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         19 GLNTIQFEAY---KAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        19 ~l~~~Q~~~i---~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      .++..|...+   +++..++++++.||||||||+++.+++..++..       +.++++.+
T Consensus        80 ~~~~~~~~~l~~~~fi~~~~nlll~Gp~GtGKThLa~al~~~a~~~-------g~~v~f~t  133 (254)
T PRK06526         80 SLKRDTIAHLGTLDFVTGKENVVFLGPPGTGKTHLAIGLGIRACQA-------GHRVLFAT  133 (254)
T ss_pred             CcchHHHHHHhcCchhhcCceEEEEeCCCCchHHHHHHHHHHHHHC-------CCchhhhh
Confidence            3444444433   344457899999999999999999999999876       66777765

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=99.09  E-value=5.1e-10  Score=74.71  Aligned_cols=48  Identities=27%  Similarity=0.439  Sum_probs=38.7

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ++.++++.||||+||||++.+++..++..       +.+|+++.     +.+++.+|+..
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~~~-------g~sv~f~~-----~~el~~~Lk~~  151 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELLKA-------GISVLFIT-----APDLLSKLKAA  151 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHc-------CCeEEEEE-----HHHHHHHHHHH
Confidence            46799999999999999999999999943       78898888     55555555443

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.08  E-value=1.3e-09  Score=80.62  Aligned_cols=73  Identities=18%  Similarity=0.128  Sum_probs=58.2

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHH-HHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALR-IVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~-~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ....+++.|.+++..+..+..+++++|||||||..... ++..+....     ...++||++||++++.|+.+.+.++.
T Consensus        25 G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~-----~~~~~LIL~PTreLa~Qv~~~l~~~~   98 (629)
T PRK11634         25 GYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPEL-----KAPQILVLAPTRELAVQVAEAMTDFS   98 (629)
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhcc-----CCCeEEEEeCcHHHHHHHHHHHHHHH
Confidence            45568999999999999999999999999999986433 333332221     24589999999999999999888764

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.08  E-value=8.6e-10  Score=65.30  Aligned_cols=55  Identities=24%  Similarity=0.350  Sum_probs=47.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +++++.||||+|||+++...+..+....     ...++++++|++.++.++.+.+..+..
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~-----~~~~~lv~~p~~~l~~~~~~~~~~~~~   55 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSL-----KGGQVLVLAPTRELANQVAERLKELFG   55 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcc-----cCCCEEEEcCcHHHHHHHHHHHHHHhh
Confidence            3578999999999999888888887652     368999999999999999998887763

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=99.07  E-value=5.6e-10  Score=70.94  Aligned_cols=48  Identities=27%  Similarity=0.495  Sum_probs=37.1

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ++.++++.||||||||+++.+++..++..       +.+++++.     ..++++.++..
T Consensus        46 ~~~~l~l~G~~G~GKThLa~ai~~~~~~~-------g~~v~f~~-----~~~L~~~l~~~   93 (178)
T PF01695_consen   46 NGENLILYGPPGTGKTHLAVAIANEAIRK-------GYSVLFIT-----ASDLLDELKQS   93 (178)
T ss_dssp             C--EEEEEESTTSSHHHHHHHHHHHHHHT-------T--EEEEE-----HHHHHHHHHCC
T ss_pred             cCeEEEEEhhHhHHHHHHHHHHHHHhccC-------CcceeEee-----cCceecccccc
Confidence            45789999999999999999999999887       78898888     56666666543

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.06  E-value=2.1e-09  Score=76.75  Aligned_cols=79  Identities=22%  Similarity=0.125  Sum_probs=59.4

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHH-HHHHHhchhh-hhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRI-VEGFLKNKEL-ARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~-~~~~~~~~~~-~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ....+++.|.+++..+..+..+++.+|||||||...... +..+...... ....+.++||++||++++.|+.+.+.++.
T Consensus        20 g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil~PtreLa~Qi~~~~~~~~   99 (456)
T PRK10590         20 GYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYS   99 (456)
T ss_pred             CCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEEeCcHHHHHHHHHHHHHHh
Confidence            445678999999999999999999999999999875443 3443332110 01123479999999999999999998875


Q ss_pred             c
Q psy16285         94 Q   94 (97)
Q Consensus        94 ~   94 (97)
                      .
T Consensus       100 ~  100 (456)
T PRK10590        100 K  100 (456)
T ss_pred             c
Confidence            3

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=99.06  E-value=9.9e-10  Score=84.25  Aligned_cols=65  Identities=18%  Similarity=0.171  Sum_probs=53.7

Q ss_pred             cCCCCCHHHHHHHHHHhc-CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVE   87 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~   87 (97)
                      ..+.|++.|++++..+.. ++.++|+|++||||||++..+...+...       +.+|+.++||..++..+.+
T Consensus       343 ~g~~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~l~~~~~~~e~~-------G~~V~~~ApTGkAA~~L~e  408 (988)
T PRK13889        343 RGLVLSGEQADALAHVTDGRDLGVVVGYAGTGKSAMLGVAREAWEAA-------GYEVRGAALSGIAAENLEG  408 (988)
T ss_pred             cCCCCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHHHHHHHHHHHHc-------CCeEEEecCcHHHHHHHhh
Confidence            357899999999999887 4578999999999999976655554333       7889999999999988865

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.05  E-value=1.9e-09  Score=82.41  Aligned_cols=72  Identities=18%  Similarity=0.101  Sum_probs=59.8

Q ss_pred             cCCCCCHHHHHHHHHHhcC------CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALTR------EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~------~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      -.+.+++.|.+++..+..+      ...+++||+|+|||.++...+...+..       +.++++++||..++.|..+.+
T Consensus       448 ~~f~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~-------g~qvlvLvPT~~LA~Q~~~~f  520 (926)
T TIGR00580       448 FPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD-------GKQVAVLVPTTLLAQQHFETF  520 (926)
T ss_pred             CCCCCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh-------CCeEEEEeCcHHHHHHHHHHH
Confidence            3567899999999998763      468999999999999877665555544       678999999999999999999


Q ss_pred             Hhhcc
Q psy16285         90 LKYTQ   94 (97)
Q Consensus        90 ~~~~~   94 (97)
                      .+++.
T Consensus       521 ~~~~~  525 (926)
T TIGR00580       521 KERFA  525 (926)
T ss_pred             HHHhc
Confidence            88654

All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.

>TIGR01054 rgy reverse gyrase

Probab=99.05  E-value=1.2e-09  Score=85.09  Aligned_cols=72  Identities=22%  Similarity=0.103  Sum_probs=61.1

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ....+.+.|+.++..+..+..+++++|||+|||+.+..++..+..       .+.++++++||++++.|+.+.+.++..
T Consensus        75 ~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~f~l~~~~~l~~-------~g~~vLIL~PTreLa~Qi~~~l~~l~~  146 (1171)
T TIGR01054        75 VGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTTFGLAMSLFLAK-------KGKRCYIILPTTLLVIQVAEKISSLAE  146 (1171)
T ss_pred             cCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHHHh-------cCCeEEEEeCHHHHHHHHHHHHHHHHH
Confidence            456788999999999999999999999999999876655544433       267899999999999999999998864

Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.05  E-value=2.6e-09  Score=75.49  Aligned_cols=78  Identities=21%  Similarity=0.070  Sum_probs=58.5

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHH-HHHHHHhchhh--hhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALR-IVEGFLKNKEL--ARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~-~~~~~~~~~~~--~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +...+++.|.+++..+.++..+++.+|+|||||..... ++..+......  ....+.+++|++|+++++.|+.+.+..+
T Consensus        27 g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~lil~PtreLa~Qi~~~~~~l  106 (423)
T PRK04837         27 GFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPL  106 (423)
T ss_pred             CCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEEECCcHHHHHHHHHHHHHH
Confidence            44567899999999999999999999999999986433 33444332110  0012467999999999999999888776


Q ss_pred             c
Q psy16285         93 T   93 (97)
Q Consensus        93 ~   93 (97)
                      .
T Consensus       107 ~  107 (423)
T PRK04837        107 A  107 (423)
T ss_pred             h
Confidence            5

>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional

Probab=99.05  E-value=1.6e-09  Score=84.08  Aligned_cols=72  Identities=25%  Similarity=0.231  Sum_probs=61.6

Q ss_pred             CCCCCHHHHHHHHHHhc-----CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         17 ELGLNTIQFEAYKAALT-----REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~-----~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      .+.++++|.+++..+..     .+..+|..|+|||||.++..++..+++..     ..++|||+++++++++|..+.+.+
T Consensus       411 ~~~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li~~L~~~~-----~~~rVLfLvDR~~L~~Qa~~~F~~  485 (1123)
T PRK11448        411 GLGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALMYRLLKAK-----RFRRILFLVDRSALGEQAEDAFKD  485 (1123)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHHHHHHhcC-----ccCeEEEEecHHHHHHHHHHHHHh
Confidence            36789999999987753     35789999999999999998988887763     357999999999999999999988


Q ss_pred             hc
Q psy16285         92 YT   93 (97)
Q Consensus        92 ~~   93 (97)
                      +.
T Consensus       486 ~~  487 (1123)
T PRK11448        486 TK  487 (1123)
T ss_pred             cc
Confidence            74

>PRK02362 ski2-like helicase; Provisional

Probab=99.01  E-value=3.2e-09  Score=79.61  Aligned_cols=71  Identities=20%  Similarity=0.139  Sum_probs=58.4

Q ss_pred             cCCCCCHHHHHHHHH-HhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKA-ALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~-~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +...+++.|.+++.. +.+++++++.+|||+|||.++...+...+..       +.++++++|+++++.|..+++.++.
T Consensus        20 g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~-------~~kal~i~P~raLa~q~~~~~~~~~   91 (737)
T PRK02362         20 GIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIAR-------GGKALYIVPLRALASEKFEEFERFE   91 (737)
T ss_pred             CCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhc-------CCcEEEEeChHHHHHHHHHHHHHhh
Confidence            345689999999987 5578899999999999999876544443333       6789999999999999999998873

>PTZ00110 helicase; Provisional

Probab=99.00  E-value=3.9e-09  Score=76.96  Aligned_cols=78  Identities=21%  Similarity=0.135  Sum_probs=58.6

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHH-HHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVAL-RIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~-~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ...+++.|.+++..++++..+++.+|||+|||.... -++..+..+.......+..+||++||++++.|+.+.+.++..
T Consensus       150 ~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~  228 (545)
T PTZ00110        150 FTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGA  228 (545)
T ss_pred             CCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHHHHHHHHHHHHhc
Confidence            345789999999999999999999999999998532 233333332111111245799999999999999999998864

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=98.99  E-value=5.4e-09  Score=76.61  Aligned_cols=80  Identities=24%  Similarity=0.181  Sum_probs=60.8

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHH-HHHHHHhchhhh--hcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALR-IVEGFLKNKELA--RYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~-~~~~~~~~~~~~--~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ....+++.|.++|..++++..+++++|+|||||..... ++..+.......  .....++||++|+++++.|+.+.+.++
T Consensus        28 g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PTreLa~Qi~~~~~~l  107 (572)
T PRK04537         28 GFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKF  107 (572)
T ss_pred             CCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCcHHHHHHHHHHHHHH
Confidence            44568999999999999999999999999999986444 444444321100  001368999999999999999999888


Q ss_pred             ccC
Q psy16285         93 TQN   95 (97)
Q Consensus        93 ~~~   95 (97)
                      +.+
T Consensus       108 ~~~  110 (572)
T PRK04537        108 GAD  110 (572)
T ss_pred             hcc
Confidence            643

>PRK13766 Hef nuclease; Provisional

Probab=98.99  E-value=4.8e-09  Score=78.89  Aligned_cols=71  Identities=25%  Similarity=0.309  Sum_probs=61.3

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..+..+++|.+++..+..+ +.+|..|+|+|||.++..++...+..      .+.++||++|+..++.|+.+.++++.
T Consensus        12 ~~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~------~~~~vLvl~Pt~~L~~Q~~~~~~~~~   82 (773)
T PRK13766         12 NTIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHK------KGGKVLILAPTKPLVEQHAEFFRKFL   82 (773)
T ss_pred             CcCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHh------CCCeEEEEeCcHHHHHHHHHHHHHHh
Confidence            5577899999999887766 89999999999999888777776654      47899999999999999999998875

>PRK10689 transcription-repair coupling factor; Provisional

Probab=98.99  E-value=4e-09  Score=82.13  Aligned_cols=73  Identities=21%  Similarity=0.133  Sum_probs=60.1

Q ss_pred             ccCCCCCHHHHHHHHHHhcC------CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALTR------EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~------~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      .-.+.+++.|.+++..+..+      ...+++||+|+|||.++...+...+..       +.+++|++||..++.|+.+.
T Consensus       596 ~~~~~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~-------g~qvlvLvPT~eLA~Q~~~~  668 (1147)
T PRK10689        596 SFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVEN-------HKQVAVLVPTTLLAQQHYDN  668 (1147)
T ss_pred             hCCCCCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHc-------CCeEEEEeCcHHHHHHHHHH
Confidence            34568899999999998764      578999999999999876555555443       78899999999999999999


Q ss_pred             HHhhcc
Q psy16285         89 VLKYTQ   94 (97)
Q Consensus        89 l~~~~~   94 (97)
                      +.+.+.
T Consensus       669 f~~~~~  674 (1147)
T PRK10689        669 FRDRFA  674 (1147)
T ss_pred             HHHhhc
Confidence            887543

>PRK00254 ski2-like helicase; Provisional

Probab=98.97  E-value=4.8e-09  Score=78.54  Aligned_cols=70  Identities=21%  Similarity=0.252  Sum_probs=57.7

Q ss_pred             cCCCCCHHHHHHHHH-HhcCCceEEeCCCCCchHHHH-HHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         16 EELGLNTIQFEAYKA-ALTREFAIIQGPPGTGKTYVA-LRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~-~~~~~~~~v~Gp~GtGKT~~~-~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +...+++.|.+++.. +.+++++++.+|||+|||.++ ..++..+...       +.++++++|+++++.+..+++.++
T Consensus        20 g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~-------~~~~l~l~P~~aLa~q~~~~~~~~   91 (720)
T PRK00254         20 GIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE-------GGKAVYLVPLKALAEEKYREFKDW   91 (720)
T ss_pred             CCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc-------CCeEEEEeChHHHHHHHHHHHHHH
Confidence            445689999999986 567889999999999999987 4445555443       678999999999999999998875

>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=98.96  E-value=3.4e-09  Score=79.28  Aligned_cols=76  Identities=21%  Similarity=0.276  Sum_probs=66.8

Q ss_pred             ccCCCCCHHHHHHHHHHhc-----CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALT-----REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~-----~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      .....++.+|..||.....     ++..+|..+||||||.+|.+++..+.+.++     .++|||++-++.+++|-...+
T Consensus       161 ~s~i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAiaii~rL~r~~~-----~KRVLFLaDR~~Lv~QA~~af  235 (875)
T COG4096         161 DSAIGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAIAIIDRLIKSGW-----VKRVLFLADRNALVDQAYGAF  235 (875)
T ss_pred             cccccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHHHHHHHHHhcch-----hheeeEEechHHHHHHHHHHH
Confidence            4567789999999998764     357999999999999999999999999875     689999999999999999988


Q ss_pred             HhhccC
Q psy16285         90 LKYTQN   95 (97)
Q Consensus        90 ~~~~~~   95 (97)
                      .+|..+
T Consensus       236 ~~~~P~  241 (875)
T COG4096         236 EDFLPF  241 (875)
T ss_pred             HHhCCC
Confidence            888753

>PRK12377 putative replication protein; Provisional

Probab=98.95  E-value=1.3e-08  Score=67.77  Aligned_cols=43  Identities=23%  Similarity=0.444  Sum_probs=33.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQF   85 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~   85 (97)
                      .++++.|||||||||++.+++..+.+.       +.+++++. ..+.+..+
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~l~~~-------g~~v~~i~-~~~l~~~l  144 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNRLLAK-------GRSVIVVT-VPDVMSRL  144 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc-------CCCeEEEE-HHHHHHHH
Confidence            578999999999999999999999876       66777766 23444433

>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional

Probab=98.94  E-value=9.5e-09  Score=74.50  Aligned_cols=79  Identities=18%  Similarity=0.102  Sum_probs=58.5

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHH-HHHHHHhchh--hhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALR-IVEGFLKNKE--LARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~-~~~~~~~~~~--~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +...+++.|.+++..+..++++++.+|||+|||..... ++..+.....  .....+.+++|++||++++.|+.+.++.+
T Consensus       140 g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l  219 (518)
T PLN00206        140 GYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVL  219 (518)
T ss_pred             CCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHHHHHHHHHHHHH
Confidence            34568999999999999999999999999999975333 3333332110  00113568999999999999998888776


Q ss_pred             cc
Q psy16285         93 TQ   94 (97)
Q Consensus        93 ~~   94 (97)
                      ..
T Consensus       220 ~~  221 (518)
T PLN00206        220 GK  221 (518)
T ss_pred             hC
Confidence            54

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=98.94  E-value=6.1e-09  Score=80.60  Aligned_cols=66  Identities=17%  Similarity=0.130  Sum_probs=56.1

Q ss_pred             cCCCCCHHHHHHHHHHhc-CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      ..+.|++.|.+++..+.. ++..+|+|++||||||++..+...+-..       +.+|+.++||..++.++.+.
T Consensus       378 ~~~~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l~~~~~~~e~~-------G~~V~g~ApTgkAA~~L~e~  444 (1102)
T PRK13826        378 RHARLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMMKAAREAWEAA-------GYRVVGGALAGKAAEGLEKE  444 (1102)
T ss_pred             cCCCCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHHHHHHHHHHHc-------CCeEEEEcCcHHHHHHHHHh
Confidence            357899999999998754 5688999999999999988887766554       78999999999999998653

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=98.93  E-value=1.4e-08  Score=72.84  Aligned_cols=77  Identities=23%  Similarity=0.152  Sum_probs=58.0

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHH-HHHHHHHhchhhh--hcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVAL-RIVEGFLKNKELA--RYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~-~~~~~~~~~~~~~--~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...+++.|.+++..+.++.++++.+|+|||||.... .++..+.+.....  .....++||++||++++.|+.+.+.++.
T Consensus       107 ~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~PtreLa~Q~~~~~~~l~  186 (475)
T PRK01297        107 FPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALT  186 (475)
T ss_pred             CCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCcHHHHHHHHHHHHHhh
Confidence            345789999999999999999999999999997533 3344454431000  0013579999999999999999888775

>PRK09183 transposase/IS protein; Provisional

Probab=98.93  E-value=7e-09  Score=69.39  Aligned_cols=50  Identities=18%  Similarity=0.268  Sum_probs=37.5

Q ss_pred             CCHHHHHHHHH---HhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         20 LNTIQFEAYKA---ALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        20 l~~~Q~~~i~~---~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ++..|...+..   +.++.++++.||||+||||++.+++..++..       +.+++++.
T Consensus        85 ~~~~~i~~L~~~~~i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~-------G~~v~~~~  137 (259)
T PRK09183         85 APQKQLQSLRSLSFIERNENIVLLGPSGVGKTHLAIALGYEAVRA-------GIKVRFTT  137 (259)
T ss_pred             CCHHHHHHHhcCCchhcCCeEEEEeCCCCCHHHHHHHHHHHHHHc-------CCeEEEEe
Confidence            34445555543   3456789999999999999999998887765       67787765

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.93  E-value=1.1e-08  Score=70.57  Aligned_cols=36  Identities=25%  Similarity=0.421  Sum_probs=32.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      +.++++.|||||||||++.+++..++..       +.+|++++
T Consensus       183 ~~~Lll~G~~GtGKThLa~aIa~~l~~~-------g~~V~y~t  218 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSNCIAKELLDR-------GKSVIYRT  218 (329)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHHHC-------CCeEEEEE
Confidence            4789999999999999999999999876       67888877

>PRK14701 reverse gyrase; Provisional

Probab=98.93  E-value=7.8e-09  Score=82.63  Aligned_cols=71  Identities=21%  Similarity=0.132  Sum_probs=58.6

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+.+++.|.+++..+..++.+++++|||+|||.....++..+ ..      ++.+++|++||.+++.|+.+++..+..
T Consensus        77 G~~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~-~~------~g~~aLVl~PTreLa~Qi~~~l~~l~~  147 (1638)
T PRK14701         77 GFEFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFL-AL------KGKKCYIILPTTLLVKQTVEKIESFCE  147 (1638)
T ss_pred             CCCCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHH-Hh------cCCeEEEEECHHHHHHHHHHHHHHHHh
Confidence            447899999999999999999999999999998544333333 22      367899999999999999999998754

>PRK07952 DNA replication protein DnaC; Validated

Probab=98.92  E-value=1.5e-08  Score=67.28  Aligned_cols=58  Identities=26%  Similarity=0.348  Sum_probs=41.9

Q ss_pred             CHHHHHHHHHHhc------C--CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         21 NTIQFEAYKAALT------R--EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        21 ~~~Q~~~i~~~~~------~--~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      ++.|..++..+.+      .  ..+++.|+||||||+++.+++..+...       +.+++++.     +.++...++
T Consensus        78 ~~~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~~~-------g~~v~~it-----~~~l~~~l~  143 (244)
T PRK07952         78 CEGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLR-------GKSVLIIT-----VADIMSAMK  143 (244)
T ss_pred             CchHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHhc-------CCeEEEEE-----HHHHHHHHH
Confidence            4556556555442      1  468999999999999999999999876       67888876     444444443

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=98.92  E-value=4.1e-09  Score=68.38  Aligned_cols=56  Identities=32%  Similarity=0.385  Sum_probs=41.5

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCCh
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN   79 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~   79 (97)
                      +.+..|..+++.+.+.+.+++.||+|||||+++.+.+..++.++     .-.+++++-|.-
T Consensus         4 p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g-----~~~kiii~Rp~v   59 (205)
T PF02562_consen    4 PKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEG-----EYDKIIITRPPV   59 (205)
T ss_dssp             --SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTT-----S-SEEEEEE-S-
T ss_pred             CCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhC-----CCcEEEEEecCC
Confidence            56889999999999899999999999999999999998888773     345666666644

; GO: 0005524 ATP binding; PDB: 3B85_A.

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=98.92  E-value=3.9e-09  Score=78.09  Aligned_cols=71  Identities=25%  Similarity=0.253  Sum_probs=62.3

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .|++.|++++...  .+.++|.++||||||.++...+.+++.....   .+.+|+.+++||.|+.++.+++.+...
T Consensus         2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v---~p~~Il~vTFTnkAA~em~~Rl~~~~~   72 (655)
T COG0210           2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAAGGV---DPEQILAITFTNKAAAEMRERLLKLLG   72 (655)
T ss_pred             CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHcCCc---ChHHeeeeechHHHHHHHHHHHHHHhC
Confidence            5789999998864  6778899999999999999999999998544   577899999999999999999998764

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=98.89  E-value=6.7e-09  Score=74.97  Aligned_cols=72  Identities=15%  Similarity=0.244  Sum_probs=59.9

Q ss_pred             cccCCCCCHHHHHHHHHHhcC-----CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         14 VQEELGLNTIQFEAYKAALTR-----EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        14 ~~~~~~l~~~Q~~~i~~~~~~-----~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      ....+.....|-+||..+..+     +.-++.|.+|||||++...++...          +++.||++|++.++.|+...
T Consensus         7 l~s~f~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~AnVI~~~----------~rPtLV~AhNKTLAaQLy~E   76 (663)
T COG0556           7 LHSPFKPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMANVIAKV----------QRPTLVLAHNKTLAAQLYSE   76 (663)
T ss_pred             eccCCCCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHHHHHHHh----------CCCeEEEecchhHHHHHHHH
Confidence            344556667788888887642     467899999999999988888776          77899999999999999999


Q ss_pred             HHhhccC
Q psy16285         89 VLKYTQN   95 (97)
Q Consensus        89 l~~~~~~   95 (97)
                      +++|+.+
T Consensus        77 fk~fFP~   83 (663)
T COG0556          77 FKEFFPE   83 (663)
T ss_pred             HHHhCcC
Confidence            9999964

>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase

Probab=98.88  E-value=1.8e-08  Score=75.74  Aligned_cols=71  Identities=13%  Similarity=0.064  Sum_probs=59.3

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHH-HHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALR-IVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~-~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...+.+.|.+++..+.+++++++..|||||||..... ++..+...      +..++|+++|+++++.+..+.+.++.
T Consensus        34 ~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~------~~~~aL~l~PtraLa~q~~~~l~~l~  105 (742)
T TIGR03817        34 IHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD------PRATALYLAPTKALAADQLRAVRELT  105 (742)
T ss_pred             CCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC------CCcEEEEEcChHHHHHHHHHHHHHhc
Confidence            3468999999999999999999999999999986443 34444443      36789999999999999999999875

A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=98.87  E-value=7.5e-09  Score=65.29  Aligned_cols=51  Identities=27%  Similarity=0.387  Sum_probs=41.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .++|.||||||||+++..++....++       +.++++++. .+..+++.+++.+++.
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~~~-------g~~v~~~s~-e~~~~~~~~~~~~~g~   51 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGLAR-------GEPGLYVTL-EESPEELIENAESLGW   51 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHC-------CCcEEEEEC-CCCHHHHHHHHHHcCC
Confidence            36899999999999999999888766       778888874 4567788877776653

A related protein is found in archaea.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=98.85  E-value=2.6e-08  Score=71.46  Aligned_cols=67  Identities=16%  Similarity=0.173  Sum_probs=54.1

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...+++.|.+++..+..++.+++.+|||+|||.....  -.+. .       ....+|++|+.+++.+..+++..++
T Consensus         9 ~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~l--p~l~-~-------~~~~lVi~P~~~L~~dq~~~l~~~g   75 (470)
T TIGR00614         9 LSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQL--PALC-S-------DGITLVISPLISLMEDQVLQLKASG   75 (470)
T ss_pred             CCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHH--HHHH-c-------CCcEEEEecHHHHHHHHHHHHHHcC
Confidence            3457899999999999999999999999999965322  2222 2       4579999999999999999888765

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=98.84  E-value=1.6e-08  Score=79.51  Aligned_cols=68  Identities=19%  Similarity=0.210  Sum_probs=55.7

Q ss_pred             CCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         20 LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        20 l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +++.|+++|.  ..+.+++|.+++|||||+++...+..++..+.    ...++|++|+|+.++.++.+++.+..
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~----~~~~il~~tFt~~aa~e~~~ri~~~l   69 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRGV----DIDRLLVVTFTNAAAREMKERIEEAL   69 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcCC----CHhhEEEEeccHHHHHHHHHHHHHHH
Confidence            5788999987  35778999999999999988777666655421    34679999999999999999988754

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.

>PRK10536 hypothetical protein; Provisional

Probab=98.84  E-value=1.7e-08  Score=67.45  Aligned_cols=45  Identities=24%  Similarity=0.296  Sum_probs=39.0

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      -.+.+..|...+..+.+.+.+++.||+|||||+++.+++...+..
T Consensus        57 i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~  101 (262)
T PRK10536         57 ILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIH  101 (262)
T ss_pred             ccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            356789999999988888899999999999999999999876644

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=98.82  E-value=2.6e-08  Score=80.88  Aligned_cols=67  Identities=22%  Similarity=0.267  Sum_probs=58.3

Q ss_pred             cCCCCCHHHHHHHHHHhcC--CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALTR--EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~--~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      ..+.|++.|++++..+..+  +..+|+|+||||||+++..+...+-..       +.+|.+++||..++.++.+..
T Consensus       426 ~~~~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l~~l~~~~~~~-------G~~V~~lAPTgrAA~~L~e~~  494 (1960)
T TIGR02760       426 SEFALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIAQLLLHLASEQ-------GYEIQIITAGSLSAQELRQKI  494 (1960)
T ss_pred             ccCCCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHHHHHHHHHHhc-------CCeEEEEeCCHHHHHHHHHHh
Confidence            3578999999999998864  688999999999999988888776554       789999999999999998763

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PRK13767 ATP-dependent helicase; Provisional

Probab=98.80  E-value=4.5e-08  Score=74.83  Aligned_cols=74  Identities=16%  Similarity=0.086  Sum_probs=55.6

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHH-HHHHHHhchhhh-hcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         18 LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALR-IVEGFLKNKELA-RYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~-~~~~~~~~~~~~-~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      ..+++.|.+++..+.++++++|.+|||+|||..+.. ++..+....... ...+.++++++|+++++.++.+++.+
T Consensus        31 ~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraLa~di~~~L~~  106 (876)
T PRK13767         31 GTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRALNNDIHRNLEE  106 (876)
T ss_pred             CCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHHHHHHHHHHHH
Confidence            458999999999999999999999999999987543 344444321100 01245799999999999998876653

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=98.79  E-value=3.5e-08  Score=78.65  Aligned_cols=67  Identities=21%  Similarity=0.177  Sum_probs=53.4

Q ss_pred             CCCCHHHHHHHHHHhc--CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHH
Q psy16285         18 LGLNTIQFEAYKAALT--REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVE   87 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~--~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~   87 (97)
                      ..|++.|++++..++.  ++.++|+|++||||||++..++..+..-..   ..+.+|+.++||+.++.++.+
T Consensus       834 ~~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e---~~g~~V~glAPTgkAa~~L~e  902 (1623)
T PRK14712        834 EKLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPE---SERPRVVGLGPTHRAVGEMRS  902 (1623)
T ss_pred             cccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhh---ccCceEEEEechHHHHHHHHH
Confidence            4789999999999885  478999999999999998887665533100   035679999999999988854

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=98.78  E-value=2.8e-08  Score=72.74  Aligned_cols=73  Identities=21%  Similarity=0.245  Sum_probs=57.2

Q ss_pred             CHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         21 NTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        21 ~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      -.+|-++|+. ..+..++|+|.+|||||+++.+.+++++..-+-. ...+.||++.|+..-++-+...|.+++++
T Consensus       214 QkEQneIIR~-ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~-l~~k~vlvl~PN~vFleYis~VLPeLGe~  286 (747)
T COG3973         214 QKEQNEIIRF-EKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGP-LQAKPVLVLGPNRVFLEYISRVLPELGEE  286 (747)
T ss_pred             hHhHHHHHhc-cCCCeEEEecCCCCCchhHHHHHHHHHHhccccc-cccCceEEEcCcHHHHHHHHHhchhhccC
Confidence            3445555554 3467899999999999999999999998863211 13456999999999999999999998864

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]

Probab=98.77  E-value=4e-08  Score=75.52  Aligned_cols=74  Identities=19%  Similarity=0.171  Sum_probs=67.2

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .-.+.+++.|++++..+.++.+++|.+|+|+|||.++-..+...+..       ++++.+++|.+++..|...++..-+.
T Consensus       115 ~~~F~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~-------~qrviYTsPIKALsNQKyrdl~~~fg  187 (1041)
T COG4581         115 EYPFELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRD-------GQRVIYTSPIKALSNQKYRDLLAKFG  187 (1041)
T ss_pred             hCCCCcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHc-------CCceEeccchhhhhhhHHHHHHHHhh
Confidence            46789999999999999999999999999999999999999888887       78899999999999999998887665


Q ss_pred             C
Q psy16285         95 N   95 (97)
Q Consensus        95 ~   95 (97)
                      +
T Consensus       188 d  188 (1041)
T COG4581         188 D  188 (1041)
T ss_pred             h
Confidence            4

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=98.77  E-value=4.7e-08  Score=78.53  Aligned_cols=68  Identities=22%  Similarity=0.209  Sum_probs=54.6

Q ss_pred             CCCCCHHHHHHHHHHhcC--CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHH
Q psy16285         17 ELGLNTIQFEAYKAALTR--EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVE   87 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~--~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~   87 (97)
                      ...|++.|++++..++.+  +..+|+|.|||||||++..++..+......   .+.+|+.++||+.++.++.+
T Consensus       965 ~~~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l~~v~~~~~~l~~~---~~~~V~glAPTgrAAk~L~e 1034 (1747)
T PRK13709        965 MEGLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQFRAVMSAVNTLPES---ERPRVVGLGPTHRAVGEMRS 1034 (1747)
T ss_pred             cCCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhhcc---cCceEEEECCcHHHHHHHHh
Confidence            457899999999998864  689999999999999988888776431100   25679999999999998764

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=98.75  E-value=7.7e-08  Score=71.02  Aligned_cols=68  Identities=19%  Similarity=0.195  Sum_probs=54.9

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ...+++.|.+++..+..++.+++.+|||+|||....  +-.+..        ...++|++|+.+++.+..+.+..++.
T Consensus        23 ~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~--lpal~~--------~g~tlVisPl~sL~~dqv~~l~~~gi   90 (607)
T PRK11057         23 YQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQ--IPALVL--------DGLTLVVSPLISLMKDQVDQLLANGV   90 (607)
T ss_pred             CCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHH--HHHHHc--------CCCEEEEecHHHHHHHHHHHHHHcCC
Confidence            346789999999999999999999999999996533  222322        45799999999999999998887653

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=98.74  E-value=9e-08  Score=73.26  Aligned_cols=73  Identities=21%  Similarity=0.178  Sum_probs=63.8

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      ..+.+-..|+.......++.++.+.+|||.||||....+...+-..       +++++++.||..++.|..+++.++.++
T Consensus        79 ~G~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~k-------gkr~yii~PT~~Lv~Q~~~kl~~~~e~  151 (1187)
T COG1110          79 TGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAKK-------GKRVYIIVPTTTLVRQVYERLKKFAED  151 (1187)
T ss_pred             hCCCchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHhc-------CCeEEEEecCHHHHHHHHHHHHHHHhh
Confidence            3456677899999999999999999999999999987777766555       799999999999999999999998853

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family

Probab=98.74  E-value=4.6e-08  Score=72.89  Aligned_cols=73  Identities=16%  Similarity=0.122  Sum_probs=60.6

Q ss_pred             CCCCCHHHHHHHHHHhc----------CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHH
Q psy16285         17 ELGLNTIQFEAYKAALT----------REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFV   86 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~----------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~   86 (97)
                      ....+..|..++..+..          .+..+|+.|+|||||.++..++..+....     ...+|+|++++.++.+|+.
T Consensus       236 k~~~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~~~~-----~~~~vl~lvdR~~L~~Q~~  310 (667)
T TIGR00348       236 KPYQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALELL-----KNPKVFFVVDRRELDYQLM  310 (667)
T ss_pred             eeehHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHHhhc-----CCCeEEEEECcHHHHHHHH
Confidence            34467889999988652          24789999999999999999988887542     4678999999999999999


Q ss_pred             HHHHhhcc
Q psy16285         87 EGVLKYTQ   94 (97)
Q Consensus        87 ~~l~~~~~   94 (97)
                      +.+.+++.
T Consensus       311 ~~f~~~~~  318 (667)
T TIGR00348       311 KEFQSLQK  318 (667)
T ss_pred             HHHHhhCC
Confidence            99998873

Members of this family are assumed to differ from each other in DNA site specificity.

>PRK08116 hypothetical protein; Validated

Probab=98.74  E-value=1.3e-07  Score=63.61  Aligned_cols=34  Identities=32%  Similarity=0.549  Sum_probs=29.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      .+++.|+|||||||++.+++..+.+.       +.+++++.
T Consensus       116 gl~l~G~~GtGKThLa~aia~~l~~~-------~~~v~~~~  149 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAACIANELIEK-------GVPVIFVN  149 (268)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHc-------CCeEEEEE
Confidence            48999999999999999999999876       56677766

>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]

Probab=98.73  E-value=1.4e-07  Score=68.42  Aligned_cols=76  Identities=28%  Similarity=0.207  Sum_probs=59.1

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHH-HHHHHHHHHhchhhhhcCCCC-EEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYV-ALRIVEGFLKNKELARYMSGP-ILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~-~~~~~~~~~~~~~~~~~~~~~-ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .....++.|..++..+..+..+++.+++|||||.. +.-++..+.....    .... .||++||++++.|+.+.+..+.
T Consensus        48 gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~----~~~~~aLil~PTRELA~Qi~~~~~~~~  123 (513)
T COG0513          48 GFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVE----RKYVSALILAPTRELAVQIAEELRKLG  123 (513)
T ss_pred             CCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccc----cCCCceEEECCCHHHHHHHHHHHHHHH
Confidence            45667999999999999999999999999999863 3444555442100    1222 9999999999999999999887


Q ss_pred             cC
Q psy16285         94 QN   95 (97)
Q Consensus        94 ~~   95 (97)
                      ..
T Consensus       124 ~~  125 (513)
T COG0513         124 KN  125 (513)
T ss_pred             hh
Confidence            64

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=98.72  E-value=1e-07  Score=69.99  Aligned_cols=68  Identities=15%  Similarity=0.088  Sum_probs=55.3

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .-.+++.|.+++..+..+..+++..|||+|||.....  -.+. .       ....+|++|+..++.+..+.+.+++.
T Consensus        11 ~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~l--pal~-~-------~g~~lVisPl~sL~~dq~~~l~~~gi   78 (591)
T TIGR01389        11 YDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQV--PALL-L-------KGLTVVISPLISLMKDQVDQLRAAGV   78 (591)
T ss_pred             CCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHH--HHHH-c-------CCcEEEEcCCHHHHHHHHHHHHHcCC
Confidence            3457899999999999999999999999999977542  2232 2       45689999999999999999888653

The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=98.71  E-value=1.5e-07  Score=64.37  Aligned_cols=35  Identities=20%  Similarity=0.273  Sum_probs=30.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ..+++.||+|+|||+++.+++..+...       +.++.++.
T Consensus       157 ~gl~L~G~~G~GKThLa~Aia~~l~~~-------g~~v~~~~  191 (306)
T PRK08939        157 KGLYLYGDFGVGKSYLLAAIANELAKK-------GVSSTLLH  191 (306)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc-------CCCEEEEE
Confidence            478999999999999999999999866       67777776

>KOG1806|consensus

Probab=98.71  E-value=4e-08  Score=75.09  Aligned_cols=76  Identities=30%  Similarity=0.487  Sum_probs=66.6

Q ss_pred             ccccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         13 NVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        13 ~~~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +..+...+++.|.+++......+..++.||||||||.++..++..+..+.     +.++.+|++++|.++.++++++.+.
T Consensus       732 p~~n~v~ft~~qveai~sg~qpgltmvvgppgtgktd~avqil~~lyhn~-----p~qrTlivthsnqaln~lfeKi~~~  806 (1320)
T KOG1806|consen  732 PKKNQVKFTPTQVEAILSGMQPGLTMVVGPPGTGKTDVAVQILSVLYHNS-----PNQRTLIVTHSNQALNQLFEKIMAL  806 (1320)
T ss_pred             cccchhccCHHHHHHHHhcCCCCceeeecCCCCCCcchhhhhhhhhhhcC-----CCcceEEEEecccchhHHHHHHHhc
Confidence            33455667889999999988899999999999999999999999998875     6899999999999999999988765


Q ss_pred             c
Q psy16285         93 T   93 (97)
Q Consensus        93 ~   93 (97)
                      .
T Consensus       807 d  807 (1320)
T KOG1806|consen  807 D  807 (1320)
T ss_pred             c
Confidence            3

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=98.70  E-value=8.8e-08  Score=77.94  Aligned_cols=68  Identities=21%  Similarity=0.171  Sum_probs=52.3

Q ss_pred             CCCCCHHHHHHHHHHhcC--CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHH
Q psy16285         17 ELGLNTIQFEAYKAALTR--EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVE   87 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~--~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~   87 (97)
                      ...|++.|++++..+..+  +.++|+|++|||||+++..++..+.+....   .+.+|+.++||+.++.++.+
T Consensus      1017 ~~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~---~g~~v~glApT~~Aa~~L~~ 1086 (1960)
T TIGR02760      1017 LERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES---EQLQVIGLAPTHEAVGELKS 1086 (1960)
T ss_pred             cCCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh---cCCeEEEEeChHHHHHHHHh
Confidence            467999999999998753  577899999999999986554433221110   37789999999999998864

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype

Probab=98.70  E-value=2.5e-08  Score=75.56  Aligned_cols=75  Identities=15%  Similarity=0.097  Sum_probs=55.1

Q ss_pred             cCCCCCHHHHHHHHHHhcCC-ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTRE-FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~-~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ..+...++|.+++..+..+. ..++..|+|||||..+..-...+....    ...+++++++|++++++|+.+.+++++.
T Consensus        12 ~G~~PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~~~~~----~~~~rLv~~vPtReLa~Qi~~~~~~~~k   87 (844)
T TIGR02621        12 HGYSPFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAVEIGA----KVPRRLVYVVNRRTVVDQVTEEAEKIGE   87 (844)
T ss_pred             hCCCCCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccccccc----cccceEEEeCchHHHHHHHHHHHHHHHH
Confidence            45568999999999999886 577789999999975321111111111    1355677788999999999999998875

This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=98.70  E-value=1.4e-07  Score=70.74  Aligned_cols=73  Identities=25%  Similarity=0.237  Sum_probs=65.9

Q ss_pred             cCCCCCHHHHHHHHHHhcC----CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         16 EELGLNTIQFEAYKAALTR----EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~----~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      ....++..|..++..+...    ...++.|.||+|||-+...++...+.+       ++++|+++|......|+.++++.
T Consensus       195 ~~~~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~-------GkqvLvLVPEI~Ltpq~~~rf~~  267 (730)
T COG1198         195 EWLALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQ-------GKQVLVLVPEIALTPQLLARFKA  267 (730)
T ss_pred             cccccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHc-------CCEEEEEeccccchHHHHHHHHH
Confidence            4578999999999998765    578999999999999999999999998       89999999999999999999998


Q ss_pred             hccC
Q psy16285         92 YTQN   95 (97)
Q Consensus        92 ~~~~   95 (97)
                      .+..
T Consensus       268 rFg~  271 (730)
T COG1198         268 RFGA  271 (730)
T ss_pred             HhCC
Confidence            8753

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.69  E-value=2.7e-07  Score=62.69  Aligned_cols=72  Identities=21%  Similarity=0.240  Sum_probs=50.6

Q ss_pred             CCCHHHHHHHHHHh----cCCceEEeCCCCCchHHHHHHHH-HHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         19 GLNTIQFEAYKAAL----TREFAIIQGPPGTGKTYVALRIV-EGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~----~~~~~~v~Gp~GtGKT~~~~~~~-~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ..++.|.+.+..+.    +++.+++.+|+|||||..+...+ .++......  ..+.+++++++|....++....+++.
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~--~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER--IQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc--ccccceeEEeccHHHHHHHHHHHHhc
Confidence            34889999666544    46799999999999997544443 444443100  01238999999999999988888765

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.69  E-value=2.7e-07  Score=62.69  Aligned_cols=72  Identities=21%  Similarity=0.240  Sum_probs=50.6

Q ss_pred             CCCHHHHHHHHHHh----cCCceEEeCCCCCchHHHHHHHH-HHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         19 GLNTIQFEAYKAAL----TREFAIIQGPPGTGKTYVALRIV-EGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~----~~~~~~v~Gp~GtGKT~~~~~~~-~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ..++.|.+.+..+.    +++.+++.+|+|||||..+...+ .++......  ..+.+++++++|....++....+++.
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~--~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER--IQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc--ccccceeEEeccHHHHHHHHHHHHhc
Confidence            34889999666544    46799999999999997544443 444443100  01238999999999999988888765

>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]

Probab=98.68  E-value=1.6e-07  Score=67.46  Aligned_cols=73  Identities=23%  Similarity=0.276  Sum_probs=61.1

Q ss_pred             cccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         14 VQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        14 ~~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .+.....+.+|......+..+ +.+|.-|+|-|||+++..++...+..      .++++++++||..++.|=.+.+++..
T Consensus        10 ~p~~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~------~~~kvlfLAPTKPLV~Qh~~~~~~v~   82 (542)
T COG1111          10 KPNTIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRW------FGGKVLFLAPTKPLVLQHAEFCRKVT   82 (542)
T ss_pred             ccccccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHh------cCCeEEEecCCchHHHHHHHHHHHHh
Confidence            345667899999998887766 78888999999999999888866666      35589999999999999888887765

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=98.67  E-value=2.3e-07  Score=70.50  Aligned_cols=66  Identities=14%  Similarity=0.168  Sum_probs=48.9

Q ss_pred             CHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         21 NTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        21 ~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...-.+.++.+.+++.+++.|+||||||+.....+.....       ...+++++.|++.++.++.+++.+..
T Consensus         4 ~~~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~-------~~~~ilvlqPrR~aA~qiA~rva~~~   69 (819)
T TIGR01970         4 HAVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG-------IGGKIIMLEPRRLAARSAAQRLASQL   69 (819)
T ss_pred             hHHHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc-------cCCeEEEEeCcHHHHHHHHHHHHHHh
Confidence            3444456666667889999999999999975544332221       25689999999999999999996543

This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>PRK06921 hypothetical protein; Provisional

Probab=98.67  E-value=1.7e-07  Score=62.97  Aligned_cols=45  Identities=18%  Similarity=0.405  Sum_probs=34.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQF   85 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~   85 (97)
                      +.++++.||||+||||++.+++..+.+.      .+..++++.. ...++++
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~------~g~~v~y~~~-~~l~~~l  161 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRK------KGVPVLYFPF-VEGFGDL  161 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhh------cCceEEEEEH-HHHHHHH
Confidence            4679999999999999999999998765      2566777763 3333443

>PRK09694 helicase Cas3; Provisional

Probab=98.67  E-value=1.3e-07  Score=72.20  Aligned_cols=72  Identities=18%  Similarity=0.240  Sum_probs=58.1

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .+..++.|..+.......+.++|.+|+|+|||..+...+..+...+     ...++++..|+..+++++.+++.++.
T Consensus       284 ~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~~-----~~~gi~~aLPT~Atan~m~~Rl~~~~  355 (878)
T PRK09694        284 GYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQG-----LADSIIFALPTQATANAMLSRLEALA  355 (878)
T ss_pred             CCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHhC-----CCCeEEEECcHHHHHHHHHHHHHHHH
Confidence            4567888987754433467899999999999999988888776652     35789999999999999999998643

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=98.66  E-value=1e-07  Score=65.80  Aligned_cols=52  Identities=21%  Similarity=0.275  Sum_probs=43.1

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ++|.+|||+|||.++...+.......     ...++++++|+..++.++.+++.+++
T Consensus         2 vvi~apTGsGKT~~~~~~~l~~~~~~-----~~~~ii~v~P~~~L~~q~~~~l~~~f   53 (358)
T TIGR01587         2 LVIEAPTGYGKTEAALLWALHSIKSQ-----KADRVIIALPTRATINAMYRRAKELF   53 (358)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhhC-----CCCeEEEEeehHHHHHHHHHHHHHHh
Confidence            68999999999998776655554332     36799999999999999999999974

This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.

>COG1204 Superfamily II helicase [General function prediction only]

Probab=98.65  E-value=1.3e-07  Score=71.33  Aligned_cols=66  Identities=26%  Similarity=0.293  Sum_probs=54.7

Q ss_pred             CCCHHHHHHHHHHh-cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         19 GLNTIQFEAYKAAL-TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~-~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      .+.+.|++++.... ++++++|..|||+|||.++...+..-+.+      .+.++++++|.+.++.+..+++.
T Consensus        31 el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~------~~~k~vYivPlkALa~Ek~~~~~   97 (766)
T COG1204          31 ELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLE------GGGKVVYIVPLKALAEEKYEEFS   97 (766)
T ss_pred             HhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHh------cCCcEEEEeChHHHHHHHHHHhh
Confidence            55666777777765 45899999999999999977766665555      36899999999999999999988

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=98.64  E-value=9.1e-08  Score=63.11  Aligned_cols=53  Identities=21%  Similarity=0.313  Sum_probs=43.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +..++|.||||+|||+++..++...+.+       +.++++++ +.+..+++.+++.+++-
T Consensus        21 gs~~lI~G~pGsGKT~la~~~l~~~~~~-------ge~~lyvs-~ee~~~~i~~~~~~~g~   73 (237)
T TIGR03877        21 RNVVLLSGGPGTGKSIFSQQFLWNGLQM-------GEPGIYVA-LEEHPVQVRRNMAQFGW   73 (237)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHHc-------CCcEEEEE-eeCCHHHHHHHHHHhCC
Confidence            4578999999999999999988877655       77888888 45678888888887664

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>PHA00729 NTP-binding motif containing protein

Probab=98.64  E-value=1.4e-07  Score=62.06  Aligned_cols=25  Identities=36%  Similarity=0.538  Sum_probs=22.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      .+++|+|+|||||||++..++..+.
T Consensus        18 ~nIlItG~pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYALKVARDVF   42 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3789999999999999999998875

>KOG0330|consensus

Probab=98.64  E-value=1.6e-07  Score=65.82  Aligned_cols=74  Identities=26%  Similarity=0.140  Sum_probs=63.4

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHH-HHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTY-VALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~-~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      -..++..|+++|..+..++.++..+.+|+|||- .+.=++..++++.     .....+|++||++++.|+.+.++.++..
T Consensus        81 ~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p-----~~~~~lVLtPtRELA~QI~e~fe~Lg~~  155 (476)
T KOG0330|consen   81 WKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEP-----KLFFALVLTPTRELAQQIAEQFEALGSG  155 (476)
T ss_pred             cCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCC-----CCceEEEecCcHHHHHHHHHHHHHhccc
Confidence            345688899999999999999999999999996 4666778887763     4678999999999999999999988754

>PHA02653 RNA helicase NPH-II; Provisional

Probab=98.64  E-value=1.4e-07  Score=70.40  Aligned_cols=71  Identities=20%  Similarity=0.363  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHH------Hhchh-h-hhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         22 TIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGF------LKNKE-L-ARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        22 ~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~------~~~~~-~-~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +.|.+++..+.+++.++++|+||||||+.+-..+.+.      +.... . ......++++++|+++++.++.+++.+.
T Consensus       167 ~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~  245 (675)
T PHA02653        167 DVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKS  245 (675)
T ss_pred             HHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHH
Confidence            4577888888889999999999999998643332211      11000 0 0113568999999999999999988753

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=98.63  E-value=3.2e-07  Score=54.60  Aligned_cols=39  Identities=31%  Similarity=0.572  Sum_probs=30.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCCh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN   79 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~   79 (97)
                      +..++|.||||+|||+++..++..+...       ...++++..+.
T Consensus        19 ~~~v~i~G~~G~GKT~l~~~i~~~~~~~-------~~~v~~~~~~~   57 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLARAIANELFRP-------GAPFLYLNASD   57 (151)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhhcC-------CCCeEEEehhh
Confidence            4689999999999999999999888643       45566665443

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=98.62  E-value=2.3e-07  Score=70.54  Aligned_cols=67  Identities=16%  Similarity=0.212  Sum_probs=48.3

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +....-.+.++.+.+++.++++||||||||+.....+   ++...    ...+++++.|++.++.++.+++.+.
T Consensus         5 Pi~~~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~l---L~~~~----~~~~ilvlqPrR~aA~qia~rva~~   71 (812)
T PRK11664          5 PVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQL---LQHGG----INGKIIMLEPRRLAARNVAQRLAEQ   71 (812)
T ss_pred             CHHHHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHH---HHcCC----cCCeEEEECChHHHHHHHHHHHHHH
Confidence            3344444566666678899999999999999754322   22211    1358999999999999999998654

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=98.62  E-value=1.4e-07  Score=62.16  Aligned_cols=54  Identities=24%  Similarity=0.448  Sum_probs=41.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+..++|.||||||||+++..++..+.++       +.++++++ +.+...++.+.+.+++.
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~~~~~-------g~~~~yi~-~e~~~~~~~~~~~~~g~   76 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYGFLQN-------GYSVSYVS-TQLTTTEFIKQMMSLGY   76 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhC-------CCcEEEEe-CCCCHHHHHHHHHHhCC
Confidence            45688999999999999998888887665       67788887 44456777777766553

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=98.62  E-value=3.1e-07  Score=64.31  Aligned_cols=74  Identities=24%  Similarity=0.288  Sum_probs=59.2

Q ss_pred             ccCCCCCHHHHHHHHHHhc-------CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCC-CEEEEeCChHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALT-------REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSG-PILIVCYTNHALDQFV   86 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~-------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~-~ilv~~~~~~~~~~~~   86 (97)
                      +..++.++.|.+.+..++.       ..+++|.||||||||.++..++.++.....     .. .+.|.|.......+++
T Consensus        16 P~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~-----~~~~~yINc~~~~t~~~i~   90 (366)
T COG1474          16 PEELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSA-----NVEVVYINCLELRTPYQVL   90 (366)
T ss_pred             cccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhc-----cCceEEEeeeeCCCHHHHH
Confidence            3458889999998887663       247999999999999999999999987742     23 5888998888888888


Q ss_pred             HHHHhhc
Q psy16285         87 EGVLKYT   93 (97)
Q Consensus        87 ~~l~~~~   93 (97)
                      .++.+..
T Consensus        91 ~~i~~~~   97 (366)
T COG1474          91 SKILNKL   97 (366)
T ss_pred             HHHHHHc
Confidence            8777644

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.62  E-value=3.1e-07  Score=60.60  Aligned_cols=50  Identities=14%  Similarity=0.175  Sum_probs=37.2

Q ss_pred             CHHHHHHHHHHhc---CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         21 NTIQFEAYKAALT---REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        21 ~~~Q~~~i~~~~~---~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +.....++..+..   .+.+++.||+|+||||++.+++..+...       +.++.++..
T Consensus        29 n~~a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~-------~~~v~y~~~   81 (235)
T PRK08084         29 NDSLLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAELSQR-------GRAVGYVPL   81 (235)
T ss_pred             cHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHhC-------CCeEEEEEH
Confidence            4555555555442   3578999999999999999999888765       567777664

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=98.60  E-value=3.4e-07  Score=63.72  Aligned_cols=60  Identities=18%  Similarity=0.329  Sum_probs=48.0

Q ss_pred             HHHHHHHHhcCC--ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         24 QFEAYKAALTRE--FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        24 Q~~~i~~~~~~~--~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      |.+++..+.++.  ++++.+|||+|||..+...+.   ..       ..+.++++|++.++.+..+++.++.
T Consensus         2 Q~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l---~~-------~~~~~~~~P~~aL~~~~~~~~~~~~   63 (357)
T TIGR03158         2 QVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLL---HG-------ENDTIALYPTNALIEDQTEAIKEFV   63 (357)
T ss_pred             HHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHH---Hc-------CCCEEEEeChHHHHHHHHHHHHHHH
Confidence            778888888665  578899999999987643322   22       4578999999999999999998886

subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.

>TIGR00595 priA primosomal protein N'

Probab=98.60  E-value=1.3e-07  Score=68.60  Aligned_cols=49  Identities=22%  Similarity=0.270  Sum_probs=43.5

Q ss_pred             EEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         38 IIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        38 ~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +|.||+|+|||.+...++..++..       ++++++++|+..++.|+.+++++.+
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~-------g~~vLvlvP~i~L~~Q~~~~l~~~f   49 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLAL-------GKSVLVLVPEIALTPQMIQRFKYRF   49 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHc-------CCeEEEEeCcHHHHHHHHHHHHHHh
Confidence            478999999999988888777766       7789999999999999999998765

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=98.59  E-value=8.4e-07  Score=58.06  Aligned_cols=51  Identities=24%  Similarity=0.320  Sum_probs=36.3

Q ss_pred             CHHHHHHHHHHhcC-----CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         21 NTIQFEAYKAALTR-----EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        21 ~~~Q~~~i~~~~~~-----~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      |..-..++..+..+     ..++|.||+|+||||++.+++..+.+..     ++.+++++.
T Consensus        16 N~~a~~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~-----~~~~v~y~~   71 (219)
T PF00308_consen   16 NELAYAAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIANEAQKQH-----PGKRVVYLS   71 (219)
T ss_dssp             THHHHHHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHHHHHHHC-----TTS-EEEEE
T ss_pred             HHHHHHHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHHHHHhcc-----ccccceeec
Confidence            44444455544432     2589999999999999999999987753     366788777

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PRK06893 DNA replication initiation factor; Validated

Probab=98.59  E-value=1.1e-07  Score=62.49  Aligned_cols=36  Identities=19%  Similarity=0.289  Sum_probs=28.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +.+++.|||||||||++.+++..+..+       +.++.++..
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~~~~~~~-------~~~~~y~~~   75 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVSNHYLLN-------QRTAIYIPL   75 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc-------CCCeEEeeH
Confidence            467999999999999999999998776       445555553

>COG1201 Lhr Lhr-like helicases [General function prediction only]

Probab=98.59  E-value=3.4e-07  Score=69.28  Aligned_cols=79  Identities=18%  Similarity=0.072  Sum_probs=61.9

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHH-HHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVA-LRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~-~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ....+++.|..++..+.++.+++|.+|||+|||-.| .-++..+.+........+-.+|+++|-+.+...+..+|+.++.
T Consensus        19 ~~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn~Di~~rL~~~~~   98 (814)
T COG1201          19 KFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALNNDIRRRLEEPLR   98 (814)
T ss_pred             hcCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHHHHHHHHHHHHHH
Confidence            467789999999999999999999999999999864 3445566555211111346899999999999999999987763

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=98.58  E-value=1.7e-07  Score=65.10  Aligned_cols=53  Identities=25%  Similarity=0.417  Sum_probs=43.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ..++|.|.||||||.++..++..+....     .+.++++++++......+.+.+.+-
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l~~~~-----~~~~~~~l~~n~~l~~~l~~~l~~~   54 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKELQNSE-----EGKKVLYLCGNHPLRNKLREQLAKK   54 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHhhccc-----cCCceEEEEecchHHHHHHHHHhhh
Confidence            3579999999999999999999992221     3788999999999888888777654

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK08727 hypothetical protein; Validated

Probab=98.58  E-value=8.9e-07  Score=58.37  Aligned_cols=35  Identities=26%  Similarity=0.410  Sum_probs=29.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ..+++.||+||||||++.+++..+.+.       +.++.++.
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~-------~~~~~y~~   76 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQA-------GRSSAYLP   76 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc-------CCcEEEEe
Confidence            468999999999999999999998776       56777766

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=98.57  E-value=1.3e-07  Score=61.73  Aligned_cols=54  Identities=30%  Similarity=0.568  Sum_probs=40.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +..++|.||||||||.++..++...+++      .+.++++++. .+..+++.+.+++++-
T Consensus        19 gs~~li~G~~GsGKT~l~~q~l~~~~~~------~ge~vlyvs~-ee~~~~l~~~~~s~g~   72 (226)
T PF06745_consen   19 GSVVLISGPPGSGKTTLALQFLYNGLKN------FGEKVLYVSF-EEPPEELIENMKSFGW   72 (226)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHH------HT--EEEEES-SS-HHHHHHHHHTTTS
T ss_pred             CcEEEEEeCCCCCcHHHHHHHHHHhhhh------cCCcEEEEEe-cCCHHHHHHHHHHcCC
Confidence            4578999999999999999888776665      2567888884 5556888888888764

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.57  E-value=5.2e-07  Score=67.68  Aligned_cols=68  Identities=24%  Similarity=0.198  Sum_probs=53.2

Q ss_pred             CCHHHHHHHHHHhc----CCceEEeCCCCCchHH-HHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         20 LNTIQFEAYKAALT----REFAIIQGPPGTGKTY-VALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        20 l~~~Q~~~i~~~~~----~~~~~v~Gp~GtGKT~-~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +++.|.+.+..+.+    ++.+++.+|||||||. +++..+.+..+..     ...+|++++.|+.-+.|+++.+++.
T Consensus        11 ~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~-----~~~kIiy~sRThsQl~q~i~Elk~~   83 (705)
T TIGR00604        11 IYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP-----EVRKIIYASRTHSQLEQATEELRKL   83 (705)
T ss_pred             CCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc-----ccccEEEEcccchHHHHHHHHHHhh
Confidence            46889888887663    6799999999999995 4445555544331     2478999999999999999999984

All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=98.56  E-value=2e-07  Score=62.13  Aligned_cols=54  Identities=30%  Similarity=0.521  Sum_probs=44.2

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+..++|.|+||||||.++...+....+.       +.++++++ +.+...++.+.+.+++-
T Consensus        22 ~g~~~lI~G~pGsGKT~f~~qfl~~~~~~-------ge~vlyvs-~~e~~~~l~~~~~~~g~   75 (260)
T COG0467          22 RGSVVLITGPPGTGKTIFALQFLYEGARE-------GEPVLYVS-TEESPEELLENARSFGW   75 (260)
T ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHHHhc-------CCcEEEEE-ecCCHHHHHHHHHHcCC
Confidence            45789999999999999999999988887       78888888 55567777777776653

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.55  E-value=9.1e-08  Score=56.42  Aligned_cols=39  Identities=28%  Similarity=0.480  Sum_probs=29.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCCh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN   79 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~   79 (97)
                      +..++|.||||||||+++..++..+...       ...++++..+.
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~-------~~~~~~~~~~~   40 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPP-------GGGVIYIDGED   40 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCC-------CCCEEEECCEE
Confidence            4678999999999999999998887554       23466666543

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]

Probab=98.55  E-value=3e-07  Score=68.01  Aligned_cols=74  Identities=23%  Similarity=0.229  Sum_probs=64.4

Q ss_pred             ccCCCCCHHHHHHHHHHhcC------CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALTR------EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~------~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      .-.|.|+..|+.++..+...      -+-+|+|..|||||.++...+..++..       +.++.+++||..++.|-.+.
T Consensus       258 ~LPF~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~-------G~Q~ALMAPTEILA~QH~~~  330 (677)
T COG1200         258 ALPFKLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEA-------GYQAALMAPTEILAEQHYES  330 (677)
T ss_pred             hCCCCccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHc-------CCeeEEeccHHHHHHHHHHH
Confidence            45788999999999998752      256899999999999988888877777       88999999999999999999


Q ss_pred             HHhhccC
Q psy16285         89 VLKYTQN   95 (97)
Q Consensus        89 l~~~~~~   95 (97)
                      +.+++.+
T Consensus       331 ~~~~l~~  337 (677)
T COG1200         331 LRKWLEP  337 (677)
T ss_pred             HHHHhhh
Confidence            9998864

>PRK05642 DNA replication initiation factor; Validated

Probab=98.54  E-value=3e-07  Score=60.65  Aligned_cols=36  Identities=14%  Similarity=0.254  Sum_probs=29.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ..+++.||+|+||||++.+++..+...       +.+++++..
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~-------~~~v~y~~~   81 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQR-------GEPAVYLPL   81 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhC-------CCcEEEeeH
Confidence            467899999999999999998887654       567777773

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.53  E-value=5.7e-07  Score=58.71  Aligned_cols=41  Identities=15%  Similarity=0.216  Sum_probs=31.1

Q ss_pred             CHHHHHHHHHHhc----CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         21 NTIQFEAYKAALT----REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        21 ~~~Q~~~i~~~~~----~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +......+..+..    .+.+++.||+|||||+++.++...+...
T Consensus        25 ~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~   69 (227)
T PRK08903         25 NAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASYG   69 (227)
T ss_pred             cHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            3445555555533    3579999999999999999999887665

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=98.53  E-value=2.9e-07  Score=60.44  Aligned_cols=53  Identities=19%  Similarity=0.371  Sum_probs=42.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +..++|.|+||+|||+++..++...+.+       +.++++++.. +..+++.+++.+++-
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~~~~~-------g~~~~y~~~e-~~~~~~~~~~~~~g~   77 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYGALKQ-------GKKVYVITTE-NTSKSYLKQMESVKI   77 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHhC-------CCEEEEEEcC-CCHHHHHHHHHHCCC
Confidence            4578999999999999999998877665       7788888864 456788888887764

>PRK04328 hypothetical protein; Provisional

Probab=98.52  E-value=3.2e-07  Score=61.01  Aligned_cols=53  Identities=21%  Similarity=0.300  Sum_probs=41.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +..++|.||||||||+++..++...+++       +.++++++ +.+..+++.+.+.+++-
T Consensus        23 gs~ili~G~pGsGKT~l~~~fl~~~~~~-------ge~~lyis-~ee~~~~i~~~~~~~g~   75 (249)
T PRK04328         23 RNVVLLSGGPGTGKSIFSQQFLWNGLQM-------GEPGVYVA-LEEHPVQVRRNMRQFGW   75 (249)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhc-------CCcEEEEE-eeCCHHHHHHHHHHcCC
Confidence            4578999999999999999988887666       67788887 44456677777777653

>PRK05973 replicative DNA helicase; Provisional

Probab=98.50  E-value=3.6e-07  Score=60.55  Aligned_cols=54  Identities=13%  Similarity=0.238  Sum_probs=41.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+..++|.|+||+|||+++..++.....+       +.++++++.. +..+++.+++..++-
T Consensus        63 ~Gsl~LIaG~PG~GKT~lalqfa~~~a~~-------Ge~vlyfSlE-es~~~i~~R~~s~g~  116 (237)
T PRK05973         63 PGDLVLLGARPGHGKTLLGLELAVEAMKS-------GRTGVFFTLE-YTEQDVRDRLRALGA  116 (237)
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHHhc-------CCeEEEEEEe-CCHHHHHHHHHHcCC
Confidence            45678999999999999999998888766       6778887743 335777777776653

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=98.49  E-value=4.4e-07  Score=59.15  Aligned_cols=54  Identities=19%  Similarity=0.218  Sum_probs=43.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      +..++|.|+||+|||+++..++...+++       +.++++++. ....+++.+++..++.+
T Consensus        16 g~~~li~G~~G~GKt~~~~~~~~~~~~~-------g~~~~y~s~-e~~~~~l~~~~~~~~~~   69 (224)
T TIGR03880        16 GHVIVVIGEYGTGKTTFSLQFLYQGLKN-------GEKAMYISL-EEREERILGYAKSKGWD   69 (224)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC-------CCeEEEEEC-CCCHHHHHHHHHHcCCC
Confidence            4578999999999999999998887766       678888875 44688888888777643

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.48  E-value=1.1e-06  Score=56.94  Aligned_cols=41  Identities=17%  Similarity=0.221  Sum_probs=30.0

Q ss_pred             CHHHHHHHHHHh---cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         21 NTIQFEAYKAAL---TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        21 ~~~Q~~~i~~~~---~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..-.+.+..+.   .+..++|.||+|||||+++..++..+.+.
T Consensus        22 ~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~~~   65 (226)
T TIGR03420        22 NAELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEER   65 (226)
T ss_pred             cHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            333444555542   24689999999999999999998887654

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=98.47  E-value=2e-06  Score=64.19  Aligned_cols=71  Identities=14%  Similarity=0.240  Sum_probs=57.7

Q ss_pred             ccCCCCCHHHHHHHHHHhcC-----CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALTR-----EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~-----~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      ...+.....|..++..+.++     ...++.|.+|||||+++..++..+          ++++||++|+...+.++.+.+
T Consensus         5 ~~~~~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a~~~~~~----------~~p~Lvi~~n~~~A~ql~~el   74 (655)
T TIGR00631         5 HSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMANVIAQV----------NRPTLVIAHNKTLAAQLYNEF   74 (655)
T ss_pred             ccCCCCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHHHHHHHh----------CCCEEEEECCHHHHHHHHHHH
Confidence            34566778898888887542     256799999999999987776554          678999999999999999999


Q ss_pred             HhhccC
Q psy16285         90 LKYTQN   95 (97)
Q Consensus        90 ~~~~~~   95 (97)
                      +.|+.+
T Consensus        75 ~~f~p~   80 (655)
T TIGR00631        75 KEFFPE   80 (655)
T ss_pred             HHhCCC
Confidence            999743

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=98.46  E-value=3.9e-07  Score=54.11  Aligned_cols=22  Identities=41%  Similarity=0.777  Sum_probs=20.2

Q ss_pred             eEEeCCCCCchHHHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++.||||||||+++..++..+
T Consensus         1 ill~G~~G~GKT~l~~~la~~l   22 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL   22 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT
T ss_pred             CEEECcCCCCeeHHHHHHHhhc
Confidence            5799999999999999998887

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=98.46  E-value=1.3e-06  Score=66.80  Aligned_cols=66  Identities=26%  Similarity=0.269  Sum_probs=48.2

Q ss_pred             cCCCCCHHHHHHHHHHh----cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAAL----TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~----~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      ..+..++.|.+.+..+.    ++..+++.+|||||||.....-+......       +++++|.+||+.+.+|+..+
T Consensus       242 ~~~~~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~~-------~~~vvi~t~t~~Lq~Ql~~~  311 (850)
T TIGR01407       242 LGLEYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAIT-------EKPVVISTNTKVLQSQLLEK  311 (850)
T ss_pred             cCCccCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhcC-------CCeEEEEeCcHHHHHHHHHH
Confidence            45778999998666433    46788999999999996533332222222       67999999999999998763

This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=98.46  E-value=4.3e-07  Score=65.55  Aligned_cols=53  Identities=17%  Similarity=0.315  Sum_probs=44.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +..++|.||||+|||+++...+....++       +.++++++ ..+..+++..+.++++-
T Consensus       263 gs~~li~G~~G~GKt~l~~~f~~~~~~~-------ge~~~y~s-~eEs~~~i~~~~~~lg~  315 (484)
T TIGR02655       263 DSIILATGATGTGKTLLVSKFLENACAN-------KERAILFA-YEESRAQLLRNAYSWGI  315 (484)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHC-------CCeEEEEE-eeCCHHHHHHHHHHcCC
Confidence            3478999999999999999999988776       67888877 56678888888888764

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.46  E-value=8.4e-07  Score=61.41  Aligned_cols=46  Identities=26%  Similarity=0.300  Sum_probs=36.7

Q ss_pred             cCCCCCHHHHHHHHHHhc-------CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         16 EELGLNTIQFEAYKAALT-------REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~-------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+.-++.|.+.+.....       .++++|.||||||||+++..++..+.+.
T Consensus        15 ~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~   67 (365)
T TIGR02928        15 DRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEA   67 (365)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHH
Confidence            456778888877777653       2579999999999999999999887543

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=98.45  E-value=1.1e-06  Score=58.85  Aligned_cols=28  Identities=29%  Similarity=0.404  Sum_probs=23.6

Q ss_pred             HhcCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         31 ALTREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        31 ~~~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+..+++.||||||||+++..++..+
T Consensus        18 l~~g~~vLL~G~~GtGKT~lA~~la~~l   45 (262)
T TIGR02640        18 LKSGYPVHLRGPAGTGKTTLAMHVARKR   45 (262)
T ss_pred             HhcCCeEEEEcCCCCCHHHHHHHHHHHh
Confidence            3356789999999999999999988744

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=98.44  E-value=1.1e-06  Score=56.75  Aligned_cols=45  Identities=18%  Similarity=0.313  Sum_probs=33.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC---ChHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY---TNHALDQFVE   87 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~---~~~~~~~~~~   87 (97)
                      .+++.||+|+||||++..++.++..+       +.++.++|.   ...+.+|+..
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~-------~~~v~lis~D~~R~ga~eQL~~   50 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLK-------GKKVALISADTYRIGAVEQLKT   50 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT-------T--EEEEEESTSSTHHHHHHHH
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhc-------cccceeecCCCCCccHHHHHHH
Confidence            57899999999999999999998776       566777764   4456666544

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=98.44  E-value=5.7e-07  Score=64.92  Aligned_cols=55  Identities=15%  Similarity=0.352  Sum_probs=43.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      +..++|.||||||||+++..++..-+.+      .+.++++++.. +..+++.+..++++-+
T Consensus        21 g~~~Li~G~pGsGKT~la~qfl~~g~~~------~ge~~lyvs~e-E~~~~l~~~~~~~G~~   75 (484)
T TIGR02655        21 GRSTLVSGTSGTGKTLFSIQFLYNGIIH------FDEPGVFVTFE-ESPQDIIKNARSFGWD   75 (484)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHHh------CCCCEEEEEEe-cCHHHHHHHHHHcCCC
Confidence            4578999999999999999988765554      36788888854 6788888888887643

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=98.44  E-value=6.5e-07  Score=58.45  Aligned_cols=52  Identities=23%  Similarity=0.452  Sum_probs=38.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +..++|.||||+|||+++..++...+.+       +.++++++. ....+++.++.++++
T Consensus        20 G~~~~i~G~~G~GKT~l~~~~~~~~~~~-------g~~~~~is~-e~~~~~i~~~~~~~g   71 (229)
T TIGR03881        20 GFFVAVTGEPGTGKTIFCLHFAYKGLRD-------GDPVIYVTT-EESRESIIRQAAQFG   71 (229)
T ss_pred             CeEEEEECCCCCChHHHHHHHHHHHHhc-------CCeEEEEEc-cCCHHHHHHHHHHhC
Confidence            5688999999999999999988776655       567777774 334566666655544

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>KOG0952|consensus

Probab=98.43  E-value=1e-06  Score=67.74  Aligned_cols=78  Identities=23%  Similarity=0.188  Sum_probs=60.0

Q ss_pred             CCCCCHHHHHHHHHHhc-CCceEEeCCCCCchHHHHHHHHHHHHhchh---hhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         17 ELGLNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEGFLKNKE---LARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~---~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      .-.+|..|..+...+.+ +++.+|.+|+|+|||.++...+-..+++..   ....+..+|++++|.+.++.++.+.+.+-
T Consensus       108 f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~~kk  187 (1230)
T KOG0952|consen  108 FEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFSKK  187 (1230)
T ss_pred             HHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHHhhh
Confidence            34578889999988885 579999999999999987766666666411   01114679999999999999999887665


Q ss_pred             cc
Q psy16285         93 TQ   94 (97)
Q Consensus        93 ~~   94 (97)
                      +.
T Consensus       188 l~  189 (1230)
T KOG0952|consen  188 LA  189 (1230)
T ss_pred             cc
Confidence            43

>COG4889 Predicted helicase [General function prediction only]

Probab=98.43  E-value=9.9e-07  Score=67.38  Aligned_cols=69  Identities=23%  Similarity=0.216  Sum_probs=57.4

Q ss_pred             cccCCCCCHHHHHHHHHHhc----CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         14 VQEELGLNTIQFEAYKAALT----REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        14 ~~~~~~l~~~Q~~~i~~~~~----~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      ......+++.|+.|++.+.+    +.+.=++.++|||||++++.+.+++.         ..++|+++|+..++.|-++.+
T Consensus       156 l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsLkisEala---------~~~iL~LvPSIsLLsQTlrew  226 (1518)
T COG4889         156 LKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSLKISEALA---------AARILFLVPSISLLSQTLREW  226 (1518)
T ss_pred             cCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHHHHHHHHh---------hhheEeecchHHHHHHHHHHH
Confidence            34567789999999999886    35666778999999999999999884         458999999999999977766


Q ss_pred             Hh
Q psy16285         90 LK   91 (97)
Q Consensus        90 ~~   91 (97)
                      ..
T Consensus       227 ~~  228 (1518)
T COG4889         227 TA  228 (1518)
T ss_pred             hh
Confidence            54

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=98.42  E-value=6.1e-07  Score=55.29  Aligned_cols=52  Identities=25%  Similarity=0.349  Sum_probs=41.5

Q ss_pred             CCceEEeCCCCCchHH-HHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         34 REFAIIQGPPGTGKTY-VALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~-~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +...+|.-.||+|||+ ++-.++.+.++.       ..++|++.||+..++++.+.|+..
T Consensus         4 g~~~~~d~hpGaGKTr~vlp~~~~~~i~~-------~~rvLvL~PTRvva~em~~aL~~~   56 (148)
T PF07652_consen    4 GELTVLDLHPGAGKTRRVLPEIVREAIKR-------RLRVLVLAPTRVVAEEMYEALKGL   56 (148)
T ss_dssp             TEEEEEE--TTSSTTTTHHHHHHHHHHHT-------T--EEEEESSHHHHHHHHHHTTTS
T ss_pred             CceeEEecCCCCCCcccccHHHHHHHHHc-------cCeEEEecccHHHHHHHHHHHhcC
Confidence            4567889999999999 678888888777       789999999999999999988754

The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=98.42  E-value=3.1e-07  Score=60.39  Aligned_cols=24  Identities=38%  Similarity=0.657  Sum_probs=21.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++++.||||+||||+|..++..+
T Consensus        51 ~h~lf~GPPG~GKTTLA~IIA~e~   74 (233)
T PF05496_consen   51 DHMLFYGPPGLGKTTLARIIANEL   74 (233)
T ss_dssp             -EEEEESSTTSSHHHHHHHHHHHC
T ss_pred             ceEEEECCCccchhHHHHHHHhcc
Confidence            478999999999999999888876

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=98.42  E-value=1.3e-06  Score=60.33  Aligned_cols=42  Identities=24%  Similarity=0.352  Sum_probs=34.9

Q ss_pred             CCCHHHHHHHHHHhc-CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         19 GLNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .+++.|.+.+..+.. +.+++|.|++|+||||++.+++..+..
T Consensus       128 ~~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll~aL~~~i~~  170 (323)
T PRK13833        128 IMTEAQASVIRSAIDSRLNIVISGGTGSGKTTLANAVIAEIVA  170 (323)
T ss_pred             CCCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHHHhc
Confidence            467778888888775 568999999999999999999887753

>TIGR00609 recB exodeoxyribonuclease V, beta subunit

Probab=98.42  E-value=6.9e-07  Score=69.75  Aligned_cols=56  Identities=25%  Similarity=0.360  Sum_probs=47.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhch-hhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNK-ELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~-~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ++..+|.+.+|||||+++..+...++-+. ..   ...+||++++|+.|..++.+++++.
T Consensus         9 ~G~~lieAsAGtGKT~ti~~~~lrll~~~~~~---~~~~iLvvTFT~aAt~el~~RIr~r   65 (1087)
T TIGR00609         9 NGTFLIEASAGTGKTFTIAQLYLRLLLEGGPL---TVEEILVVTFTNAATEELKTRIRGR   65 (1087)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHhcCCCC---ChhhEEEEehhHHHHHHHHHHHHHH
Confidence            46789999999999999888887777753 11   4689999999999999999999874

All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=98.41  E-value=1.7e-06  Score=57.94  Aligned_cols=38  Identities=21%  Similarity=0.276  Sum_probs=31.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      +..++|.||||||||+++..++.....+       +.++++++..
T Consensus        36 gs~~lI~G~pGtGKT~l~~qf~~~~a~~-------Ge~vlyis~E   73 (259)
T TIGR03878        36 YSVINITGVSDTGKSLMVEQFAVTQASR-------GNPVLFVTVE   73 (259)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhC-------CCcEEEEEec
Confidence            4578999999999999999988877665       6778888754

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional

Probab=98.40  E-value=2.5e-06  Score=66.57  Aligned_cols=67  Identities=15%  Similarity=0.176  Sum_probs=52.3

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +...+++.|.++|..++.++.+++..|||+|||.....  -.+. .       +..++|++|+.+++.+.+.++...
T Consensus       457 G~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQL--PAL~-~-------~GiTLVISPLiSLmqDQV~~L~~~  523 (1195)
T PLN03137        457 GNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQL--PALI-C-------PGITLVISPLVSLIQDQIMNLLQA  523 (1195)
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHH--HHHH-c-------CCcEEEEeCHHHHHHHHHHHHHhC
Confidence            34578999999999999999999999999999965332  2232 2       457999999999987666666544

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=98.40  E-value=8.9e-07  Score=60.52  Aligned_cols=29  Identities=24%  Similarity=0.536  Sum_probs=26.7

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+.++|+||+||||||++.+++.++.+.
T Consensus       124 ~~GLILVTGpTGSGKSTTlAamId~iN~~  152 (353)
T COG2805         124 PRGLILVTGPTGSGKSTTLAAMIDYINKH  152 (353)
T ss_pred             CCceEEEeCCCCCcHHHHHHHHHHHHhcc
Confidence            45789999999999999999999999887

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

Probab=98.40  E-value=2.8e-06  Score=63.13  Aligned_cols=72  Identities=24%  Similarity=0.219  Sum_probs=55.7

Q ss_pred             ccCCCCCHHHHHHHHHHh---cC-CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAAL---TR-EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~---~~-~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      ...+..++.|.+.+..+.   .+ ..+++.+|+|||||.-.+..+......      .+.++++.+.|+...+|+.++..
T Consensus        11 ~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~------~~~~viist~t~~lq~q~~~~~~   84 (654)
T COG1199          11 FPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYARE------EGKKVIISTRTKALQEQLLEEDL   84 (654)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHH------cCCcEEEECCCHHHHHHHHHhhc
Confidence            456778999999887655   34 459999999999998655544444333      36899999999999999999887


Q ss_pred             hh
Q psy16285         91 KY   92 (97)
Q Consensus        91 ~~   92 (97)
                      ..
T Consensus        85 ~~   86 (654)
T COG1199          85 PI   86 (654)
T ss_pred             ch
Confidence            65

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=98.40  E-value=8e-07  Score=62.55  Aligned_cols=47  Identities=26%  Similarity=0.324  Sum_probs=31.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      .+++++||||||||+++..++...          +..+.-++.+...+.++.+.+++
T Consensus        49 ~SmIl~GPPG~GKTTlA~liA~~~----------~~~f~~~sAv~~gvkdlr~i~e~   95 (436)
T COG2256          49 HSMILWGPPGTGKTTLARLIAGTT----------NAAFEALSAVTSGVKDLREIIEE   95 (436)
T ss_pred             ceeEEECCCCCCHHHHHHHHHHhh----------CCceEEeccccccHHHHHHHHHH
Confidence            478999999999999998887755          33455555444444444444433

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.40  E-value=2.2e-06  Score=59.90  Aligned_cols=47  Identities=34%  Similarity=0.406  Sum_probs=36.2

Q ss_pred             ccCCCCCHHHHHHHHHHhc-------CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         15 QEELGLNTIQFEAYKAALT-------REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~-------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..+.-++.+.+.+.....       .++++|.||||||||+++..++..+...
T Consensus        29 P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~   82 (394)
T PRK00411         29 PENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEI   82 (394)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            3556667777777766542       2578999999999999999999887654

>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]

Probab=98.40  E-value=2.3e-06  Score=65.47  Aligned_cols=71  Identities=21%  Similarity=0.266  Sum_probs=61.3

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHH-HHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYV-ALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~-~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      .+...|.+|++.+.++++++|+-|||+|||-. ..-++..+++.      +..+.|++-|+|.++..=.++++++..+
T Consensus        70 ~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~------~~a~AL~lYPtnALa~DQ~~rl~~~~~~  141 (851)
T COG1205          70 RLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRD------PSARALLLYPTNALANDQAERLRELISD  141 (851)
T ss_pred             cccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhC------cCccEEEEechhhhHhhHHHHHHHHHHh
Confidence            37788999999999999999999999999975 55667777776      4668999999999999999999988754

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.39  E-value=3.1e-07  Score=54.72  Aligned_cols=58  Identities=24%  Similarity=0.502  Sum_probs=34.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ++.++|.||||+|||+++..++..+........ ...-+.+.++.......+...+.+.
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~i~~~   61 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKN-HPDVIYVNCPSSRTPRDFAQEILEA   61 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCC-CEEEEEEEHHHHSSHHHHHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccC-CCcEEEEEeCCCCCHHHHHHHHHHH
Confidence            467899999999999999999988866421100 1223445555444455555555443

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=98.38  E-value=2.4e-06  Score=63.51  Aligned_cols=55  Identities=16%  Similarity=0.217  Sum_probs=42.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHH-HHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIV-EGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~-~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ++..+++.+|+|||||.....-+ ..+...      .+.+++|.+||+.+.+|+.+.+..+.
T Consensus        15 ~~~~lliEA~TGtGKTlAYLlpal~~~~~~------~~~rvlIstpT~~Lq~Ql~~~l~~l~   70 (636)
T TIGR03117        15 QKRIGMLEASTGVGKTLAMIMAALTMLKER------PDQKIAIAVPTLALMGQLWSELERLT   70 (636)
T ss_pred             cCCeEEEEcCCCCcHHHHHHHHHHHHHHhc------cCceEEEECCcHHHHHHHHHHHHHHH
Confidence            45788999999999996433333 333322      36899999999999999999887765

Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.

>KOG0331|consensus

Probab=98.38  E-value=1e-06  Score=63.80  Aligned_cols=80  Identities=18%  Similarity=0.132  Sum_probs=60.9

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHH-HHHHHHHHHh-chhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYV-ALRIVEGFLK-NKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~-~~~~~~~~~~-~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ....+.+.|.+.+..++.++.++....+|||||.- ++=.+.++.. .....+..+.++||++||++++.|+...+.+|.
T Consensus       110 g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTRELA~QV~~~~~~~~  189 (519)
T KOG0331|consen  110 GFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTRELAVQVQAEAREFG  189 (519)
T ss_pred             CCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcHHHHHHHHHHHHHHc
Confidence            44557888999999999999999999999999963 2223344443 222233357789999999999999999999987


Q ss_pred             cC
Q psy16285         94 QN   95 (97)
Q Consensus        94 ~~   95 (97)
                      ..
T Consensus       190 ~~  191 (519)
T KOG0331|consen  190 KS  191 (519)
T ss_pred             CC
Confidence            53

>KOG1123|consensus

Probab=98.38  E-value=1.5e-07  Score=68.06  Aligned_cols=81  Identities=19%  Similarity=0.349  Sum_probs=63.8

Q ss_pred             cccccccCCccc---------ccCCCCCHHHHHHHHHHhcC---CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCC
Q psy16285          3 SILDAYDLSANV---------QEELGLNTIQFEAYKAALTR---EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSG   70 (97)
Q Consensus         3 ~~~~~~~~~~~~---------~~~~~l~~~Q~~~i~~~~~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~   70 (97)
                      +++++|++..+.         .....++++|...+.....+   ++.+|.-|.|+|||.+....+..+          .+
T Consensus       277 PlLeEYDFRND~~npdl~idLKPst~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~ti----------kK  346 (776)
T KOG1123|consen  277 PLLEEYDFRNDNVNPDLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACTI----------KK  346 (776)
T ss_pred             hhhhhhccccCCCCCCCCcCcCcccccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeeee----------cc
Confidence            467777774332         23456899999999998854   467889999999998765555444          67


Q ss_pred             CEEEEeCChHHHHHHHHHHHhhc
Q psy16285         71 PILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        71 ~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ++||+|.+..+++||..++..|.
T Consensus       347 ~clvLcts~VSVeQWkqQfk~ws  369 (776)
T KOG1123|consen  347 SCLVLCTSAVSVEQWKQQFKQWS  369 (776)
T ss_pred             cEEEEecCccCHHHHHHHHHhhc
Confidence            89999999999999999988775

>PLN03025 replication factor C subunit; Provisional

Probab=98.36  E-value=1e-06  Score=60.42  Aligned_cols=43  Identities=28%  Similarity=0.330  Sum_probs=31.7

Q ss_pred             CCCHHHHHHHHHHhcC---CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         19 GLNTIQFEAYKAALTR---EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .-++...+.+..+...   +++++.||||||||+++..++..+...
T Consensus        16 ~g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~~~   61 (319)
T PLN03025         16 VGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGP   61 (319)
T ss_pred             cCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhcc
Confidence            3345555566655433   478999999999999999999888543

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=98.35  E-value=1.5e-06  Score=52.99  Aligned_cols=36  Identities=28%  Similarity=0.529  Sum_probs=29.4

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCCh
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN   79 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~   79 (97)
                      ++|.||||+|||+++..++..+...       +.+++++....
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~-------~~~v~~~~~e~   37 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATK-------GGKVVYVDIEE   37 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhc-------CCEEEEEECCc
Confidence            6899999999999999999888664       66777776543

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>KOG0744|consensus

Probab=98.35  E-value=7.5e-07  Score=61.52  Aligned_cols=59  Identities=17%  Similarity=0.322  Sum_probs=37.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC-----------ChHHHHHHHHHHHhhcc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY-----------TNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~-----------~~~~~~~~~~~l~~~~~   94 (97)
                      ++.+++.||||||||++..+++..+--+.  .+...+.+++=..           +...+..+++++.+.-+
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~--~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~  246 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIRT--NDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVE  246 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheeee--cCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence            35678999999999999888887763321  1112333443322           55667777777766543

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=98.35  E-value=2.2e-06  Score=58.56  Aligned_cols=42  Identities=24%  Similarity=0.350  Sum_probs=33.7

Q ss_pred             CCCHHHHHHHHHHhc-CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         19 GLNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .+++.+.+.+..+.. +.+++|.||+|+||||++.+++..+-.
T Consensus       116 ~~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll~al~~~i~~  158 (299)
T TIGR02782       116 IMTAAQRDVLREAVLARKNILVVGGTGSGKTTLANALLAEIAK  158 (299)
T ss_pred             CCCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHHhhc
Confidence            356667777777665 568999999999999999999887754

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=98.35  E-value=6.5e-07  Score=54.17  Aligned_cols=23  Identities=39%  Similarity=0.647  Sum_probs=21.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.||||||||+++..++..+
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~   23 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALL   23 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999999888

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=98.34  E-value=2.5e-06  Score=58.75  Aligned_cols=40  Identities=28%  Similarity=0.390  Sum_probs=33.0

Q ss_pred             CCHHHHHHHHHHh-cCCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         20 LNTIQFEAYKAAL-TREFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        20 l~~~Q~~~i~~~~-~~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +++.|.+.+..+. .+.+++|.|+||+||||++.+++..+.
T Consensus       133 ~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll~aL~~~~~  173 (319)
T PRK13894        133 MTAAQREAIIAAVRAHRNILVIGGTGSGKTTLVNAIINEMV  173 (319)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHhhh
Confidence            5667778887765 467999999999999999999987764

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=98.34  E-value=7.5e-06  Score=58.61  Aligned_cols=37  Identities=24%  Similarity=0.243  Sum_probs=29.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ..+++.||||+||||++.+++..+.+..     ++.+++++.
T Consensus       149 ~~l~l~G~~G~GKThL~~ai~~~~~~~~-----~~~~v~yi~  185 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHAIGNYILEKN-----PNAKVVYVT  185 (450)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhC-----CCCeEEEEE
Confidence            3589999999999999999999987752     245666665

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=98.33  E-value=5.6e-07  Score=53.08  Aligned_cols=22  Identities=45%  Similarity=0.859  Sum_probs=20.0

Q ss_pred             eEEeCCCCCchHHHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++|.||||+||||++..++..+
T Consensus         2 I~I~G~~gsGKST~a~~La~~~   23 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERL   23 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999999999998875

...

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=98.33  E-value=2.8e-06  Score=53.85  Aligned_cols=59  Identities=24%  Similarity=0.454  Sum_probs=38.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhh---cCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELAR---YMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~---~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +...+|.||||+|||+++..++..+.....-.+   ..+.+++++..... ..++.+++....
T Consensus        32 g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~   93 (193)
T PF13481_consen   32 GELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALL   93 (193)
T ss_dssp             TSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHh
Confidence            567899999999999999999998876321111   13678888886555 666777776544

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.33  E-value=5e-06  Score=59.52  Aligned_cols=37  Identities=22%  Similarity=0.186  Sum_probs=30.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+++.||||+||||++.+++..+.+..     ++.+++++..
T Consensus       132 ~l~lyG~~G~GKTHLl~ai~~~l~~~~-----~~~~v~yi~~  168 (440)
T PRK14088        132 PLFIYGGVGLGKTHLLQSIGNYVVQNE-----PDLRVMYITS  168 (440)
T ss_pred             eEEEEcCCCCcHHHHHHHHHHHHHHhC-----CCCeEEEEEH
Confidence            589999999999999999999887652     2456777663

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=98.32  E-value=1.9e-06  Score=67.56  Aligned_cols=57  Identities=26%  Similarity=0.282  Sum_probs=47.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...+++|.+++|||||+++...+..++..+.    .+.+|+++++|+.++.+|.+++.+..
T Consensus         9 p~~~~~~~a~agsgkt~~l~~~~~~~~~~~~----~~~~i~~~t~t~~aa~em~~Ri~~~L   65 (1141)
T TIGR02784         9 PKTSAWVSANAGSGKTHVLTQRVIRLLLNGV----PPSKILCLTYTKAAAAEMQNRVFDRL   65 (1141)
T ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHHHHcCC----CCCeEEEEecCHHHHHHHHHHHHHHH
Confidence            3468899999999999988877777765432    47899999999999999999988765

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=98.32  E-value=2.2e-06  Score=57.55  Aligned_cols=45  Identities=27%  Similarity=0.519  Sum_probs=36.1

Q ss_pred             cCCCCCHHHHHHHHHHhc--CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         16 EELGLNTIQFEAYKAALT--REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~--~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ..+.+.+.|.+.+..+..  ++.++|.||+|+||||++.+++..+..
T Consensus        60 ~~lg~~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l~all~~i~~  106 (264)
T cd01129          60 EKLGLKPENLEIFRKLLEKPHGIILVTGPTGSGKTTTLYSALSELNT  106 (264)
T ss_pred             HHcCCCHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHHHHHHhhhCC
Confidence            345578888888877664  467899999999999999988887754

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=98.31  E-value=2e-06  Score=55.43  Aligned_cols=38  Identities=21%  Similarity=0.420  Sum_probs=30.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      +..+.|.||||+|||+++..++......       +.+++++...
T Consensus        12 g~i~~i~G~~GsGKT~l~~~~~~~~~~~-------g~~v~yi~~e   49 (209)
T TIGR02237        12 GTITQIYGPPGSGKTNICMILAVNAARQ-------GKKVVYIDTE   49 (209)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC-------CCeEEEEECC
Confidence            4578999999999999999998887765       5667777754

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK14974 cell division protein FtsY; Provisional

Probab=98.31  E-value=3.1e-06  Score=58.70  Aligned_cols=51  Identities=24%  Similarity=0.260  Sum_probs=36.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC---hHHHHHHHHHHHhh
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT---NHALDQFVEGVLKY   92 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~---~~~~~~~~~~l~~~   92 (97)
                      ..+++.||||+||||++..++..+...       +.++++++..   ..+.+|+.......
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA~~l~~~-------g~~V~li~~Dt~R~~a~eqL~~~a~~l  194 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLAYYLKKN-------GFSVVIAAGDTFRAGAIEQLEEHAERL  194 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHHHc-------CCeEEEecCCcCcHHHHHHHHHHHHHc
Confidence            367899999999999999999877554       5677666543   55666665544443

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=98.31  E-value=7.2e-06  Score=62.65  Aligned_cols=69  Identities=23%  Similarity=0.115  Sum_probs=49.1

Q ss_pred             cCCCCCHHHHHHHHHHh----cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHH-HHHH
Q psy16285         16 EELGLNTIQFEAYKAAL----TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFV-EGVL   90 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~----~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~-~~l~   90 (97)
                      ..+..++.|.+....+.    ++..+++.++||||||.....-  .+...      .+.+++|.+||.++.+|+. +.+.
T Consensus       242 ~~~e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp--~l~~~------~~~~vvI~t~T~~Lq~Ql~~~~i~  313 (820)
T PRK07246        242 LGLEERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLP--LLAQS------DQRQIIVSVPTKILQDQIMAEEVK  313 (820)
T ss_pred             CCCccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHH--HHHhc------CCCcEEEEeCcHHHHHHHHHHHHH
Confidence            45788999999554443    3567889999999999743222  22222      2678999999999999995 4454


Q ss_pred             hh
Q psy16285         91 KY   92 (97)
Q Consensus        91 ~~   92 (97)
                      .+
T Consensus       314 ~l  315 (820)
T PRK07246        314 AI  315 (820)
T ss_pred             HH
Confidence            43

>KOG0335|consensus

Probab=98.31  E-value=1.3e-06  Score=62.63  Aligned_cols=80  Identities=18%  Similarity=0.116  Sum_probs=62.3

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHH-HHHHHHHHHHhchhhhhc-----CCCCEEEEeCChHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTY-VALRIVEGFLKNKELARY-----MSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~-~~~~~~~~~~~~~~~~~~-----~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      ......++.|+-++..+..++-++..+++|+|||. .+.=++..+++.+....+     ...+.++++||+++++|+.++
T Consensus        92 ~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~ne  171 (482)
T KOG0335|consen   92 SGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNE  171 (482)
T ss_pred             ccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHH
Confidence            34566788999999988888999999999999997 345556666665432111     246899999999999999999


Q ss_pred             HHhhcc
Q psy16285         89 VLKYTQ   94 (97)
Q Consensus        89 l~~~~~   94 (97)
                      .+++..
T Consensus       172 a~k~~~  177 (482)
T KOG0335|consen  172 ARKFSY  177 (482)
T ss_pred             HHhhcc
Confidence            998864

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=98.30  E-value=2.8e-06  Score=60.90  Aligned_cols=35  Identities=31%  Similarity=0.421  Sum_probs=30.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+++.||+|+||||++.+++..+...       +.+++++..
T Consensus       143 pl~L~G~~G~GKTHLl~Ai~~~l~~~-------~~~v~yi~~  177 (445)
T PRK12422        143 PIYLFGPEGSGKTHLMQAAVHALRES-------GGKILYVRS  177 (445)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHc-------CCCEEEeeH
Confidence            58999999999999999999998765       677877764

>KOG0991|consensus

Probab=98.29  E-value=2.1e-06  Score=57.22  Aligned_cols=71  Identities=24%  Similarity=0.299  Sum_probs=44.0

Q ss_pred             CCCHHHHHHHHHHhcC---CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEE-EEeCChHHHHHHHHHHHhhcc
Q psy16285         19 GLNTIQFEAYKAALTR---EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPIL-IVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~il-v~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .-|+.-.+.+..+.+.   +++++.|||||||||.+..++..++-...+     .-+| +.+....-.+.+..+++.|.+
T Consensus        30 VGNe~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~k-----e~vLELNASdeRGIDvVRn~IK~FAQ  104 (333)
T KOG0991|consen   30 VGNEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLGDSYK-----EAVLELNASDERGIDVVRNKIKMFAQ  104 (333)
T ss_pred             hCCHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhChhhh-----hHhhhccCccccccHHHHHHHHHHHH
Confidence            3345555555554432   689999999999999999999988775321     1122 233333445555666665553

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=98.29  E-value=7.7e-07  Score=59.43  Aligned_cols=26  Identities=42%  Similarity=0.505  Sum_probs=22.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .++++.||||||||+++..++..+..
T Consensus        43 ~~vll~GppGtGKTtlA~~ia~~l~~   68 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVARILGKLFKE   68 (261)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            46799999999999999999887754

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=98.29  E-value=1.9e-06  Score=54.90  Aligned_cols=41  Identities=22%  Similarity=0.229  Sum_probs=34.1

Q ss_pred             CCCCHHHHHHHHHHhc-CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         18 LGLNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      -.+++.+.+.+....+ +.+++|.||+|+||||++..++..+
T Consensus         8 g~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll~aL~~~i   49 (186)
T cd01130           8 GTFSPLQAAYLWLAVEARKNILISGGTGSGKTTLLNALLAFI   49 (186)
T ss_pred             CCCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            3567888888888775 5789999999999999988887665

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PRK04195 replication factor C large subunit; Provisional

Probab=98.27  E-value=4e-06  Score=60.50  Aligned_cols=53  Identities=21%  Similarity=0.379  Sum_probs=36.9

Q ss_pred             ccccccCCcccccCCCCCHHHHHHHHHHhc-------CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285          4 ILDAYDLSANVQEELGLNTIQFEAYKAALT-------REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus         4 ~~~~~~~~~~~~~~~~l~~~Q~~~i~~~~~-------~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      |.+.|.+.  ....+..++.+.+.+..+..       ...++|.||||+|||+++..++..+
T Consensus         4 W~eKyrP~--~l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el   63 (482)
T PRK04195          4 WVEKYRPK--TLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDY   63 (482)
T ss_pred             chhhcCCC--CHHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence            44555332  22345566767667766553       3578999999999999999998776

>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e

Probab=98.27  E-value=7.7e-06  Score=54.70  Aligned_cols=57  Identities=21%  Similarity=0.227  Sum_probs=39.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +..++.-.+|+|||..+..++..+.......  ...++||+||+ ..+.+|...+.++..
T Consensus        26 ~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~--~~~~~LIv~P~-~l~~~W~~E~~~~~~   82 (299)
T PF00176_consen   26 RGGLLADEMGLGKTITAIALISYLKNEFPQR--GEKKTLIVVPS-SLLSQWKEEIEKWFD   82 (299)
T ss_dssp             -EEEE---TTSSHHHHHHHHHHHHHHCCTTS--S-S-EEEEE-T-TTHHHHHHHHHHHSG
T ss_pred             CCEEEEECCCCCchhhhhhhhhhhhhccccc--cccceeEeecc-chhhhhhhhhccccc
Confidence            4567777899999999999998777663110  11259999999 778999999999873

g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1) [, ]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Proteins that contain this domain appear to be distantly related to the DEAX box helicases IPR001410 from INTERPRO, however no helicase activity has ever been demonstrated for these proteins. ; GO: 0003677 DNA binding, 0005524 ATP binding; PDB: 1Z63_B 1Z3I_X 3DMQ_A 3MWY_W.

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=98.27  E-value=1e-05  Score=60.40  Aligned_cols=73  Identities=14%  Similarity=0.216  Sum_probs=59.3

Q ss_pred             cccccCCCCCHHHHHHHHHHhcC-----CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHH
Q psy16285         12 ANVQEELGLNTIQFEAYKAALTR-----EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFV   86 (97)
Q Consensus        12 ~~~~~~~~l~~~Q~~~i~~~~~~-----~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~   86 (97)
                      +.....+.++..|..++..+.+.     ...+|.|.+|+||+.++..++...          ++++|+++|+...+.++.
T Consensus         5 ~~~~~~~~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia~l~~~~----------~r~vLIVt~~~~~A~~l~   74 (652)
T PRK05298          5 FKLVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMANVIARL----------QRPTLVLAHNKTLAAQLY   74 (652)
T ss_pred             cccccCCCCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHHHHHHHh----------CCCEEEEECCHHHHHHHH
Confidence            34567788999999999887532     256799999999999977655432          678999999999999999


Q ss_pred             HHHHhhcc
Q psy16285         87 EGVLKYTQ   94 (97)
Q Consensus        87 ~~l~~~~~   94 (97)
                      +.|..|..
T Consensus        75 ~dL~~~~~   82 (652)
T PRK05298         75 SEFKEFFP   82 (652)
T ss_pred             HHHHHhcC
Confidence            99999864

>KOG0345|consensus

Probab=98.26  E-value=9.5e-06  Score=58.25  Aligned_cols=79  Identities=16%  Similarity=0.134  Sum_probs=58.1

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHH-HHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALR-IVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~-~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +....++.|..+|...+.+.-+++.+++|||||.-... +++.+.+......+..-.-+|++||++++.||.+.+..|..
T Consensus        25 GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRELa~QI~~V~~~F~~  104 (567)
T KOG0345|consen   25 GFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELARQIREVAQPFLE  104 (567)
T ss_pred             CCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEEecCcHHHHHHHHHHHHHHHH
Confidence            44567899999999999999999999999999974333 33444333221111123679999999999999998887754

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=98.26  E-value=3.9e-06  Score=59.23  Aligned_cols=37  Identities=27%  Similarity=0.279  Sum_probs=30.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+++.||+|+||||++.+++..+.+..     ++.+++++..
T Consensus       138 ~l~l~G~~G~GKThL~~ai~~~l~~~~-----~~~~v~yi~~  174 (405)
T TIGR00362       138 PLFIYGGVGLGKTHLLHAIGNEILENN-----PNAKVVYVSS  174 (405)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHHHHhC-----CCCcEEEEEH
Confidence            578999999999999999999987652     2567777763

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=98.26  E-value=3.6e-06  Score=55.23  Aligned_cols=40  Identities=33%  Similarity=0.507  Sum_probs=33.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      .+..++|.|+||+|||+++..++..+..+      .+.++++++..
T Consensus        12 ~G~l~lI~G~~G~GKT~~~~~~~~~~~~~------~g~~vly~s~E   51 (242)
T cd00984          12 PGDLIIIAARPSMGKTAFALNIAENIAKK------QGKPVLFFSLE   51 (242)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHh------CCCceEEEeCC
Confidence            45688999999999999999998888776      37788888853

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=98.26  E-value=8.9e-06  Score=62.85  Aligned_cols=67  Identities=28%  Similarity=0.325  Sum_probs=48.9

Q ss_pred             cCCCCCHHHHHHHHHHh----cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAAL----TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~----~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      ..+..++.|.+....+.    ++..++|.+|||||||.--..-+......      .+++++|.++|..+-+|++++
T Consensus       254 ~~~e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~------~~~~vvIsT~T~~LQ~Ql~~k  324 (928)
T PRK08074        254 PKYEKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKK------KEEPVVISTYTIQLQQQLLEK  324 (928)
T ss_pred             CCCcCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhc------cCCeEEEEcCCHHHHHHHHHh
Confidence            45788999999666544    35678899999999997432222222222      378999999999999999774

>cd01131 PilT Pilus retraction ATPase PilT

Probab=98.26  E-value=1.9e-06  Score=55.44  Aligned_cols=27  Identities=26%  Similarity=0.560  Sum_probs=23.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +.++|.||+|+||||++..++..+...
T Consensus         2 GlilI~GptGSGKTTll~~ll~~~~~~   28 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDYINKN   28 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhhhc
Confidence            568999999999999999888887644

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=98.25  E-value=8.3e-06  Score=51.02  Aligned_cols=42  Identities=17%  Similarity=0.289  Sum_probs=29.4

Q ss_pred             CCHHHHHHHHHHhc------CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         20 LNTIQFEAYKAALT------REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        20 l~~~Q~~~i~~~~~------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      -++.|.+.+.....      ...++|.|++|+|||+++..+...+...
T Consensus         4 gR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen    4 GREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAER   51 (185)
T ss_dssp             T-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            35677777777661      3589999999999999999988888766

>CHL00181 cbbX CbbX; Provisional

Probab=98.25  E-value=3.9e-06  Score=57.04  Aligned_cols=26  Identities=42%  Similarity=0.616  Sum_probs=23.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++++.||||||||++|..++..+...
T Consensus        61 ~ill~G~pGtGKT~lAr~la~~~~~~   86 (287)
T CHL00181         61 HMSFTGSPGTGKTTVALKMADILYKL   86 (287)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            57899999999999999999887654

>PRK11823 DNA repair protein RadA; Provisional

Probab=98.24  E-value=3.1e-06  Score=60.64  Aligned_cols=52  Identities=21%  Similarity=0.345  Sum_probs=40.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +..++|.|+||+|||+++..++..+.+.       +.++++++. .+..+++..+..+++
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~~-------g~~vlYvs~-Ees~~qi~~ra~rlg  131 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLAAA-------GGKVLYVSG-EESASQIKLRAERLG  131 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhc-------CCeEEEEEc-cccHHHHHHHHHHcC
Confidence            3477999999999999999998887654       678888874 456677777766654

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=98.24  E-value=2.8e-06  Score=61.23  Aligned_cols=46  Identities=24%  Similarity=0.452  Sum_probs=37.8

Q ss_pred             cCCCCCHHHHHHHHHHhc--CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         16 EELGLNTIQFEAYKAALT--REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~--~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ....+.+.|.+.+..+.+  ++.++|+||+|+||||++..++..+...
T Consensus       238 ~~Lg~~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTTLY~~L~~ln~~  285 (500)
T COG2804         238 EKLGMSPFQLARLLRLLNRPQGLILVTGPTGSGKTTTLYAALSELNTP  285 (500)
T ss_pred             HHhCCCHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHHHHHHHHhcCC
Confidence            445567788888888775  4688999999999999999999988766

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.24  E-value=1.1e-05  Score=62.10  Aligned_cols=69  Identities=17%  Similarity=0.110  Sum_probs=54.1

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHH-HHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         18 LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVE-GFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~-~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +.+++.|.+.+..+..+...+...+||+|||..+..-+. .++.        +..++|++||..++.|..+.+..+..
T Consensus        91 ~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~--------g~~v~IVTpTrELA~Qdae~m~~L~k  160 (970)
T PRK12899         91 WDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALT--------GKPVHLVTVNDYLAQRDCEWVGSVLR  160 (970)
T ss_pred             CCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhh--------cCCeEEEeCCHHHHHHHHHHHHHHHh
Confidence            347888999999888888899999999999986543333 3322        34589999999999999998887753

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=98.23  E-value=3.5e-06  Score=57.14  Aligned_cols=26  Identities=42%  Similarity=0.581  Sum_probs=23.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+++.||||||||++|..++..+...
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~l~~~   85 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQILHRL   85 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            68999999999999999998888765

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=98.23  E-value=3.1e-06  Score=61.36  Aligned_cols=54  Identities=22%  Similarity=0.379  Sum_probs=42.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +..++|.|+||+|||+++..++...+.+      .+.++++++ ..+..+++.+.+..++-
T Consensus        31 Gs~~li~G~pGsGKT~l~~qf~~~~~~~------~ge~~lyis-~ee~~~~i~~~~~~~g~   84 (509)
T PRK09302         31 GRPTLVSGTAGTGKTLFALQFLVNGIKR------FDEPGVFVT-FEESPEDIIRNVASFGW   84 (509)
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHh------cCCCEEEEE-ccCCHHHHHHHHHHcCC
Confidence            4578999999999999999998776655      367888887 45567788888877764

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=98.23  E-value=5.1e-06  Score=55.21  Aligned_cols=43  Identities=19%  Similarity=0.158  Sum_probs=31.3

Q ss_pred             CCCCCHHHHHHHHHHh---c--CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         17 ELGLNTIQFEAYKAAL---T--REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~---~--~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      .+..+..+.+++....   +  .+.++|.||+|+|||+++..+...+.
T Consensus        21 ~~~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~~l~~~l~   68 (269)
T TIGR03015        21 FFYPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIRNLLKRLD   68 (269)
T ss_pred             HhCCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHHhcC
Confidence            4455666666666543   2  34789999999999999998877663

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=98.23  E-value=6.2e-06  Score=55.68  Aligned_cols=36  Identities=19%  Similarity=0.342  Sum_probs=29.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ..+++.||+|+||||++..++..+.+.       +.+++++.-
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~l~~~-------g~~V~li~~  108 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANKLKKQ-------GKSVLLAAG  108 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHHhc-------CCEEEEEeC
Confidence            367788999999999999999887554       677877763

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>KOG0989|consensus

Probab=98.23  E-value=1.6e-06  Score=59.35  Aligned_cols=27  Identities=37%  Similarity=0.524  Sum_probs=24.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .+++++.||||||||.++.+.+++++-
T Consensus        57 lp~~LFyGPpGTGKTStalafar~L~~   83 (346)
T KOG0989|consen   57 LPHYLFYGPPGTGKTSTALAFARALNC   83 (346)
T ss_pred             CceEEeeCCCCCcHhHHHHHHHHHhcC
Confidence            368999999999999999999998877

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=98.23  E-value=6.2e-06  Score=65.19  Aligned_cols=72  Identities=18%  Similarity=0.156  Sum_probs=52.6

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..++......+.+..+..++.++|.|+|||||||.+-.++......      ...+|+++-|.+.++..+.+++.+..
T Consensus        64 ~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTTqlPq~lle~~~~------~~~~I~~tQPRRlAA~svA~RvA~el  135 (1283)
T TIGR01967        64 DNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRG------SHGLIGHTQPRRLAARTVAQRIAEEL  135 (1283)
T ss_pred             CCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHHHHHHHHHHcCCC------CCceEecCCccHHHHHHHHHHHHHHh
Confidence            4455666566677777678899999999999999766555433211      23467778899999999998887754

This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=98.22  E-value=4.3e-06  Score=57.75  Aligned_cols=44  Identities=20%  Similarity=0.211  Sum_probs=35.4

Q ss_pred             ccCCCCCHHHHHHHHHHh-cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAAL-TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~-~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...+.+++.-..++..+. .++.+++.||||||||+++..++..+
T Consensus        44 d~~y~f~~~~~~~vl~~l~~~~~ilL~G~pGtGKTtla~~lA~~l   88 (327)
T TIGR01650        44 DPAYLFDKATTKAICAGFAYDRRVMVQGYHGTGKSTHIEQIAARL   88 (327)
T ss_pred             CCCccCCHHHHHHHHHHHhcCCcEEEEeCCCChHHHHHHHHHHHH
Confidence            346778877766666555 46789999999999999999998877

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.22  E-value=7e-06  Score=55.66  Aligned_cols=24  Identities=38%  Similarity=0.674  Sum_probs=21.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||+|||+++..++..+
T Consensus        31 ~~~ll~Gp~G~GKT~la~~ia~~~   54 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLAHIIANEM   54 (305)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh
Confidence            368999999999999999988776

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.21  E-value=6.8e-06  Score=59.02  Aligned_cols=38  Identities=18%  Similarity=0.046  Sum_probs=30.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ..++|.|++|+||||++.+++..+.+..     ++.+++++..
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~-----~~~~v~yv~~  179 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNF-----SDLKVSYMSG  179 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhC-----CCCeEEEEEH
Confidence            3588999999999999999998886642     3567777663

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=98.20  E-value=1.1e-05  Score=60.16  Aligned_cols=70  Identities=14%  Similarity=0.037  Sum_probs=55.6

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      -.+...+.|..++..+..+.  +....||+|||.++...+.....       .+..++|++||..++.|..+.+..+..
T Consensus       100 lg~~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al-------~G~~v~VvTptreLA~qdae~~~~l~~  169 (656)
T PRK12898        100 LGQRHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAAL-------AGLPVHVITVNDYLAERDAELMRPLYE  169 (656)
T ss_pred             hCCCCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhh-------cCCeEEEEcCcHHHHHHHHHHHHHHHh
Confidence            35566788999988887776  89999999999876554444333       377999999999999999999888753

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=98.20  E-value=3.8e-06  Score=60.21  Aligned_cols=34  Identities=38%  Similarity=0.566  Sum_probs=27.3

Q ss_pred             HHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         27 AYKAALTREFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        27 ~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .+.....++++++.||||||||+++..++..+..
T Consensus       187 l~~~L~~~~~iil~GppGtGKT~lA~~la~~l~~  220 (459)
T PRK11331        187 ILKRLTIKKNIILQGPPGVGKTFVARRLAYLLTG  220 (459)
T ss_pred             HHHHHhcCCCEEEECCCCCCHHHHHHHHHHHhcC
Confidence            3333345789999999999999999999887754

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.20  E-value=1.4e-05  Score=60.16  Aligned_cols=67  Identities=16%  Similarity=0.079  Sum_probs=47.6

Q ss_pred             cCCCCCHHHHHHHHHHh---cC------CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAAL---TR------EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFV   86 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~---~~------~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~   86 (97)
                      ..+..++.|.+....+.   .+      +.++|.+|||||||.--+.-+......      .+++|+|-+.|..+-+|++
T Consensus        22 ~~~e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~------~~k~vVIST~T~~LQeQL~   95 (697)
T PRK11747         22 PGFIPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARA------EKKKLVISTATVALQEQLV   95 (697)
T ss_pred             CCCCcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHH------cCCeEEEEcCCHHHHHHHH
Confidence            46889999999655544   33      578899999999996322222111122      3789999999999999997


Q ss_pred             HH
Q psy16285         87 EG   88 (97)
Q Consensus        87 ~~   88 (97)
                      .+
T Consensus        96 ~k   97 (697)
T PRK11747         96 SK   97 (697)
T ss_pred             hh
Confidence            53

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=98.20  E-value=4.7e-06  Score=59.37  Aligned_cols=32  Identities=28%  Similarity=0.317  Sum_probs=26.7

Q ss_pred             HHhcCCceEEeCCCCCchHHHHHHHHHH-HHhc
Q psy16285         30 AALTREFAIIQGPPGTGKTYVALRIVEG-FLKN   61 (97)
Q Consensus        30 ~~~~~~~~~v~Gp~GtGKT~~~~~~~~~-~~~~   61 (97)
                      .+.++.++++.||+||||||++.++... ++..
T Consensus       205 fve~~~Nli~lGp~GTGKThla~~l~~~~a~~s  237 (449)
T TIGR02688       205 LVEPNYNLIELGPKGTGKSYIYNNLSPYVILIS  237 (449)
T ss_pred             HHhcCCcEEEECCCCCCHHHHHHHHhHHHHHHc
Confidence            3346789999999999999999998877 5555

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=98.19  E-value=5.9e-06  Score=55.16  Aligned_cols=51  Identities=14%  Similarity=0.178  Sum_probs=37.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      .+..++|.||||+|||+++..++..+..+      .+.++++++... ..+++..++.
T Consensus        29 ~g~~~~i~g~~G~GKT~l~~~~~~~~~~~------~g~~vl~iS~E~-~~~~~~~r~~   79 (271)
T cd01122          29 KGELIILTAGTGVGKTTFLREYALDLITQ------HGVRVGTISLEE-PVVRTARRLL   79 (271)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHHh------cCceEEEEEccc-CHHHHHHHHH
Confidence            45688999999999999999998887655      367888888533 3444554443

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK04296 thymidine kinase; Provisional

Probab=98.19  E-value=3.2e-06  Score=54.15  Aligned_cols=36  Identities=17%  Similarity=0.229  Sum_probs=29.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ...+++||+|+|||+.+..++..+...       +.+++++.|
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~-------g~~v~i~k~   38 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEER-------GMKVLVFKP   38 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHc-------CCeEEEEec
Confidence            356899999999999999998888765       667777755

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=98.19  E-value=6.6e-06  Score=56.71  Aligned_cols=36  Identities=17%  Similarity=0.269  Sum_probs=29.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ..+++.||+|+||||++..++..+...       +.+|++++.
T Consensus       115 ~vi~lvGpnGsGKTTt~~kLA~~l~~~-------g~~V~Li~~  150 (318)
T PRK10416        115 FVILVVGVNGVGKTTTIGKLAHKYKAQ-------GKKVLLAAG  150 (318)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHHhc-------CCeEEEEec
Confidence            467889999999999999999887654       667777763

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=98.18  E-value=3.6e-06  Score=59.11  Aligned_cols=39  Identities=15%  Similarity=0.261  Sum_probs=30.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ++.+++.||+|+||||++..++..+....     +..+|.+++.
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~-----G~~~V~lit~  175 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRF-----GASKVALLTT  175 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhc-----CCCeEEEEec
Confidence            46889999999999999999998876541     1356766664

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=98.18  E-value=8.9e-06  Score=57.17  Aligned_cols=42  Identities=21%  Similarity=0.356  Sum_probs=30.6

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         18 LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +.+.+...+.+.  ..++.++|.||+|+||||++.+++..+.+.
T Consensus       135 lgl~~~~~~~l~--~~~GlilI~G~TGSGKTT~l~al~~~i~~~  176 (372)
T TIGR02525       135 MGIEPDLFNSLL--PAAGLGLICGETGSGKSTLAASIYQHCGET  176 (372)
T ss_pred             cCCCHHHHHHHH--hcCCEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            444554444332  246788999999999999999998888653

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=98.18  E-value=1.2e-05  Score=63.72  Aligned_cols=73  Identities=18%  Similarity=0.175  Sum_probs=51.1

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...++......+.+..+.+++.++|.|+|||||||.+-.++..+...      ....|.++.|.+.++..+..++.+-.
T Consensus        70 ~~~LPi~~~r~~Il~ai~~~~VviI~GeTGSGKTTqlPq~lle~g~g------~~g~I~~TQPRRlAArsLA~RVA~El  142 (1294)
T PRK11131         70 PENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRG------VKGLIGHTQPRRLAARTVANRIAEEL  142 (1294)
T ss_pred             CCCCCHHHHHHHHHHHHHhCCeEEEECCCCCCHHHHHHHHHHHcCCC------CCCceeeCCCcHHHHHHHHHHHHHHH
Confidence            45566677777777777788899999999999999755554433111      13456677788888777777776543

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=98.18  E-value=3.4e-06  Score=61.52  Aligned_cols=55  Identities=20%  Similarity=0.382  Sum_probs=37.1

Q ss_pred             cccccccCCcccccCCCCCHHHHHHHHHHhc--------CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285          3 SILDAYDLSANVQEELGLNTIQFEAYKAALT--------REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus         3 ~~~~~~~~~~~~~~~~~l~~~Q~~~i~~~~~--------~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      .|.|.|.+.  ...++..+....+.++.|+.        .+.++++||||||||+++..++..+.
T Consensus         8 ~W~~ky~P~--~~~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~elg   70 (519)
T PF03215_consen    8 PWVEKYAPK--TLDELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKELG   70 (519)
T ss_pred             ccchhcCCC--CHHHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHhC
Confidence            355555432  23345556666666666653        23578999999999999988887763

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=98.17  E-value=5.2e-06  Score=58.32  Aligned_cols=52  Identities=23%  Similarity=0.359  Sum_probs=39.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +..++|.|+||+|||+++..++..+...       +.++++++.. +..+++..+..+++
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~a~~-------g~~VlYvs~E-Es~~qi~~Ra~rlg  133 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARLAKR-------GGKVLYVSGE-ESPEQIKLRADRLG  133 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhc-------CCeEEEEECC-cCHHHHHHHHHHcC
Confidence            3578999999999999999998887665       5678887743 45667766666554

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=98.17  E-value=1.3e-05  Score=54.63  Aligned_cols=43  Identities=28%  Similarity=0.363  Sum_probs=29.8

Q ss_pred             cCCCCCHHHHHHHHHHhcC---Cce-EEeCCCCCchHHHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALTR---EFA-IIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~---~~~-~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ......+...+.+..+...   ++. ++.||||+|||+++..++..+
T Consensus        21 ~~~~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~   67 (316)
T PHA02544         21 DECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEV   67 (316)
T ss_pred             HHhcCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHh
Confidence            4455566666666665532   234 448999999999999887765

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=98.17  E-value=7.9e-06  Score=58.28  Aligned_cols=38  Identities=16%  Similarity=0.309  Sum_probs=30.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH-hchhhhhcCCCCEEEEeC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL-KNKELARYMSGPILIVCY   77 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~-~~~~~~~~~~~~ilv~~~   77 (97)
                      ++.+++.||+|+||||++..++..+. ..      .+.+|.+++.
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~------~g~~V~li~~  259 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLY------GKKKVALITL  259 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhc------CCCeEEEEEC
Confidence            35789999999999999999988886 33      2567777764

>PHA02244 ATPase-like protein

Probab=98.17  E-value=4.6e-06  Score=58.52  Aligned_cols=29  Identities=24%  Similarity=0.369  Sum_probs=24.3

Q ss_pred             HHhcCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         30 AALTREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        30 ~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..+.+++|.||||||||+++.+++..+
T Consensus       115 ~l~~~~PVLL~GppGtGKTtLA~aLA~~l  143 (383)
T PHA02244        115 IVNANIPVFLKGGAGSGKNHIAEQIAEAL  143 (383)
T ss_pred             HHhcCCCEEEECCCCCCHHHHHHHHHHHh
Confidence            33356789999999999999999998774

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=98.17  E-value=1.4e-05  Score=60.48  Aligned_cols=68  Identities=15%  Similarity=0.032  Sum_probs=48.3

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .++++|.+++..+.-+.-.++..+||+|||.++...+.....       .+..++|++|+..++.++.+.+..+.
T Consensus        68 glrpydVQlig~l~l~~G~Iaem~TGeGKTLta~Lpa~l~aL-------~g~~V~VVTpn~yLA~Rdae~m~~l~  135 (762)
T TIGR03714        68 GMFPYDVQVLGAIVLHQGNIAEMKTGEGKTLTATMPLYLNAL-------TGKGAMLVTTNDYLAKRDAEEMGPVY  135 (762)
T ss_pred             CCCccHHHHHHHHHhcCCceeEecCCcchHHHHHHHHHHHhh-------cCCceEEeCCCHHHHHHHHHHHHHHH
Confidence            345555556665554444689999999999876555322211       36679999999999999999886654

Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.

>PRK10436 hypothetical protein; Provisional

Probab=98.17  E-value=6.5e-06  Score=59.28  Aligned_cols=46  Identities=26%  Similarity=0.549  Sum_probs=36.8

Q ss_pred             cCCCCCHHHHHHHHHHh--cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         16 EELGLNTIQFEAYKAAL--TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~--~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+.+.+.|.+.+..+.  .++.++|.||+|+||||++.+++..+...
T Consensus       198 ~~LG~~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL~a~l~~~~~~  245 (462)
T PRK10436        198 ETLGMTPAQLAQFRQALQQPQGLILVTGPTGSGKTVTLYSALQTLNTA  245 (462)
T ss_pred             HHcCcCHHHHHHHHHHHHhcCCeEEEECCCCCChHHHHHHHHHhhCCC
Confidence            45667888888888765  35789999999999999998888877443

>cd01394 radB RadB

Probab=98.16  E-value=6.6e-06  Score=53.35  Aligned_cols=36  Identities=25%  Similarity=0.435  Sum_probs=29.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      +..+.|.|+||+|||+++..++..+...       +.+++++.
T Consensus        19 g~i~~i~G~~GsGKT~l~~~~a~~~~~~-------g~~v~yi~   54 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQLAVETAGQ-------GKKVAYID   54 (218)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhc-------CCeEEEEE
Confidence            4568999999999999999998888655       56676664

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>TIGR00416 sms DNA repair protein RadA

Probab=98.16  E-value=6.5e-06  Score=59.17  Aligned_cols=52  Identities=25%  Similarity=0.392  Sum_probs=40.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +..++|.|+||+|||+++..++..+...       +.++++++. .+...++..+..+++
T Consensus        94 GsvilI~G~pGsGKTTL~lq~a~~~a~~-------g~kvlYvs~-EEs~~qi~~ra~rlg  145 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQVACQLAKN-------QMKVLYVSG-EESLQQIKMRAIRLG  145 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHhc-------CCcEEEEEC-cCCHHHHHHHHHHcC
Confidence            3478999999999999999998887665       567888874 345677777766654

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=98.16  E-value=6.7e-06  Score=53.58  Aligned_cols=38  Identities=29%  Similarity=0.495  Sum_probs=31.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      +..+.|.||||+|||+++..++......       +.+++++...
T Consensus        23 g~i~~i~G~~GsGKT~l~~~la~~~~~~-------~~~v~yi~~e   60 (225)
T PRK09361         23 GTITQIYGPPGSGKTNICLQLAVEAAKN-------GKKVIYIDTE   60 (225)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHC-------CCeEEEEECC
Confidence            3478999999999999999999888765       5677777654

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.15  E-value=5.5e-06  Score=56.62  Aligned_cols=43  Identities=23%  Similarity=0.343  Sum_probs=32.9

Q ss_pred             CCCHHHHHHHHHHhcCC---ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         19 GLNTIQFEAYKAALTRE---FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~---~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .-++...+.+..+...+   .+++.||||||||+++..++..+...
T Consensus        18 ~g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~~~   63 (337)
T PRK12402         18 LGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGD   63 (337)
T ss_pred             cCCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhcCc
Confidence            34566666666665432   68999999999999999999888644

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=98.15  E-value=5.1e-06  Score=60.18  Aligned_cols=45  Identities=20%  Similarity=0.434  Sum_probs=36.2

Q ss_pred             cCCCCCHHHHHHHHHHhc--CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         16 EELGLNTIQFEAYKAALT--REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~--~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ..+.+.+.|.+.+..+..  ++.++|.||+|+||||++.+++..+..
T Consensus       222 ~~Lg~~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL~a~L~~l~~  268 (486)
T TIGR02533       222 ETLGMSPELLSRFERLIRRPHGIILVTGPTGSGKTTTLYAALSRLNT  268 (486)
T ss_pred             HHcCCCHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHhccCC
Confidence            456678888888888765  357899999999999999888777743

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>KOG0328|consensus

Probab=98.15  E-value=8.2e-07  Score=60.33  Aligned_cols=72  Identities=22%  Similarity=0.179  Sum_probs=55.5

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEeCCCCCchHHH-HHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         18 LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYV-ALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~-~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ...+..|+.|+..+++++.++.++.+|||||.+ .+.++..+--..     ..-++|+++||++++.|+.+.+...+.
T Consensus        48 ekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~-----r~tQ~lilsPTRELa~Qi~~vi~alg~  120 (400)
T KOG0328|consen   48 EKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISV-----RETQALILSPTRELAVQIQKVILALGD  120 (400)
T ss_pred             CCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeeccccc-----ceeeEEEecChHHHHHHHHHHHHHhcc
Confidence            445788999999999999999999999999975 333333221111     246899999999999999998877664

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.15  E-value=4e-06  Score=58.45  Aligned_cols=24  Identities=38%  Similarity=0.634  Sum_probs=20.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .-+++.||||||||.+|.+++.+-
T Consensus       186 KGVLLYGPPGTGKTLLAkAVA~~T  209 (406)
T COG1222         186 KGVLLYGPPGTGKTLLAKAVANQT  209 (406)
T ss_pred             CceEeeCCCCCcHHHHHHHHHhcc
Confidence            468999999999999999987543

>PRK08118 topology modulation protein; Reviewed

Probab=98.14  E-value=2.5e-06  Score=53.63  Aligned_cols=23  Identities=30%  Similarity=0.453  Sum_probs=20.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||+||||++..+...+
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l   25 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKL   25 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999999998775

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=98.14  E-value=6.7e-06  Score=59.64  Aligned_cols=53  Identities=19%  Similarity=0.380  Sum_probs=42.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +..++|.|+||+|||+++..++...+..       +.++++++... ..+++.+.+..++-
T Consensus       273 g~~~li~G~~G~GKT~l~~~~~~~~~~~-------g~~~~yis~e~-~~~~i~~~~~~~g~  325 (509)
T PRK09302        273 GSIILVSGATGTGKTLLASKFAEAACRR-------GERCLLFAFEE-SRAQLIRNARSWGI  325 (509)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhC-------CCcEEEEEecC-CHHHHHHHHHHcCC
Confidence            4577899999999999999998887766       77888887543 47778887777653

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=98.14  E-value=1.4e-05  Score=54.10  Aligned_cols=39  Identities=18%  Similarity=0.359  Sum_probs=29.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      ..+++.||+|+||||++..++..+....     .+.+|.+++..
T Consensus       195 ~vi~~vGptGvGKTTt~~kLa~~~~~~~-----g~~~V~li~~D  233 (282)
T TIGR03499       195 GVIALVGPTGVGKTTTLAKLAARFVLEH-----GNKKVALITTD  233 (282)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHHc-----CCCeEEEEECC
Confidence            4788999999999999999998886541     13567776643

>KOG2028|consensus

Probab=98.14  E-value=5.3e-06  Score=58.40  Aligned_cols=49  Identities=31%  Similarity=0.284  Sum_probs=32.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      +.++++||||||||+++..++...-..       ..+++=++.++..+..+.+-++
T Consensus       163 pSmIlWGppG~GKTtlArlia~tsk~~-------SyrfvelSAt~a~t~dvR~ife  211 (554)
T KOG2028|consen  163 PSMILWGPPGTGKTTLARLIASTSKKH-------SYRFVELSATNAKTNDVRDIFE  211 (554)
T ss_pred             CceEEecCCCCchHHHHHHHHhhcCCC-------ceEEEEEeccccchHHHHHHHH
Confidence            588999999999999988877654222       3445555555555544444333

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=98.13  E-value=2.2e-05  Score=60.02  Aligned_cols=74  Identities=22%  Similarity=0.152  Sum_probs=57.8

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ...++......+.+..+.+++.++|.||||+||||-+-..+......      ....|.++-|.+.++..+.+++.+-..
T Consensus        46 ~~~LPv~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~~------~~g~I~~tQPRRlAArsvA~RvAeel~  119 (845)
T COG1643          46 RSGLPVTAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGLG------IAGKIGCTQPRRLAARSVAERVAEELG  119 (845)
T ss_pred             cccCCcHHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhcc------cCCeEEecCchHHHHHHHHHHHHHHhC
Confidence            44566677777777777789999999999999999765555444332      367899999999999999999887554

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.13  E-value=1.8e-05  Score=60.97  Aligned_cols=47  Identities=21%  Similarity=0.270  Sum_probs=36.9

Q ss_pred             ccCCCCCHHHHHHHHHHhc------CC-c-eEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         15 QEELGLNTIQFEAYKAALT------RE-F-AIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~------~~-~-~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++.++-++.|.+.+...+.      ++ . ++|.|+||||||.++..++..+.+.
T Consensus       754 PD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqee  808 (1164)
T PTZ00112        754 PKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHK  808 (1164)
T ss_pred             CCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHH
Confidence            4667789999988877663      12 3 4699999999999999999887654

>KOG0922|consensus

Probab=98.12  E-value=8.7e-06  Score=60.21  Aligned_cols=71  Identities=20%  Similarity=0.168  Sum_probs=53.3

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHH-HHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYV-ALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~-~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..++..+...+.+..+.+++.++|.|.+|+||||= -..+.++-...       ..+|.+.-|.+.|+-.+.+++.+-.
T Consensus        48 ~~LPI~~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~~-------~g~I~~TQPRRVAavslA~RVAeE~  119 (674)
T KOG0922|consen   48 ESLPIYKYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFAS-------SGKIACTQPRRVAAVSLAKRVAEEM  119 (674)
T ss_pred             ccCCHHHHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhccccc-------CCcEEeecCchHHHHHHHHHHHHHh
Confidence            44566666677788888899999999999999984 33333333333       3449999999999999999987643

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.12  E-value=9e-06  Score=57.66  Aligned_cols=24  Identities=46%  Similarity=0.602  Sum_probs=20.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++..++...
T Consensus        37 ~~ilL~GppGtGKTtLA~~ia~~~   60 (413)
T PRK13342         37 SSMILWGPPGTGKTTLARIIAGAT   60 (413)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999887654

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=98.12  E-value=5.7e-06  Score=58.37  Aligned_cols=48  Identities=21%  Similarity=0.289  Sum_probs=34.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC---hHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT---NHALDQFVEG   88 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~---~~~~~~~~~~   88 (97)
                      ++.+++.||+|+||||++..++..+...       +.++.+++-.   ..+++||...
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~~l~~~-------g~~V~lItaDtyR~gAveQLk~y  256 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGWQLLKQ-------NRTVGFITTDTFRSGAVEQFQGY  256 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc-------CCeEEEEeCCccCccHHHHHHHH
Confidence            4578999999999999999999887665       5667666642   2345555443

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=98.12  E-value=6.8e-06  Score=51.51  Aligned_cols=34  Identities=26%  Similarity=0.402  Sum_probs=27.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      .+++.|+||+|||+++..++..+.+.       +.+++++.
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~-------g~~v~~i~   35 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKK-------GKKVLLVA   35 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-------CCcEEEEE
Confidence            46789999999999999998887665       56666555

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=98.12  E-value=2.1e-05  Score=55.66  Aligned_cols=48  Identities=21%  Similarity=0.357  Sum_probs=35.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC---ChHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY---TNHALDQFV   86 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~---~~~~~~~~~   86 (97)
                      ++.+.+.||+|.||||++..++..+....     ..++|-+++-   ...|++|+.
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~-----~~~kVaiITtDtYRIGA~EQLk  253 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLK-----KKKKVAIITTDTYRIGAVEQLK  253 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhc-----cCcceEEEEeccchhhHHHHHH
Confidence            56889999999999999999988887221     3677777763   445666553

>TIGR02012 tigrfam_recA protein RecA

Probab=98.12  E-value=9e-06  Score=56.10  Aligned_cols=37  Identities=27%  Similarity=0.346  Sum_probs=29.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +..+.|.||||||||+++..++......       +.+++++..
T Consensus        55 G~iteI~G~~GsGKTtLaL~~~~~~~~~-------g~~v~yId~   91 (321)
T TIGR02012        55 GRIIEIYGPESSGKTTLALHAIAEAQKA-------GGTAAFIDA   91 (321)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc-------CCcEEEEcc
Confidence            3578899999999999999998888765       556665543

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=98.12  E-value=3.1e-06  Score=49.99  Aligned_cols=22  Identities=41%  Similarity=0.611  Sum_probs=19.8

Q ss_pred             eEEeCCCCCchHHHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++|.|+||+||||++..+...+
T Consensus         1 I~i~G~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAERL   22 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            4799999999999999998884

...

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=98.12  E-value=6.1e-06  Score=64.87  Aligned_cols=58  Identities=26%  Similarity=0.345  Sum_probs=45.8

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhch-hhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNK-ELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~-~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .+++++|.+..|||||+++..++-.++-.. ..   ...++|++++|+.|+.+|.+|+.+-.
T Consensus        15 ~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~---~v~~ILvvTFT~aAa~Emk~RI~~~L   73 (1139)
T COG1074          15 PGQSVLVEASAGTGKTFVLAERVLRLLLEGGPL---DVDEILVVTFTKAAAAEMKERIRDRL   73 (1139)
T ss_pred             CCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCC---ChhHeeeeeccHHHHHHHHHHHHHHH
Confidence            456899999999999997666655554442 12   46899999999999999999988754

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=98.10  E-value=1.3e-05  Score=56.96  Aligned_cols=46  Identities=17%  Similarity=0.270  Sum_probs=34.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC---hHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT---NHALDQFVE   87 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~---~~~~~~~~~   87 (97)
                      ..+++.||+|+||||++..++..+...       +.++.+++..   ..+++|+..
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~~~-------GkkVglI~aDt~RiaAvEQLk~  290 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFHGK-------KKTVGFITTDHSRIGTVQQLQD  290 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHc-------CCcEEEEecCCcchHHHHHHHH
Confidence            467899999999999999999888654       6677766642   235556554

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=98.10  E-value=9.3e-06  Score=59.76  Aligned_cols=44  Identities=23%  Similarity=0.423  Sum_probs=36.3

Q ss_pred             cCCCCCHHHHHHHHHHhc--CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALT--REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~--~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      ..+.+.+.|.+.+..+..  ++.++|.||+|+||||++.+++..+.
T Consensus       296 ~~lg~~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl~a~l~~~~  341 (564)
T TIGR02538       296 DKLGFEPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSLYTALNILN  341 (564)
T ss_pred             HHcCCCHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHhhC
Confidence            456678888888887664  56889999999999999988888774

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>KOG0731|consensus

Probab=98.10  E-value=4.9e-06  Score=62.68  Aligned_cols=24  Identities=42%  Similarity=0.627  Sum_probs=21.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +-+++.||||||||.+|.+++...
T Consensus       345 kGvLL~GPPGTGKTLLAKAiAGEA  368 (774)
T KOG0731|consen  345 KGVLLVGPPGTGKTLLAKAIAGEA  368 (774)
T ss_pred             CceEEECCCCCcHHHHHHHHhccc
Confidence            458999999999999999997765

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=98.10  E-value=2.4e-06  Score=51.60  Aligned_cols=21  Identities=43%  Similarity=0.838  Sum_probs=18.3

Q ss_pred             eEEeCCCCCchHHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +++.||||+||||++..+...
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~   22 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKR   22 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            689999999999998888644

...

>KOG0948|consensus

Probab=98.09  E-value=1.1e-05  Score=60.76  Aligned_cols=73  Identities=18%  Similarity=0.139  Sum_probs=62.6

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      -.|.|++.|..+|..+.++++++|.+-+.+|||.+|-..++..++.       .+||++.+|=..+-.|=.+.+.+-+.+
T Consensus       126 YPF~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~-------kQRVIYTSPIKALSNQKYREl~~EF~D  198 (1041)
T KOG0948|consen  126 YPFTLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLRE-------KQRVIYTSPIKALSNQKYRELLEEFKD  198 (1041)
T ss_pred             CCcccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHh-------cCeEEeeChhhhhcchhHHHHHHHhcc
Confidence            4688999999999999899999999999999999999999998887       899999999777777766665554443

>PF05729 NACHT: NACHT domain

Probab=98.09  E-value=4.4e-06  Score=51.23  Aligned_cols=27  Identities=22%  Similarity=0.511  Sum_probs=24.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhch
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNK   62 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~   62 (97)
                      .++|.|+||+|||+++..++..+....
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~~   28 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEEE   28 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhcC
Confidence            578999999999999999999888874

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=98.09  E-value=6.5e-06  Score=52.01  Aligned_cols=47  Identities=15%  Similarity=0.222  Sum_probs=33.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      .++|.||||||||+++..++..+          +.++++++.....-+++.+++..+
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~----------~~~~~~iat~~~~~~e~~~ri~~h   49 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQS----------GLQVLYIATAQPFDDEMAARIAHH   49 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHc----------CCCcEeCcCCCCChHHHHHHHHHH
Confidence            57899999999999988886553          345666665555556666666544

>PRK06620 hypothetical protein; Validated

Probab=98.08  E-value=6.5e-06  Score=53.74  Aligned_cols=22  Identities=32%  Similarity=0.502  Sum_probs=18.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +.+++.||||+||||++..+..
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~   66 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQN   66 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHh
Confidence            3489999999999999887644

>PRK10876 recB exonuclease V subunit beta; Provisional

Probab=98.08  E-value=1.3e-05  Score=63.33  Aligned_cols=60  Identities=20%  Similarity=0.240  Sum_probs=44.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh-chhh--hh--cCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK-NKEL--AR--YMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~-~~~~--~~--~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .+..+|.+..|||||+++..+.-.++- .+..  +.  ....+||++++|+.|+.++.+|+++..
T Consensus        17 ~G~~LIEASAGTGKTyTIa~lyLrLlL~~g~~~~~~~~L~~~~ILvvTFT~aAt~Elr~RIr~rL   81 (1181)
T PRK10876         17 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEEILVVTFTEAATEELRGRIRSNI   81 (1181)
T ss_pred             CCCEEEEeCCCCcHHHHHHHHHHHHHccCCccccccCCCChhhEEEEechHHHHHHHHHHHHHHH
Confidence            467899999999999988777655544 2110  00  023689999999999999999997643

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=98.08  E-value=1.6e-05  Score=55.60  Aligned_cols=28  Identities=21%  Similarity=0.450  Sum_probs=24.9

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .++.++|.||+|+||||++.+++..+..
T Consensus       133 ~~glilI~GpTGSGKTTtL~aLl~~i~~  160 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLLAAIIRELAE  160 (358)
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            4679999999999999999999888754

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>PRK13909 putative recombination protein RecB; Provisional

Probab=98.07  E-value=1.1e-05  Score=62.30  Aligned_cols=52  Identities=19%  Similarity=0.317  Sum_probs=41.5

Q ss_pred             EEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         38 IIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        38 ~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ++.++.|||||+++....-.++..+.    .+..||++++||.|+.+|.+|+.+..
T Consensus         2 ~~~AsAGsGKT~~L~~~yl~ll~~~~----~~~~IlavTFT~kAa~Emk~Ri~~~L   53 (910)
T PRK13909          2 ALKASAGSGKTFALSVRFLALLFKGA----NPSEILALTFTKKAANEMKERIIDTL   53 (910)
T ss_pred             ceecCCCCchhHHHHHHHHHHHhcCC----CcceEEEEeehHHHHHHHHHHHHHHH
Confidence            57789999999976666555555432    46799999999999999999988764

>KOG0743|consensus

Probab=98.07  E-value=4.1e-06  Score=59.64  Aligned_cols=24  Identities=29%  Similarity=0.503  Sum_probs=21.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +-.++.||||||||+++.+|+..+
T Consensus       236 RGYLLYGPPGTGKSS~IaAmAn~L  259 (457)
T KOG0743|consen  236 RGYLLYGPPGTGKSSFIAAMANYL  259 (457)
T ss_pred             ccceeeCCCCCCHHHHHHHHHhhc
Confidence            457999999999999999998877

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=98.07  E-value=1.5e-05  Score=59.04  Aligned_cols=37  Identities=22%  Similarity=0.059  Sum_probs=30.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .++|.|++|+||||++.+++..+.+..     .+.+++++..
T Consensus       316 pL~LyG~sGsGKTHLL~AIa~~a~~~~-----~g~~V~Yita  352 (617)
T PRK14086        316 PLFIYGESGLGKTHLLHAIGHYARRLY-----PGTRVRYVSS  352 (617)
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHHHhC-----CCCeEEEeeH
Confidence            489999999999999999999987642     3567777763

>KOG0342|consensus

Probab=98.07  E-value=6.9e-06  Score=59.03  Aligned_cols=77  Identities=21%  Similarity=0.157  Sum_probs=57.8

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHH-HHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVA-LRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~-~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +.....+.|...+..++.++.++..+-+|||||.-. .-.++.+..... ....+-.++|+|||++++-|++..+++..
T Consensus       101 GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~-~~r~~~~vlIi~PTRELA~Q~~~eak~Ll  178 (543)
T KOG0342|consen  101 GFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKF-KPRNGTGVLIICPTRELAMQIFAEAKELL  178 (543)
T ss_pred             CccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhccc-CCCCCeeEEEecccHHHHHHHHHHHHHHH
Confidence            445578889888888888999999999999999743 333444444322 12246689999999999999999887754

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.07  E-value=9.5e-06  Score=55.84  Aligned_cols=43  Identities=28%  Similarity=0.356  Sum_probs=30.5

Q ss_pred             cCCCCCHHHHHHHHHHhc--------CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALT--------REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~--------~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+.-.+...+.+..+..        .+.+++.||||||||+++..++..+
T Consensus        25 ~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l   75 (328)
T PRK00080         25 DEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEM   75 (328)
T ss_pred             HHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHh
Confidence            344455555555544332        2478999999999999999998776

>PF13173 AAA_14: AAA domain

Probab=98.05  E-value=2e-05  Score=47.29  Aligned_cols=41  Identities=27%  Similarity=0.500  Sum_probs=30.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHAL   82 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~   82 (97)
                      ++.++|.||.|+|||+++..++..+. .       +.+++++.......
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~-~-------~~~~~yi~~~~~~~   42 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL-P-------PENILYINFDDPRD   42 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc-c-------cccceeeccCCHHH
Confidence            46789999999999999999988876 2       45566665544433

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=98.05  E-value=1.4e-05  Score=55.20  Aligned_cols=38  Identities=26%  Similarity=0.347  Sum_probs=30.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      +..+.|.||||+|||+++..++......       +.+++++...
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~~~-------g~~~vyId~E   92 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQKL-------GGTVAFIDAE   92 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc-------CCCEEEECcc
Confidence            3578899999999999999998887665       5566666643

RecA couples ATP hydrolysis to DNA strand exchange.

>KOG0920|consensus

Probab=98.05  E-value=1.6e-05  Score=61.08  Aligned_cols=72  Identities=21%  Similarity=0.203  Sum_probs=57.8

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHH-HHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTY-VALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~-~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      ...++....+.+.++.+.+++.++|.|.||||||| +-..++......+     +..+|++.-|.+.++-.+.+++..
T Consensus       169 R~~LPa~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~-----~~~~IicTQPRRIsAIsvAeRVa~  241 (924)
T KOG0920|consen  169 RESLPAYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESG-----AACNIICTQPRRISAISVAERVAK  241 (924)
T ss_pred             HHhCccHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcC-----CCCeEEecCCchHHHHHHHHHHHH
Confidence            35566677788888888889999999999999999 4555566655553     477899999999999999998865

>PF12846 AAA_10: AAA-like domain

Probab=98.04  E-value=1.1e-05  Score=53.90  Aligned_cols=40  Identities=20%  Similarity=0.380  Sum_probs=33.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNH   80 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~   80 (97)
                      +++++|.|++|+|||+++..++..+...       +..++++=+..+
T Consensus         1 n~h~~i~G~tGsGKT~~~~~l~~~~~~~-------g~~~~i~D~~g~   40 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLKNLLEQLIRR-------GPRVVIFDPKGD   40 (304)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHc-------CCCEEEEcCCch
Confidence            3578999999999999999999888887       677777766544

>PRK13531 regulatory ATPase RavA; Provisional

Probab=98.04  E-value=7.4e-06  Score=59.24  Aligned_cols=29  Identities=34%  Similarity=0.604  Sum_probs=25.3

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ..++++++.||||||||+++..+...+..
T Consensus        37 lag~hVLL~GpPGTGKT~LAraLa~~~~~   65 (498)
T PRK13531         37 LSGESVFLLGPPGIAKSLIARRLKFAFQN   65 (498)
T ss_pred             ccCCCEEEECCCChhHHHHHHHHHHHhcc
Confidence            36789999999999999999999887644

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=98.04  E-value=1.1e-05  Score=58.32  Aligned_cols=24  Identities=38%  Similarity=0.614  Sum_probs=20.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus        89 ~giLL~GppGtGKT~la~alA~~~  112 (495)
T TIGR01241        89 KGVLLVGPPGTGKTLLAKAVAGEA  112 (495)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHc
Confidence            368999999999999999997654

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=98.04  E-value=8.6e-06  Score=54.46  Aligned_cols=39  Identities=28%  Similarity=0.382  Sum_probs=28.4

Q ss_pred             HHHHHHHHHh-cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         23 IQFEAYKAAL-TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        23 ~Q~~~i~~~~-~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ...+.+.... .++++++.||+|+||||++.+++..+-..
T Consensus       115 ~~~~~l~~~v~~~~~ili~G~tGSGKTT~l~all~~i~~~  154 (270)
T PF00437_consen  115 EIAEFLRSAVRGRGNILISGPTGSGKTTLLNALLEEIPPE  154 (270)
T ss_dssp             HHHHHHHHCHHTTEEEEEEESTTSSHHHHHHHHHHHCHTT
T ss_pred             HHHHHHhhccccceEEEEECCCccccchHHHHHhhhcccc
Confidence            3444444433 36799999999999999998888766444

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=98.04  E-value=7.3e-06  Score=56.92  Aligned_cols=28  Identities=25%  Similarity=0.546  Sum_probs=24.1

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .++.++|.||+|+||||++..++..+..
T Consensus       121 ~~g~ili~G~tGSGKTT~l~al~~~i~~  148 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTLASMIDYINK  148 (343)
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHhhCc
Confidence            3578999999999999999998887654

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PRK14530 adenylate kinase; Provisional

Probab=98.04  E-value=5.6e-06  Score=53.77  Aligned_cols=25  Identities=28%  Similarity=0.534  Sum_probs=21.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++.++|.||||+||||++..++..+
T Consensus         3 ~~~I~i~G~pGsGKsT~~~~La~~~   27 (215)
T PRK14530          3 QPRILLLGAPGAGKGTQSSNLAEEF   27 (215)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            4578999999999999999887655

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=98.03  E-value=1.5e-05  Score=52.56  Aligned_cols=58  Identities=16%  Similarity=0.211  Sum_probs=38.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhh-----cCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELAR-----YMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~-----~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...++.||||+|||+++..++..+.......+     ..+.+|++++-.. ..+++.+++..+.
T Consensus         2 ~~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~~Ed-~~~~i~~Rl~~i~   64 (239)
T cd01125           2 YVSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAED-PREEIHRRLEAIL   64 (239)
T ss_pred             ceeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEECCC-CHHHHHHHHHHHH
Confidence            35789999999999999999877654321111     1356788888433 2445666666554

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>KOG0348|consensus

Probab=98.03  E-value=3.2e-05  Score=56.54  Aligned_cols=76  Identities=22%  Similarity=0.213  Sum_probs=57.8

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHH-HHHHHhch-hhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRI-VEGFLKNK-ELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~-~~~~~~~~-~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .++..|+++|..+++++-++|..++|+|||.--+.- +..+.... ++.+-.+.-.||++||++++-|+++.+.++..
T Consensus       159 ~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTREL~~Q~y~~~qKLl~  236 (708)
T KOG0348|consen  159 APTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTRELALQIYETVQKLLK  236 (708)
T ss_pred             ccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCceEEEEechHHHHHHHHHHHHHHhc
Confidence            356789999999999999999999999999754333 44443332 22333567899999999999999998877653

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=98.03  E-value=1.6e-05  Score=56.03  Aligned_cols=24  Identities=38%  Similarity=0.629  Sum_probs=21.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus       166 ~gvLL~GppGtGKT~lAkaia~~~  189 (389)
T PRK03992        166 KGVLLYGPPGTGKTLLAKAVAHET  189 (389)
T ss_pred             CceEEECCCCCChHHHHHHHHHHh
Confidence            358999999999999999998765

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=98.03  E-value=6e-05  Score=53.55  Aligned_cols=38  Identities=24%  Similarity=0.201  Sum_probs=31.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ..++|.||+|.||||++.+++..+.+..     +..+++.++.
T Consensus       114 nplfi~G~~GlGKTHLl~Aign~~~~~~-----~~a~v~y~~s  151 (408)
T COG0593         114 NPLFIYGGVGLGKTHLLQAIGNEALANG-----PNARVVYLTS  151 (408)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHhhC-----CCceEEeccH
Confidence            5789999999999999999999998883     3456666663

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=98.02  E-value=2.8e-05  Score=55.73  Aligned_cols=35  Identities=26%  Similarity=0.326  Sum_probs=28.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+++.|++|+||||++..++..+.+.       +.++++++.
T Consensus        97 vI~lvG~~GsGKTTtaakLA~~L~~~-------g~kV~lV~~  131 (437)
T PRK00771         97 TIMLVGLQGSGKTTTAAKLARYFKKK-------GLKVGLVAA  131 (437)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHc-------CCeEEEecC
Confidence            57889999999999999999887654       566776664

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=98.01  E-value=7.1e-06  Score=47.95  Aligned_cols=25  Identities=40%  Similarity=0.720  Sum_probs=22.0

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +.|.||||+|||+++..++..+.+.
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~   25 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKH   25 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHH
Confidence            4689999999999999998888865

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=98.01  E-value=1.3e-05  Score=52.10  Aligned_cols=36  Identities=33%  Similarity=0.421  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHh-cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         22 TIQFEAYKAAL-TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        22 ~~Q~~~i~~~~-~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +..+.++..+. .+.++++.||||||||+++..+...
T Consensus         9 e~aKrAL~iAAaG~h~lLl~GppGtGKTmlA~~l~~l   45 (206)
T PF01078_consen    9 EEAKRALEIAAAGGHHLLLIGPPGTGKTMLARRLPSL   45 (206)
T ss_dssp             HHHHHHHHHHHHCC--EEEES-CCCTHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHcCCCCeEEECCCCCCHHHHHHHHHHh
Confidence            34455555544 4568999999999999998888543

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>PRK10867 signal recognition particle protein; Provisional

Probab=98.01  E-value=2.7e-05  Score=55.71  Aligned_cols=36  Identities=25%  Similarity=0.351  Sum_probs=29.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+++.|++|+||||++..++.++...      .+.++++++.
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~l~~~------~G~kV~lV~~  137 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKYLKKK------KKKKVLLVAA  137 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHh------cCCcEEEEEc
Confidence            57889999999999999999988665      2667777664

>PRK03839 putative kinase; Provisional

Probab=98.01  E-value=6.3e-06  Score=51.99  Aligned_cols=23  Identities=39%  Similarity=0.613  Sum_probs=20.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.|+||+||||++..++..+
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~   24 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKL   24 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999887765

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=98.01  E-value=2.2e-05  Score=56.14  Aligned_cols=35  Identities=20%  Similarity=0.335  Sum_probs=28.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+++.|++|+||||++..++.++...       +.++++++.
T Consensus       102 vi~lvG~~GvGKTTtaaKLA~~l~~~-------G~kV~lV~~  136 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLAYYYQRK-------GFKPCLVCA  136 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-------CCCEEEEcC
Confidence            57899999999999999999877544       667777764

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=98.00  E-value=7.1e-06  Score=51.76  Aligned_cols=26  Identities=38%  Similarity=0.731  Sum_probs=21.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +++|+|+||+||||++..++..+...
T Consensus         1 ~i~iTG~pG~GKTTll~k~i~~l~~~   26 (168)
T PF03266_consen    1 HIFITGPPGVGKTTLLKKVIEELKKK   26 (168)
T ss_dssp             EEEEES-TTSSHHHHHHHHHHHHHHT
T ss_pred             CEEEECcCCCCHHHHHHHHHHHhhcc
Confidence            47899999999999999999888554

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=98.00  E-value=2.1e-05  Score=42.51  Aligned_cols=22  Identities=36%  Similarity=0.594  Sum_probs=20.0

Q ss_pred             eEEeCCCCCchHHHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.+.|+||+|||+++..+...+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5789999999999999998887

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>CHL00195 ycf46 Ycf46; Provisional

Probab=98.00  E-value=2.3e-05  Score=56.89  Aligned_cols=24  Identities=29%  Similarity=0.428  Sum_probs=21.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.+++.||||||||.++.+++..+
T Consensus       260 kGILL~GPpGTGKTllAkaiA~e~  283 (489)
T CHL00195        260 RGLLLVGIQGTGKSLTAKAIANDW  283 (489)
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHh
Confidence            468999999999999999998876

>KOG0947|consensus

Probab=98.00  E-value=3.3e-05  Score=59.52  Aligned_cols=75  Identities=16%  Similarity=0.035  Sum_probs=66.1

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .-.|.++..|++||....++.+++|.+++.+|||.+|-+.+......       ..|.++.+|=+.+-.|=+.++++.++
T Consensus       293 ~~pFelD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~h-------~TR~iYTSPIKALSNQKfRDFk~tF~  365 (1248)
T KOG0947|consen  293 IYPFELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQKH-------MTRTIYTSPIKALSNQKFRDFKETFG  365 (1248)
T ss_pred             hCCCCccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHhh-------ccceEecchhhhhccchHHHHHHhcc
Confidence            34678899999999999999999999999999999998888877766       78999999999999998888888776


Q ss_pred             CC
Q psy16285         95 NT   96 (97)
Q Consensus        95 ~~   96 (97)
                      ++
T Consensus       366 Dv  367 (1248)
T KOG0947|consen  366 DV  367 (1248)
T ss_pred             cc
Confidence            54

>PRK00131 aroK shikimate kinase; Reviewed

Probab=97.99  E-value=8e-06  Score=50.73  Aligned_cols=25  Identities=16%  Similarity=0.267  Sum_probs=21.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+++.|+||||||+++..++..+
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~l   28 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKRL   28 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHh
Confidence            4578999999999999999987765

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.99  E-value=1.9e-05  Score=53.58  Aligned_cols=44  Identities=27%  Similarity=0.394  Sum_probs=32.9

Q ss_pred             CCCCHHHHHHHHHHhcC---CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         18 LGLNTIQFEAYKAALTR---EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +.-.+...+.+..+.+.   +.+++.||||+|||+++..++..+...
T Consensus        19 ~~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~   65 (319)
T PRK00440         19 IVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGE   65 (319)
T ss_pred             hcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCC
Confidence            33455666677766543   368999999999999999998887543

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=97.99  E-value=7.2e-06  Score=51.67  Aligned_cols=23  Identities=39%  Similarity=0.598  Sum_probs=19.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +.++|.||||+||||++..++..
T Consensus         4 ~ii~i~G~~GsGKsTl~~~l~~~   26 (188)
T TIGR01360         4 KIIFIVGGPGSGKGTQCEKIVEK   26 (188)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            56889999999999998888744

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.99  E-value=1.7e-05  Score=49.81  Aligned_cols=28  Identities=29%  Similarity=0.318  Sum_probs=24.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..+++.|++|+||||++..+...+...
T Consensus         7 ~~~I~i~G~~GsGKst~a~~l~~~l~~~   34 (176)
T PRK05541          7 GYVIWITGLAGSGKTTIAKALYERLKLK   34 (176)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            4578999999999999999998888544

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=97.99  E-value=1.7e-05  Score=50.06  Aligned_cols=46  Identities=20%  Similarity=0.355  Sum_probs=34.2

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ++|.||+|+|||+.+..++..   .       +.++++++.....-.++.++++++
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~---~-------~~~~~y~at~~~~d~em~~rI~~H   47 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE---L-------GGPVTYIATAEAFDDEMAERIARH   47 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh---c-------CCCeEEEEccCcCCHHHHHHHHHH
Confidence            689999999999998887654   2       567777776655556667666554

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.99  E-value=6.9e-06  Score=51.75  Aligned_cols=22  Identities=41%  Similarity=0.742  Sum_probs=19.0

Q ss_pred             eEEeCCCCCchHHHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++|.||||+||||++..++..+
T Consensus         2 i~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            6899999999999988886654

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=97.99  E-value=7.2e-06  Score=52.21  Aligned_cols=22  Identities=36%  Similarity=0.718  Sum_probs=19.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +++|.||||+||||.+..++..
T Consensus         2 riiilG~pGaGK~T~A~~La~~   23 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKK   23 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999999766

>PRK06762 hypothetical protein; Provisional

Probab=97.98  E-value=2.7e-05  Score=48.40  Aligned_cols=24  Identities=38%  Similarity=0.639  Sum_probs=20.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.|+||+||||++..+...+
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~l   26 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQERL   26 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            357899999999999999888776

>smart00763 AAA_PrkA PrkA AAA domain

Probab=97.98  E-value=1.6e-05  Score=55.58  Aligned_cols=42  Identities=14%  Similarity=0.206  Sum_probs=30.4

Q ss_pred             CCHHHHHHHHHHhc--------CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         20 LNTIQFEAYKAALT--------REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        20 l~~~Q~~~i~~~~~--------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .++...+.+..+..        +..+++.||||+|||+++..++..+...
T Consensus        56 ~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~~y  105 (361)
T smart00763       56 MEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEEY  105 (361)
T ss_pred             cHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHhhh
Confidence            44445555554432        2467999999999999999999888663

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=97.98  E-value=1.7e-05  Score=49.84  Aligned_cols=28  Identities=25%  Similarity=0.303  Sum_probs=24.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..+++.|+||+||||++..+...+...
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~~l~~~   31 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAEKLREA   31 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            4578899999999999999999888544

>KOG0340|consensus

Probab=97.97  E-value=2.8e-05  Score=54.32  Aligned_cols=73  Identities=21%  Similarity=0.119  Sum_probs=60.5

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHH-HHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTY-VALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~-~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      -....+.|...|..++.++..+-.+-+|||||+ .+.-++..+-+..     .+-=.+|++||++.+.|+.+++.-.+.
T Consensus        27 i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP-----~giFalvlTPTrELA~QiaEQF~alGk  100 (442)
T KOG0340|consen   27 IKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDP-----YGIFALVLTPTRELALQIAEQFIALGK  100 (442)
T ss_pred             CCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCC-----CcceEEEecchHHHHHHHHHHHHHhcc
Confidence            345678899999999999999899999999998 5677777775552     345689999999999999999987764

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=97.97  E-value=1.2e-05  Score=55.98  Aligned_cols=36  Identities=22%  Similarity=0.355  Sum_probs=27.7

Q ss_pred             HHHHHHHHhc-CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         24 QFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        24 Q~~~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      ..+.+..+.+ +.+++|.||+|+||||++.+++..+-
T Consensus       151 ~~~~l~~~v~~~~nilI~G~tGSGKTTll~aLl~~i~  187 (344)
T PRK13851        151 LEAFLHACVVGRLTMLLCGPTGSGKTTMSKTLISAIP  187 (344)
T ss_pred             HHHHHHHHHHcCCeEEEECCCCccHHHHHHHHHcccC
Confidence            3444555553 57999999999999999999887653

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=97.97  E-value=2.9e-06  Score=56.97  Aligned_cols=38  Identities=37%  Similarity=0.656  Sum_probs=29.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+..+++.||+||||||+ ..|++.+++.      ....|++--.
T Consensus        26 ~gef~vliGpSGsGKTTt-LkMINrLiep------t~G~I~i~g~   63 (309)
T COG1125          26 EGEFLVLIGPSGSGKTTT-LKMINRLIEP------TSGEILIDGE   63 (309)
T ss_pred             CCeEEEEECCCCCcHHHH-HHHHhcccCC------CCceEEECCe
Confidence            467899999999999999 5677777776      4566666543

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=97.97  E-value=8.1e-06  Score=51.37  Aligned_cols=24  Identities=21%  Similarity=0.351  Sum_probs=20.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.||+|+||||++..++..+
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~~   25 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARARL   25 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            467899999999999998887764

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>PRK07261 topology modulation protein; Provisional

Probab=97.97  E-value=8.7e-06  Score=51.33  Aligned_cols=23  Identities=26%  Similarity=0.443  Sum_probs=20.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.|+||+||||++..+...+
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~   24 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHY   24 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHh
Confidence            47899999999999999887654

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=97.96  E-value=1.6e-05  Score=56.37  Aligned_cols=24  Identities=38%  Similarity=0.607  Sum_probs=20.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus       180 kgvLL~GppGTGKT~LAkalA~~l  203 (398)
T PTZ00454        180 RGVLLYGPPGTGKTMLAKAVAHHT  203 (398)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhc
Confidence            468999999999999999887654

>PRK14532 adenylate kinase; Provisional

Probab=97.96  E-value=7.5e-06  Score=51.95  Aligned_cols=22  Identities=45%  Similarity=0.638  Sum_probs=18.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      ++++.||||+||||++..++..
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~   23 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEE   23 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999998888654

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=97.95  E-value=6.4e-05  Score=56.82  Aligned_cols=69  Identities=14%  Similarity=-0.006  Sum_probs=47.4

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+.+.+.|.........+  .+...+||+|||.++...+. +..-      .+..++|++||..++.+..+.+..+..
T Consensus        54 g~~p~~vQlig~~~l~~G--~Iaem~TGeGKTLva~lpa~-l~aL------~G~~V~VvTpt~~LA~qdae~~~~l~~  122 (745)
T TIGR00963        54 GMRPFDVQLIGGIALHKG--KIAEMKTGEGKTLTATLPAY-LNAL------TGKGVHVVTVNDYLAQRDAEWMGQVYR  122 (745)
T ss_pred             CCCccchHHhhhhhhcCC--ceeeecCCCccHHHHHHHHH-HHHH------hCCCEEEEcCCHHHHHHHHHHHHHHhc
Confidence            344455565554443333  38899999999976543332 2121      256899999999999999999888765

The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.

>TIGR00959 ffh signal recognition particle protein

Probab=97.95  E-value=3.9e-05  Score=54.89  Aligned_cols=36  Identities=22%  Similarity=0.331  Sum_probs=28.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+++.|++|+||||++..++..+...      .+.++++++.
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~l~~~------~g~kV~lV~~  136 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYYLKKK------QGKKVLLVAC  136 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHh------CCCeEEEEec
Confidence            57899999999999999999987643      2567776664

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PRK14531 adenylate kinase; Provisional

Probab=97.95  E-value=1e-05  Score=51.32  Aligned_cols=24  Identities=33%  Similarity=0.596  Sum_probs=20.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||+||||++..++..+
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~   26 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAH   26 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            468999999999999988886654

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=97.95  E-value=1.7e-05  Score=48.59  Aligned_cols=35  Identities=14%  Similarity=0.333  Sum_probs=27.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+.|.|+.|+||||++..++..+.++       +.++.++-+
T Consensus         2 vv~VvG~~~sGKTTl~~~Li~~l~~~-------g~~v~~ik~   36 (140)
T PF03205_consen    2 VVQVVGPKNSGKTTLIRKLINELKRR-------GYRVAVIKH   36 (140)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT-------T--EEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhHc-------CCceEEEEE
Confidence            57899999999999999999999877       556664443

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.95  E-value=1.3e-05  Score=50.37  Aligned_cols=26  Identities=38%  Similarity=0.618  Sum_probs=23.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.|+|+||+||||++..++..+.+.
T Consensus         7 ki~ITG~PGvGKtTl~~ki~e~L~~~   32 (179)
T COG1618           7 KIFITGRPGVGKTTLVLKIAEKLREK   32 (179)
T ss_pred             EEEEeCCCCccHHHHHHHHHHHHHhc
Confidence            67899999999999999999988776

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=97.94  E-value=9.4e-06  Score=51.43  Aligned_cols=22  Identities=36%  Similarity=0.644  Sum_probs=19.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +++|.||||+||||++..++..
T Consensus         1 ~I~i~G~pGsGKst~a~~La~~   22 (194)
T cd01428           1 RILLLGPPGSGKGTQAERLAKK   22 (194)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999998888665

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=97.94  E-value=3.6e-05  Score=51.04  Aligned_cols=25  Identities=24%  Similarity=0.511  Sum_probs=21.9

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +++.|+||+||||++..+...+...
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~~~   26 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLSEK   26 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            6899999999999999999887544

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.94  E-value=4.4e-05  Score=54.01  Aligned_cols=40  Identities=28%  Similarity=0.321  Sum_probs=29.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ..+++.||+|+||||++..++..+......   .+.+|.+++-
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~~---~g~~V~lit~  214 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSDD---KSLNIKIITI  214 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhcc---CCCeEEEEec
Confidence            468899999999999999999877643110   2566776664

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=97.94  E-value=1e-05  Score=53.63  Aligned_cols=23  Identities=35%  Similarity=0.525  Sum_probs=19.3

Q ss_pred             EeCCCCCchHHHHHHHHHHHHhc
Q psy16285         39 IQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        39 v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      |.||||+||||....+..++...
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~~~   23 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWLESN   23 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhc
Confidence            68999999999988888887555

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PRK06851 hypothetical protein; Provisional

Probab=97.93  E-value=1.2e-05  Score=56.47  Aligned_cols=28  Identities=39%  Similarity=0.679  Sum_probs=25.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.++|.|+||||||+++..++..+.+.
T Consensus        30 ~~~~il~G~pGtGKStl~~~i~~~~~~~   57 (367)
T PRK06851         30 NRIFILKGGPGTGKSTLMKKIGEEFLEK   57 (367)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            4678999999999999999999988775

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=97.92  E-value=1.9e-05  Score=48.11  Aligned_cols=27  Identities=22%  Similarity=0.434  Sum_probs=23.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +..+++.|+.|+|||+++..++..+-.
T Consensus        22 ~~~i~l~G~lGaGKTtl~~~l~~~lg~   48 (133)
T TIGR00150        22 GTVVLLKGDLGAGKTTLVQGLLQGLGI   48 (133)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHcCC
Confidence            568899999999999999999988743

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=97.92  E-value=2.2e-05  Score=56.25  Aligned_cols=24  Identities=42%  Similarity=0.653  Sum_probs=21.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus       218 ~gVLL~GPPGTGKT~LAraIA~el  241 (438)
T PTZ00361        218 KGVILYGPPGTGKTLLAKAVANET  241 (438)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhh
Confidence            368999999999999999998765

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=97.92  E-value=3.3e-05  Score=57.42  Aligned_cols=29  Identities=24%  Similarity=0.456  Sum_probs=24.7

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.+++++||||||||+++..++..+...
T Consensus        36 ~~~~~ll~G~pG~GKT~la~~la~~l~~~   64 (608)
T TIGR00764        36 QKRNVLLIGEPGVGKSMLAKAMAELLPDE   64 (608)
T ss_pred             cCCCEEEECCCCCCHHHHHHHHHHHcCch
Confidence            46789999999999999999998877443

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PRK09354 recA recombinase A; Provisional

Probab=97.92  E-value=3.1e-05  Score=54.04  Aligned_cols=37  Identities=27%  Similarity=0.354  Sum_probs=29.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +..+.|.||||||||+++..++......       +.+++++..
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~~-------G~~~~yId~   96 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQKA-------GGTAAFIDA   96 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc-------CCcEEEECC
Confidence            3477899999999999999998887665       555665554

>PRK08233 hypothetical protein; Provisional

Probab=97.92  E-value=9e-06  Score=50.98  Aligned_cols=24  Identities=25%  Similarity=0.390  Sum_probs=20.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+.|.|+||+||||++..++..+
T Consensus         4 ~iI~I~G~~GsGKtTla~~L~~~l   27 (182)
T PRK08233          4 KIITIAAVSGGGKTTLTERLTHKL   27 (182)
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhC
Confidence            457789999999999999888776

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=97.92  E-value=3.3e-05  Score=53.24  Aligned_cols=30  Identities=33%  Similarity=0.609  Sum_probs=26.1

Q ss_pred             HHhcCCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         30 AALTREFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        30 ~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      .+..++.+++.||||+|||.++..++..+-
T Consensus        39 a~~~~~~vll~G~PG~gKT~la~~lA~~l~   68 (329)
T COG0714          39 ALLAGGHVLLEGPPGVGKTLLARALARALG   68 (329)
T ss_pred             HHHcCCCEEEECCCCccHHHHHHHHHHHhC
Confidence            344688999999999999999999998884

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=97.92  E-value=1.8e-05  Score=50.01  Aligned_cols=25  Identities=32%  Similarity=0.515  Sum_probs=22.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      .++++.||+|+|||.++..++..+.
T Consensus         4 ~~~ll~GpsGvGKT~la~~la~~l~   28 (171)
T PF07724_consen    4 SNFLLAGPSGVGKTELAKALAELLF   28 (171)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3689999999999999999999886

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=97.92  E-value=1.8e-05  Score=52.61  Aligned_cols=35  Identities=20%  Similarity=0.273  Sum_probs=28.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +++|.|++|||||+++..++..+...       -..+.+.++
T Consensus        15 r~viIG~sGSGKT~li~~lL~~~~~~-------f~~I~l~t~   49 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTLIKSLLYYLRHK-------FDHIFLITP   49 (241)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhhccc-------CCEEEEEec
Confidence            78999999999999999998776554       355666665

This is thought to be an ATPase involved in viral DNA packaging [].

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=97.91  E-value=8.8e-06  Score=50.46  Aligned_cols=22  Identities=23%  Similarity=0.490  Sum_probs=18.9

Q ss_pred             eEEeCCCCCchHHHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++.||+|+||||++..+...+
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRL   22 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999998887664

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.91  E-value=3.3e-05  Score=55.94  Aligned_cols=39  Identities=15%  Similarity=0.295  Sum_probs=29.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ++.+.+.||+|+||||++..++..+....     +..+|.+++-
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~-----G~~kV~LI~~  294 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRH-----GASKVALLTT  294 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhc-----CCCeEEEEeC
Confidence            35788999999999999999998875441     1346666553

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=97.91  E-value=2.2e-05  Score=54.48  Aligned_cols=34  Identities=26%  Similarity=0.300  Sum_probs=26.4

Q ss_pred             HHHHHHh-cCCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         26 EAYKAAL-TREFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        26 ~~i~~~~-~~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +.+..+. .+.+++|.||+|+||||++.+++..+-
T Consensus       151 ~~L~~~v~~~~nili~G~tgSGKTTll~aL~~~ip  185 (332)
T PRK13900        151 EFLEHAVISKKNIIISGGTSTGKTTFTNAALREIP  185 (332)
T ss_pred             HHHHHHHHcCCcEEEECCCCCCHHHHHHHHHhhCC
Confidence            3444444 367999999999999999998887664

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.91  E-value=6.4e-05  Score=57.55  Aligned_cols=41  Identities=24%  Similarity=0.390  Sum_probs=31.6

Q ss_pred             CHHHHHHHHHHhc---CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         21 NTIQFEAYKAALT---REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        21 ~~~Q~~~i~~~~~---~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++.+.+.+..++.   ..+.++.||||+|||+++..++..+...
T Consensus       184 r~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal~~~la~~i~~~  227 (821)
T CHL00095        184 REKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQRIVNR  227 (821)
T ss_pred             cHHHHHHHHHHHcccccCCeEEECCCCCCHHHHHHHHHHHHHhC
Confidence            5555555655553   3588999999999999999999888654

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=97.91  E-value=9e-05  Score=56.15  Aligned_cols=71  Identities=18%  Similarity=0.281  Sum_probs=58.3

Q ss_pred             CCHHHHHHHHHHhc---CC-ceEEeCCCCCchHHHHHHHHHHHHhch-hhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         20 LNTIQFEAYKAALT---RE-FAIIQGPPGTGKTYVALRIVEGFLKNK-ELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        20 l~~~Q~~~i~~~~~---~~-~~~v~Gp~GtGKT~~~~~~~~~~~~~~-~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ..+.|..+++.+.+   .. .+++.+|+|.|||.++...+....... +    ...+++.+-|.+.+++++.+++++++.
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~----~~~r~i~vlP~~t~ie~~~~r~~~~~~  271 (733)
T COG1203         196 GYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIK----LKSRVIYVLPFRTIIEDMYRRAKEIFG  271 (733)
T ss_pred             hhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhcccc----ccceEEEEccHHHHHHHHHHHHHhhhc
Confidence            35678888877664   34 789999999999999988888887772 2    377899999999999999999998764

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.91  E-value=2.2e-05  Score=55.99  Aligned_cols=37  Identities=19%  Similarity=0.422  Sum_probs=28.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ..+++.||+|+||||++..++..+...      .+.++.+++-
T Consensus       224 ~vi~lvGptGvGKTTtaaKLA~~~~~~------~G~~V~Lit~  260 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIAKLAAKYFLH------MGKSVSLYTT  260 (432)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHh------cCCeEEEecc
Confidence            357899999999999999999866433      2566766664

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=97.91  E-value=1.4e-05  Score=50.27  Aligned_cols=25  Identities=20%  Similarity=0.345  Sum_probs=21.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+++.|+||+||||++..+...+
T Consensus         2 ~~~i~l~G~~gsGKst~a~~l~~~~   26 (175)
T cd00227           2 GRIIILNGGSSAGKSSIARALQSVL   26 (175)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhh
Confidence            4578999999999999999887764

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.90  E-value=1e-05  Score=56.44  Aligned_cols=23  Identities=39%  Similarity=0.639  Sum_probs=20.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.||||||||+++.+++..+
T Consensus       158 gvLL~GppGtGKT~lakaia~~l  180 (364)
T TIGR01242       158 GVLLYGPPGTGKTLLAKAVAHET  180 (364)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhC
Confidence            48999999999999999987654

Many proteins may score above the trusted cutoff because an internal

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=97.90  E-value=0.00011  Score=56.02  Aligned_cols=69  Identities=12%  Similarity=-0.008  Sum_probs=49.8

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ++...+.|...+....++.  +....||+|||.++...+.....       .+..++|++||..++.+..+.+..+..
T Consensus        76 g~~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al-------~G~~v~VvTpt~~LA~qd~e~~~~l~~  144 (790)
T PRK09200         76 GMRPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNAL-------EGKGVHLITVNDYLAKRDAEEMGQVYE  144 (790)
T ss_pred             CCCCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHH-------cCCCeEEEeCCHHHHHHHHHHHHHHHh
Confidence            4556667766655444433  89999999999875544332222       378999999999999999998887754

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.90  E-value=3e-05  Score=50.65  Aligned_cols=44  Identities=18%  Similarity=0.156  Sum_probs=29.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      +..+.|.||||+|||+++..++........ .......+++++..
T Consensus        19 g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~-~~g~~~~viyi~~e   62 (235)
T cd01123          19 GSITEIFGEFGSGKTQLCHQLAVTVQLPIE-LGGLEGKAVYIDTE   62 (235)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHeeCccc-cCCCCccEEEEeCC
Confidence            467899999999999999999866543310 00013566666643

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>PRK13947 shikimate kinase; Provisional

Probab=97.90  E-value=1.3e-05  Score=49.93  Aligned_cols=23  Identities=35%  Similarity=0.443  Sum_probs=20.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++|.|+||+|||+++..++..+
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~l   25 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTL   25 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHh
Confidence            58899999999999999988765

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=97.89  E-value=2.9e-05  Score=58.67  Aligned_cols=24  Identities=42%  Similarity=0.558  Sum_probs=21.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++++.||||||||+++..++...
T Consensus        53 ~slLL~GPpGtGKTTLA~aIA~~~   76 (725)
T PRK13341         53 GSLILYGPPGVGKTTLARIIANHT   76 (725)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999888654

>TIGR00750 lao LAO/AO transport system ATPase

Probab=97.89  E-value=2.7e-05  Score=53.17  Aligned_cols=28  Identities=21%  Similarity=0.285  Sum_probs=24.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ...+.|.||||+|||+++..++..+...
T Consensus        34 ~~~i~i~G~~G~GKttl~~~l~~~~~~~   61 (300)
T TIGR00750        34 AHRVGITGTPGAGKSTLLEALGMELRRR   61 (300)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            4578899999999999999999887665

Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.

>KOG0338|consensus

Probab=97.89  E-value=3.2e-05  Score=56.27  Aligned_cols=75  Identities=21%  Similarity=0.134  Sum_probs=55.1

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHH-HHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTY-VALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~-~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +....++.|...|..++-+.-++-.+.+|||||. .+.=++..++..-..  ....||||++||++++-|+....++.
T Consensus       200 Gy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~--~~~TRVLVL~PTRELaiQv~sV~~ql  275 (691)
T KOG0338|consen  200 GYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKK--VAATRVLVLVPTRELAIQVHSVTKQL  275 (691)
T ss_pred             CCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCccc--CcceeEEEEeccHHHHHHHHHHHHHH
Confidence            4556678898888888888888899999999996 345556666554111  13569999999999988877655443

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.89  E-value=1.2e-05  Score=58.63  Aligned_cols=26  Identities=31%  Similarity=0.639  Sum_probs=22.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ..+++.||||||||+++.+++..+..
T Consensus       217 ~GILLyGPPGTGKT~LAKAlA~eL~~  242 (512)
T TIGR03689       217 KGVLLYGPPGCGKTLIAKAVANSLAQ  242 (512)
T ss_pred             cceEEECCCCCcHHHHHHHHHHhhcc
Confidence            46899999999999999999888744

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=97.88  E-value=4.1e-05  Score=48.62  Aligned_cols=25  Identities=36%  Similarity=0.523  Sum_probs=21.2

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +.|.|+||+||||++..+...+...
T Consensus         2 i~i~G~sgsGKttla~~l~~~l~~~   26 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLSNQLRVN   26 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHc
Confidence            5789999999999999888877543

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>TIGR00665 DnaB replicative DNA helicase

Probab=97.88  E-value=4.3e-05  Score=54.43  Aligned_cols=51  Identities=24%  Similarity=0.350  Sum_probs=36.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      +..++|.|+||+|||+++..++..+...      .+.++++++..- ...++.+++..
T Consensus       195 G~l~vi~g~pg~GKT~~~l~~a~~~a~~------~g~~vl~~SlEm-~~~~i~~R~~~  245 (434)
T TIGR00665       195 SDLIILAARPSMGKTAFALNIAENAAIK------EGKPVAFFSLEM-SAEQLAMRMLS  245 (434)
T ss_pred             CeEEEEEeCCCCChHHHHHHHHHHHHHh------CCCeEEEEeCcC-CHHHHHHHHHH
Confidence            4578999999999999999998887654      267788887532 34445554443

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>PRK13764 ATPase; Provisional

Probab=97.88  E-value=2.3e-05  Score=58.07  Aligned_cols=29  Identities=31%  Similarity=0.441  Sum_probs=25.2

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+++++|.||||+||||++.+++..+...
T Consensus       256 ~~~~ILIsG~TGSGKTTll~AL~~~i~~~  284 (602)
T PRK13764        256 RAEGILIAGAPGAGKSTFAQALAEFYADM  284 (602)
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHHHhhC
Confidence            36789999999999999999999888654

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=97.88  E-value=1.6e-05  Score=48.54  Aligned_cols=23  Identities=26%  Similarity=0.372  Sum_probs=19.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++|.|+||+|||+++..+...+
T Consensus         1 ~i~l~G~~GsGKstla~~la~~l   23 (154)
T cd00464           1 NIVLIGMMGAGKTTVGRLLAKAL   23 (154)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHh
Confidence            47899999999999999987654

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>KOG3347|consensus

Probab=97.88  E-value=1.5e-05  Score=49.59  Aligned_cols=25  Identities=40%  Similarity=0.672  Sum_probs=21.5

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      ..++++|+|-|||||||++..++..
T Consensus         6 ~~PNILvtGTPG~GKstl~~~lae~   30 (176)
T KOG3347|consen    6 ERPNILVTGTPGTGKSTLAERLAEK   30 (176)
T ss_pred             cCCCEEEeCCCCCCchhHHHHHHHH
Confidence            3579999999999999998888643

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=97.88  E-value=3.1e-05  Score=52.75  Aligned_cols=27  Identities=37%  Similarity=0.581  Sum_probs=23.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+++.||||.||||++..++..+-.+
T Consensus        53 DHvLl~GPPGlGKTTLA~IIA~Emgvn   79 (332)
T COG2255          53 DHVLLFGPPGLGKTTLAHIIANELGVN   79 (332)
T ss_pred             CeEEeeCCCCCcHHHHHHHHHHHhcCC
Confidence            478999999999999999998887554

>PTZ00301 uridine kinase; Provisional

Probab=97.88  E-value=3e-05  Score=50.57  Aligned_cols=26  Identities=27%  Similarity=0.489  Sum_probs=22.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.|.||||+||||++..+...+...
T Consensus         5 iIgIaG~SgSGKTTla~~l~~~l~~~   30 (210)
T PTZ00301          5 VIGISGASGSGKSSLSTNIVSELMAH   30 (210)
T ss_pred             EEEEECCCcCCHHHHHHHHHHHHHhh
Confidence            46789999999999999998887654

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=97.88  E-value=3e-05  Score=50.34  Aligned_cols=44  Identities=23%  Similarity=0.262  Sum_probs=30.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      +..+.|.||||+|||+++..++......... .....+++++...
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~-~g~~~~v~yi~~e   62 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVEAQLPGEL-GGLEGKVVYIDTE   62 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHHhhccccc-CCCcceEEEEecC
Confidence            4688999999999999999998877654100 0012566666653

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>PRK06851 hypothetical protein; Provisional

Probab=97.88  E-value=2.5e-05  Score=54.81  Aligned_cols=28  Identities=25%  Similarity=0.459  Sum_probs=25.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.++|.|+||||||+++..++..+.++
T Consensus       214 ~~~~~i~G~pG~GKstl~~~i~~~a~~~  241 (367)
T PRK06851        214 KNRYFLKGRPGTGKSTMLKKIAKAAEER  241 (367)
T ss_pred             ceEEEEeCCCCCcHHHHHHHHHHHHHhC
Confidence            3578999999999999999999999877

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.87  E-value=3.6e-05  Score=54.17  Aligned_cols=37  Identities=22%  Similarity=0.330  Sum_probs=29.5

Q ss_pred             HHHHHHHh---cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         25 FEAYKAAL---TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        25 ~~~i~~~~---~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+|+...   ++++.+|.||||+|||+++..++..+..+
T Consensus       121 ~RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~la~~i~~~  160 (380)
T PRK12608        121 MRVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAAAVAAN  160 (380)
T ss_pred             HhhhhheeecCCCceEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            34555544   46799999999999999999998888665

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=97.86  E-value=2.5e-05  Score=52.42  Aligned_cols=47  Identities=19%  Similarity=0.320  Sum_probs=32.5

Q ss_pred             HHHHHHHHHhcC----CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         23 IQFEAYKAALTR----EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        23 ~Q~~~i~~~~~~----~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      .-.+.+..+..+    ..+=|+||||.||||+.-.++..+.+.       +.+|-|++
T Consensus        14 ~~~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~~~~~~-------g~~VaVlA   64 (266)
T PF03308_consen   14 EARELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIRELRER-------GKRVAVLA   64 (266)
T ss_dssp             HHHHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHHHHHHT-------T--EEEEE
T ss_pred             HHHHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHHHHhhc-------CCceEEEE
Confidence            344556655532    255679999999999999999999876       66777766

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

Probab=97.86  E-value=0.00014  Score=57.02  Aligned_cols=74  Identities=19%  Similarity=0.105  Sum_probs=60.8

Q ss_pred             ccCCCCCHHHHHHHHHHhc----CC--ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALT----RE--FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~----~~--~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      .-.+..++.|..+|+.+.+    +.  --+|+|-.|=|||-+|...+-.++..       +++|.|++||..++.|=++.
T Consensus       590 ~FPyeET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~-------GKQVAvLVPTTlLA~QHy~t  662 (1139)
T COG1197         590 SFPYEETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMD-------GKQVAVLVPTTLLAQQHYET  662 (1139)
T ss_pred             cCCCcCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcC-------CCeEEEEcccHHhHHHHHHH
Confidence            4456778999999999874    22  34899999999999998888777776       89999999999999998887


Q ss_pred             HHhhccC
Q psy16285         89 VLKYTQN   95 (97)
Q Consensus        89 l~~~~~~   95 (97)
                      +++-+.+
T Consensus       663 FkeRF~~  669 (1139)
T COG1197         663 FKERFAG  669 (1139)
T ss_pred             HHHHhcC
Confidence            7776643

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=97.86  E-value=0.00011  Score=49.10  Aligned_cols=41  Identities=20%  Similarity=0.246  Sum_probs=30.9

Q ss_pred             CHHHHHHHHHHhc-------CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         21 NTIQFEAYKAALT-------REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        21 ~~~Q~~~i~~~~~-------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      -+.|++.+..-..       ..++++.|+.|||||+++.+++..+...
T Consensus        32 ie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~   79 (249)
T PF05673_consen   32 IERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQ   79 (249)
T ss_pred             HHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhc
Confidence            3456666554332       2589999999999999999998887665

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.85  E-value=6.1e-05  Score=55.22  Aligned_cols=38  Identities=21%  Similarity=0.409  Sum_probs=29.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ++.+.+.||+|+||||++..++..+....     .+.++.++.
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa~la~~~-----~gkkVaLId  387 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQRFAAQH-----APRDVALVT  387 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHhc-----CCCceEEEe
Confidence            56889999999999999999988876642     235566655

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=97.85  E-value=3.8e-05  Score=48.02  Aligned_cols=33  Identities=18%  Similarity=0.326  Sum_probs=27.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEE
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIV   75 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~   75 (97)
                      .+.++|.||+||||++..+...+...       +.++.++
T Consensus         4 vIwltGlsGsGKtTlA~~L~~~L~~~-------g~~~~~L   36 (156)
T PF01583_consen    4 VIWLTGLSGSGKTTLARALERRLFAR-------GIKVYLL   36 (156)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHT-------TS-EEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc-------CCcEEEe
Confidence            56889999999999999999999877       5666666

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>KOG0739|consensus

Probab=97.85  E-value=3.7e-05  Score=53.00  Aligned_cols=40  Identities=23%  Similarity=0.475  Sum_probs=28.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFV   86 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~   86 (97)
                      -+++.||||||||+++.+++....           ...|-..+..++..|.
T Consensus       168 giLLyGPPGTGKSYLAKAVATEAn-----------STFFSvSSSDLvSKWm  207 (439)
T KOG0739|consen  168 GILLYGPPGTGKSYLAKAVATEAN-----------STFFSVSSSDLVSKWM  207 (439)
T ss_pred             eEEEeCCCCCcHHHHHHHHHhhcC-----------CceEEeehHHHHHHHh
Confidence            579999999999999999987652           4445555555444443

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=97.85  E-value=0.00011  Score=55.72  Aligned_cols=28  Identities=25%  Similarity=0.448  Sum_probs=24.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+.++.||||+|||+++..++..+...
T Consensus       203 ~~n~lL~G~pG~GKT~l~~~la~~~~~~  230 (731)
T TIGR02639       203 KNNPLLVGEPGVGKTAIAEGLALRIAEG  230 (731)
T ss_pred             CCceEEECCCCCCHHHHHHHHHHHHHhC
Confidence            3589999999999999999999988765

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=97.84  E-value=1.5e-05  Score=49.58  Aligned_cols=22  Identities=32%  Similarity=0.433  Sum_probs=16.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++|+|++||||||++..+...
T Consensus         1 rI~i~G~~stGKTTL~~~L~~~   22 (163)
T PF13521_consen    1 RIVITGGPSTGKTTLIEALAAR   22 (163)
T ss_dssp             -EEEE--TTSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHc
Confidence            3789999999999999888765

>PRK02496 adk adenylate kinase; Provisional

Probab=97.84  E-value=1.9e-05  Score=49.99  Aligned_cols=23  Identities=39%  Similarity=0.618  Sum_probs=19.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||+|||+++..++..+
T Consensus         3 ~i~i~G~pGsGKst~a~~la~~~   25 (184)
T PRK02496          3 RLIFLGPPGAGKGTQAVVLAEHL   25 (184)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999988886554

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=97.84  E-value=4.9e-05  Score=47.33  Aligned_cols=25  Identities=32%  Similarity=0.480  Sum_probs=22.1

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +.|.|++|+|||+++..++..+...
T Consensus         2 i~i~G~~gsGKTtl~~~l~~~l~~~   26 (155)
T TIGR00176         2 LQIVGPKNSGKTTLIERLVKALKAR   26 (155)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhc
Confidence            5689999999999999999988655

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>PRK13768 GTPase; Provisional

Probab=97.84  E-value=3.6e-05  Score=51.38  Aligned_cols=33  Identities=21%  Similarity=0.338  Sum_probs=27.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEE
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIV   75 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~   75 (97)
                      .+++.||+|+||||++..++..+...       +.+++++
T Consensus         4 ~i~v~G~~G~GKTt~~~~~~~~l~~~-------g~~v~~i   36 (253)
T PRK13768          4 IVFFLGTAGSGKTTLTKALSDWLEEQ-------GYDVAIV   36 (253)
T ss_pred             EEEEECCCCccHHHHHHHHHHHHHhc-------CCceEEE
Confidence            46899999999999999999888665       5666665

>PRK06217 hypothetical protein; Validated

Probab=97.83  E-value=1.7e-05  Score=50.34  Aligned_cols=23  Identities=26%  Similarity=0.414  Sum_probs=20.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.|+||+||||++..+...+
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l   25 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERL   25 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            47899999999999999998765

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=97.83  E-value=1.3e-05  Score=55.57  Aligned_cols=24  Identities=33%  Similarity=0.613  Sum_probs=20.3

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +++.+++.||+||||||++..++.
T Consensus        28 ~Gef~vllGPSGcGKSTlLr~IAG   51 (338)
T COG3839          28 DGEFVVLLGPSGCGKSTLLRMIAG   51 (338)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999999666643

>KOG0350|consensus

Probab=97.83  E-value=4.8e-05  Score=55.15  Aligned_cols=74  Identities=15%  Similarity=0.203  Sum_probs=53.3

Q ss_pred             CCCHHHHHHHHHHhc---------CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         19 GLNTIQFEAYKAALT---------REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~---------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      .+=+.|...+..++.         .+-++|.+|+|+|||.--..-+-+++..+..   +.-|.+|+.|+++++.|+.+.+
T Consensus       159 ~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v---~~LRavVivPtr~L~~QV~~~f  235 (620)
T KOG0350|consen  159 RLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPV---KRLRAVVIVPTRELALQVYDTF  235 (620)
T ss_pred             cccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCc---cceEEEEEeeHHHHHHHHHHHH
Confidence            344667777777642         2468999999999997533334444444322   2358999999999999999999


Q ss_pred             HhhccC
Q psy16285         90 LKYTQN   95 (97)
Q Consensus        90 ~~~~~~   95 (97)
                      .++..+
T Consensus       236 ~~~~~~  241 (620)
T KOG0350|consen  236 KRLNSG  241 (620)
T ss_pred             HHhccC
Confidence            988754

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=97.83  E-value=1.7e-05  Score=48.47  Aligned_cols=21  Identities=29%  Similarity=0.537  Sum_probs=18.6

Q ss_pred             eEEeCCCCCchHHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +++.|+||+||||++..+...
T Consensus         2 i~l~G~~GsGKST~a~~l~~~   22 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAER   22 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhh
Confidence            678999999999999888765

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK14528 adenylate kinase; Provisional

Probab=97.83  E-value=2.1e-05  Score=50.15  Aligned_cols=23  Identities=39%  Similarity=0.564  Sum_probs=19.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+++|.||||+||||++..++..
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~   24 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCER   24 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            35789999999999998888643

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=97.83  E-value=1.8e-05  Score=49.84  Aligned_cols=22  Identities=45%  Similarity=0.671  Sum_probs=19.6

Q ss_pred             eEEeCCCCCchHHHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.|.|||||||||++..++..+
T Consensus         3 ItIsG~pGsG~TTva~~lAe~~   24 (179)
T COG1102           3 ITISGLPGSGKTTVARELAEHL   24 (179)
T ss_pred             EEeccCCCCChhHHHHHHHHHh
Confidence            5789999999999999988766

>TIGR01351 adk adenylate kinases

Probab=97.82  E-value=1.9e-05  Score=51.14  Aligned_cols=22  Identities=45%  Similarity=0.708  Sum_probs=18.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +++|.||||+||||++..++..
T Consensus         1 rI~i~G~pGsGKsT~a~~La~~   22 (210)
T TIGR01351         1 RLVLLGPPGSGKGTQAKRIAEK   22 (210)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            3789999999999998888653

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>KOG0343|consensus

Probab=97.82  E-value=3.1e-05  Score=56.80  Aligned_cols=78  Identities=21%  Similarity=0.122  Sum_probs=63.5

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHH-HHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTY-VALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~-~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ....+.+.|++.|..++.+.-++-.+-+|||||. .+.=+++.+.+.++. ...+--.||++||++++.|+++.|.+.+.
T Consensus        88 ~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs-~~DGlGalIISPTRELA~QtFevL~kvgk  166 (758)
T KOG0343|consen   88 KFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWS-PTDGLGALIISPTRELALQTFEVLNKVGK  166 (758)
T ss_pred             CCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCC-CCCCceeEEecchHHHHHHHHHHHHHHhh
Confidence            4556788999999999999999899999999996 455567777776543 12466899999999999999999987663

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=97.82  E-value=3e-05  Score=54.67  Aligned_cols=23  Identities=22%  Similarity=0.333  Sum_probs=20.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||||||.++.+++..+
T Consensus       150 gllL~GPPGcGKTllAraiA~el  172 (413)
T PLN00020        150 ILGIWGGKGQGKSFQCELVFKKM  172 (413)
T ss_pred             EEEeeCCCCCCHHHHHHHHHHHc
Confidence            46789999999999999998887

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.82  E-value=2.1e-05  Score=51.53  Aligned_cols=27  Identities=30%  Similarity=0.517  Sum_probs=24.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhch
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNK   62 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~   62 (97)
                      .++++|+||+|||+.+..++..+.++.
T Consensus         3 LiIlTGyPgsGKTtfakeLak~L~~~i   29 (261)
T COG4088           3 LIILTGYPGSGKTTFAKELAKELRQEI   29 (261)
T ss_pred             eEEEecCCCCCchHHHHHHHHHHHHhh
Confidence            478999999999999999999987763

>COG3842 PotA ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=97.82  E-value=1.5e-05  Score=55.65  Aligned_cols=25  Identities=36%  Similarity=0.485  Sum_probs=20.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.+.||+||||||++..++..
T Consensus        30 ~Gef~~lLGPSGcGKTTlLR~IAGf   54 (352)
T COG3842          30 KGEFVTLLGPSGCGKTTLLRMIAGF   54 (352)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            4678899999999999997766543

>PRK14527 adenylate kinase; Provisional

Probab=97.82  E-value=2.3e-05  Score=49.99  Aligned_cols=23  Identities=39%  Similarity=0.700  Sum_probs=19.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +..+++.||||+||||++..++.
T Consensus         6 ~~~i~i~G~pGsGKsT~a~~La~   28 (191)
T PRK14527          6 NKVVIFLGPPGAGKGTQAERLAQ   28 (191)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999888863

>KOG0327|consensus

Probab=97.82  E-value=1.2e-05  Score=56.22  Aligned_cols=74  Identities=22%  Similarity=0.092  Sum_probs=59.0

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ....+..|+.||..+.++..+.++..+|||||..-...+...+.-..    ....+++++|+++++.|+.+.....+.
T Consensus        46 FekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~----ke~qalilaPtreLa~qi~~v~~~lg~  119 (397)
T KOG0327|consen   46 FEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSV----KETQALILAPTRELAQQIQKVVRALGD  119 (397)
T ss_pred             cCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcch----HHHHHHHhcchHHHHHHHHHHHHhhhc
Confidence            44567889999999999999999999999999985555544443322    356899999999999999988777663

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.82  E-value=1.2e-05  Score=54.49  Aligned_cols=24  Identities=38%  Similarity=0.630  Sum_probs=20.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++++..||||||||.++.+++...
T Consensus       152 knVLFyGppGTGKTm~Akalane~  175 (368)
T COG1223         152 KNVLFYGPPGTGKTMMAKALANEA  175 (368)
T ss_pred             ceeEEECCCCccHHHHHHHHhccc
Confidence            589999999999999999886543

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=97.82  E-value=1.8e-05  Score=50.27  Aligned_cols=25  Identities=20%  Similarity=0.380  Sum_probs=20.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..++|.||+|+||||++..+....
T Consensus         2 g~~i~l~G~sGsGKsTl~~~l~~~~   26 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSLLAALRQRE   26 (186)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhccC
Confidence            3578999999999999988885543

>PRK05480 uridine/cytidine kinase; Provisional

Probab=97.82  E-value=4.1e-05  Score=49.40  Aligned_cols=25  Identities=40%  Similarity=0.414  Sum_probs=21.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...+.|.|++|+||||++..+...+
T Consensus         6 ~~iI~I~G~sGsGKTTl~~~l~~~l   30 (209)
T PRK05480          6 PIIIGIAGGSGSGKTTVASTIYEEL   30 (209)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHh
Confidence            3467899999999999998888876

>PHA02624 large T antigen; Provisional

Probab=97.82  E-value=2.9e-05  Score=57.55  Aligned_cols=25  Identities=28%  Similarity=0.549  Sum_probs=22.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+++.||||||||+++.+++..+
T Consensus       431 k~~il~~GPpnTGKTtf~~sLl~~L  455 (647)
T PHA02624        431 RRYWLFKGPVNSGKTTLAAALLDLC  455 (647)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHc
Confidence            4578999999999999999999888

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=97.81  E-value=4.4e-05  Score=48.85  Aligned_cols=22  Identities=45%  Similarity=0.569  Sum_probs=19.5

Q ss_pred             eEEeCCCCCchHHHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.|.||+|+||||++..+...+
T Consensus         2 igi~G~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           2 IGIAGGSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5789999999999998887776

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>PRK06696 uridine kinase; Validated

Probab=97.81  E-value=4.4e-05  Score=49.92  Aligned_cols=26  Identities=31%  Similarity=0.316  Sum_probs=22.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.|.|++|+||||++..++..+-..
T Consensus        24 iI~I~G~sgsGKSTlA~~L~~~l~~~   49 (223)
T PRK06696         24 RVAIDGITASGKTTFADELAEEIKKR   49 (223)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            67889999999999999998887443

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=97.81  E-value=5.7e-05  Score=46.56  Aligned_cols=25  Identities=24%  Similarity=0.458  Sum_probs=21.8

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +++.|+||+|||+++..+...+...
T Consensus         2 i~i~G~~GsGKSTla~~L~~~l~~~   26 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEEKLFQR   26 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            6889999999999999998887644

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=97.81  E-value=3.3e-05  Score=41.10  Aligned_cols=27  Identities=30%  Similarity=0.505  Sum_probs=22.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ...+|.||+|+|||+++-++...+...
T Consensus        24 ~~tli~G~nGsGKSTllDAi~~~L~~~   50 (62)
T PF13555_consen   24 DVTLITGPNGSGKSTLLDAIQTVLYGN   50 (62)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHcCC
Confidence            479999999999999988887776554

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.81  E-value=4.5e-05  Score=55.18  Aligned_cols=24  Identities=42%  Similarity=0.519  Sum_probs=21.6

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +++.||||||||+++..++..+..
T Consensus        39 ~Lf~GPpGtGKTTlA~~lA~~l~~   62 (472)
T PRK14962         39 YIFAGPRGTGKTTVARILAKSLNC   62 (472)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcc
Confidence            689999999999999999888754

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=97.80  E-value=0.00015  Score=43.82  Aligned_cols=26  Identities=35%  Similarity=0.473  Sum_probs=23.0

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhch
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNK   62 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~   62 (97)
                      +.+.|+||||||+++..+++.+...+
T Consensus        56 lSfHG~tGtGKn~v~~liA~~ly~~G   81 (127)
T PF06309_consen   56 LSFHGWTGTGKNFVSRLIAEHLYKSG   81 (127)
T ss_pred             EEeecCCCCcHHHHHHHHHHHHHhcc
Confidence            34799999999999999999998874

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>PRK07667 uridine kinase; Provisional

Probab=97.80  E-value=5.6e-05  Score=48.45  Aligned_cols=26  Identities=23%  Similarity=0.285  Sum_probs=22.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.|.|++|+||||++..+...+...
T Consensus        19 iIgI~G~~gsGKStla~~L~~~l~~~   44 (193)
T PRK07667         19 ILGIDGLSRSGKTTFVANLKENMKQE   44 (193)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            56789999999999998888887544

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=97.80  E-value=7.3e-06  Score=53.78  Aligned_cols=22  Identities=32%  Similarity=0.594  Sum_probs=19.2

Q ss_pred             cCCceEEeCCCCCchHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRI   54 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~   54 (97)
                      +++.++|.||+|+||||++..+
T Consensus        27 ~Gevv~iiGpSGSGKSTlLRcl   48 (240)
T COG1126          27 KGEVVVIIGPSGSGKSTLLRCL   48 (240)
T ss_pred             CCCEEEEECCCCCCHHHHHHHH
Confidence            5789999999999999996655

>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]

Probab=97.80  E-value=4e-05  Score=53.13  Aligned_cols=56  Identities=23%  Similarity=0.172  Sum_probs=46.0

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      -...++.|..-++.+.++...+-.||.|||||+++...+..++..+     .-.+|++.-|
T Consensus       126 I~~kt~~Q~~y~eai~~~di~fGiGpAGTGKTyLava~av~al~~~-----~v~rIiLtRP  181 (348)
T COG1702         126 IIPKTPGQNMYPEAIEEHDIVFGIGPAGTGKTYLAVAKAVDALGAG-----QVRRIILTRP  181 (348)
T ss_pred             eEecChhHHHHHHHHHhcCeeeeecccccCChhhhHHhHhhhhhhc-----ccceeeecCc
Confidence            3456788999999999999999999999999999999988888874     2456666555

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=97.80  E-value=5.6e-05  Score=48.05  Aligned_cols=28  Identities=32%  Similarity=0.381  Sum_probs=23.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..++|.|++|+||||++..+...+...
T Consensus         3 g~~IvieG~~GsGKsT~~~~L~~~l~~~   30 (195)
T TIGR00041         3 GMFIVIEGIDGAGKTTQANLLKKLLQEN   30 (195)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            3468999999999999999988877554

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

>PRK13949 shikimate kinase; Provisional

Probab=97.80  E-value=2.3e-05  Score=49.33  Aligned_cols=23  Identities=22%  Similarity=0.307  Sum_probs=19.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++|.|+||+|||+++..++..+
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l   25 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALAREL   25 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            58899999999999998887653

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=97.80  E-value=0.00024  Score=55.23  Aligned_cols=72  Identities=18%  Similarity=0.112  Sum_probs=58.6

Q ss_pred             cCCCCCHHHHHHHHHHhc--CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALT--REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~--~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ....+.+.|...+..+..  .++++|.=..|.|||--+..++..+...+     ..+++||+||+ .+..||...+.+.+
T Consensus       149 ~~~~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g-----~~~rvLIVvP~-sL~~QW~~El~~kF  222 (956)
T PRK04914        149 ARASLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTG-----RAERVLILVPE-TLQHQWLVEMLRRF  222 (956)
T ss_pred             CCCCCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcC-----CCCcEEEEcCH-HHHHHHHHHHHHHh
Confidence            456788999999887664  35788999999999999988888876663     35799999997 67999999996543

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=97.80  E-value=2e-05  Score=51.92  Aligned_cols=28  Identities=36%  Similarity=0.624  Sum_probs=21.3

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +++.+.|.||+||||||++. ++..+.+.
T Consensus        30 ~Ge~vaI~GpSGSGKSTLLn-iig~ld~p   57 (226)
T COG1136          30 AGEFVAIVGPSGSGKSTLLN-LLGGLDKP   57 (226)
T ss_pred             CCCEEEEECCCCCCHHHHHH-HHhcccCC
Confidence            47899999999999999954 44444443

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=97.79  E-value=5.1e-05  Score=49.73  Aligned_cols=24  Identities=21%  Similarity=0.159  Sum_probs=20.1

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +-|.||+|+||||++..+...+..
T Consensus         2 igI~G~sGSGKTTla~~L~~~l~~   25 (220)
T cd02025           2 IGIAGSVAVGKSTTARVLQALLSR   25 (220)
T ss_pred             EEeeCCCCCCHHHHHHHHHHHHhh
Confidence            458899999999999888877643

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=97.79  E-value=6.2e-05  Score=52.30  Aligned_cols=41  Identities=17%  Similarity=0.100  Sum_probs=34.1

Q ss_pred             CCCCHHHHHHHHHHhcCC-ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         18 LGLNTIQFEAYKAALTRE-FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~-~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      -.++..+.+.+..+.... +++|.|.+||||||++.++....
T Consensus       156 gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTlLNal~~~i  197 (355)
T COG4962         156 GTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTLLNALSGFI  197 (355)
T ss_pred             CCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHHHHHHHhcC
Confidence            356777888888877765 99999999999999988887665

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.79  E-value=4e-05  Score=53.56  Aligned_cols=24  Identities=25%  Similarity=0.380  Sum_probs=21.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      .+++.||+|+|||+++..++..+.
T Consensus        40 ~~L~~Gp~G~GKTtla~~la~~l~   63 (363)
T PRK14961         40 AWLLSGTRGVGKTTIARLLAKSLN   63 (363)
T ss_pred             EEEEecCCCCCHHHHHHHHHHHhc
Confidence            358999999999999999998885

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=97.79  E-value=8.4e-05  Score=52.82  Aligned_cols=50  Identities=28%  Similarity=0.430  Sum_probs=36.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      +..++|.|+||.|||+++..++..+...      .+.++++++.. ...+++..++.
T Consensus       194 g~liviag~pg~GKT~~al~ia~~~a~~------~g~~v~~fSlE-m~~~~l~~Rl~  243 (421)
T TIGR03600       194 GDLIVIGARPSMGKTTLALNIAENVALR------EGKPVLFFSLE-MSAEQLGERLL  243 (421)
T ss_pred             CceEEEEeCCCCCHHHHHHHHHHHHHHh------CCCcEEEEECC-CCHHHHHHHHH
Confidence            5678999999999999999999777533      26788888843 34555555543

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=97.78  E-value=2.2e-05  Score=48.24  Aligned_cols=20  Identities=45%  Similarity=0.846  Sum_probs=17.5

Q ss_pred             EeCCCCCchHHHHHHHHHHH
Q psy16285         39 IQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        39 v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      |.||||+|||+++..++..+
T Consensus         1 i~G~PgsGK~t~~~~la~~~   20 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRY   20 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHH
T ss_pred             CcCCCCCChHHHHHHHHHhc
Confidence            68999999999999987654

Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=97.78  E-value=7.4e-05  Score=41.60  Aligned_cols=25  Identities=28%  Similarity=0.505  Sum_probs=22.0

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +++.|.+|+|||+++..++..+.+.
T Consensus         2 ~~~~g~~G~Gktt~~~~l~~~l~~~   26 (99)
T cd01983           2 IVVTGKGGVGKTTLAANLAAALAKR   26 (99)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC
Confidence            5788999999999999999998764

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>TIGR03263 guanyl_kin guanylate kinase

Probab=97.78  E-value=2.2e-05  Score=49.30  Aligned_cols=24  Identities=29%  Similarity=0.534  Sum_probs=20.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.||+|+|||+++..++...
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~~   25 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEED   25 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHccC
Confidence            468899999999999988887643

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>KOG0923|consensus

Probab=97.78  E-value=6.5e-05  Score=56.17  Aligned_cols=70  Identities=21%  Similarity=0.088  Sum_probs=49.7

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHH-HHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVA-LRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~-~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      .++...+.-+.+..+..+..++|.|.||+||||=+ ..+.+.=+..      .+++|-+.-|.+.|+..+..++.+-
T Consensus       263 sLPVy~ykdell~av~e~QVLiI~GeTGSGKTTQiPQyL~EaGytk------~gk~IgcTQPRRVAAmSVAaRVA~E  333 (902)
T KOG0923|consen  263 SLPVYPYKDELLKAVKEHQVLIIVGETGSGKTTQIPQYLYEAGYTK------GGKKIGCTQPRRVAAMSVAARVAEE  333 (902)
T ss_pred             cCCchhhHHHHHHHHHhCcEEEEEcCCCCCccccccHHHHhccccc------CCceEeecCcchHHHHHHHHHHHHH
Confidence            34455555666777777899999999999999843 3332222222      3555888889999999999888753

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=97.78  E-value=0.00019  Score=56.12  Aligned_cols=72  Identities=14%  Similarity=0.289  Sum_probs=57.3

Q ss_pred             CCCCHHHHHHHHHHh----cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         18 LGLNTIQFEAYKAAL----TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~----~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..|+++|.+.+..+.    .+...++.=..|.|||..+..++..+.....    ...++||+||.. .+.+|.+.+.+|.
T Consensus       168 ~~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIalL~~L~~~~~----~~gp~LIVvP~S-lL~nW~~Ei~kw~  242 (1033)
T PLN03142        168 GKMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRG----ITGPHMVVAPKS-TLGNWMNEIRRFC  242 (1033)
T ss_pred             cchHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHHHHHHHHhcC----CCCCEEEEeChH-HHHHHHHHHHHHC
Confidence            478999999999875    3457788888999999998888887765422    256899999965 4799999999876


Q ss_pred             c
Q psy16285         94 Q   94 (97)
Q Consensus        94 ~   94 (97)
                      .
T Consensus       243 p  243 (1033)
T PLN03142        243 P  243 (1033)
T ss_pred             C
Confidence            4

>PLN02200 adenylate kinase family protein

Probab=97.78  E-value=2.6e-05  Score=51.60  Aligned_cols=23  Identities=39%  Similarity=0.687  Sum_probs=19.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||+||||++..++..+
T Consensus        45 ii~I~G~PGSGKsT~a~~La~~~   67 (234)
T PLN02200         45 ITFVLGGPGSGKGTQCEKIVETF   67 (234)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            67899999999999988886543

>KOG0334|consensus

Probab=97.78  E-value=5.7e-05  Score=58.23  Aligned_cols=77  Identities=22%  Similarity=0.164  Sum_probs=62.5

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHH-HHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         18 LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVA-LRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~-~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      -..++.|.+||..+..+..++.++-+|+|||.-. +=++.+...+.......+.-.+|+|||++.+.||-+.++.|..
T Consensus       386 ~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela~QI~r~~~kf~k  463 (997)
T KOG0334|consen  386 EKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLK  463 (997)
T ss_pred             CCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEcCCHHHHHHHHHHHHHHHh
Confidence            3567889999999999999999999999999843 4455666555444444567789999999999999999998864

>PLN02165 adenylate isopentenyltransferase

Probab=97.78  E-value=1.7e-05  Score=54.99  Aligned_cols=26  Identities=23%  Similarity=0.579  Sum_probs=22.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..++|.||||+|||+++..++..+
T Consensus        42 ~g~iivIiGPTGSGKStLA~~LA~~l   67 (334)
T PLN02165         42 KDKVVVIMGATGSGKSRLSVDLATRF   67 (334)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHc
Confidence            45689999999999999999987775

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=97.77  E-value=3.1e-05  Score=46.79  Aligned_cols=22  Identities=36%  Similarity=0.634  Sum_probs=19.7

Q ss_pred             eEEeCCCCCchHHHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++|.|+||||||+++..++..+
T Consensus         2 I~i~G~~GsGKst~a~~la~~~   23 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAKKL   23 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5799999999999999998765

>KOG0344|consensus

Probab=97.77  E-value=0.00015  Score=53.21  Aligned_cols=74  Identities=23%  Similarity=0.244  Sum_probs=55.5

Q ss_pred             CCHHHHHHHHHHhcCCceEEeCCCCCchHHH-HHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         20 LNTIQFEAYKAALTREFAIIQGPPGTGKTYV-ALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        20 l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~-~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..+.|+.++......+.++..+|+|+|||.- .+-++..+.......+..+-+.+|+.|+++++.|+.....+|.
T Consensus       159 Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~  233 (593)
T KOG0344|consen  159 PTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKYS  233 (593)
T ss_pred             CCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhcccCccceEEEEecchHHHHHHHHHHHHhcC
Confidence            4567888999988999999999999999752 2223444433321111246789999999999999999999987

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=97.77  E-value=9.9e-05  Score=51.10  Aligned_cols=45  Identities=18%  Similarity=0.291  Sum_probs=35.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC---ChHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY---TNHALDQFVE   87 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~---~~~~~~~~~~   87 (97)
                      .+++.|-.|+||||++..++.++.++       +++|++.+-   ...|++|+..
T Consensus       141 Vil~vGVNG~GKTTTIaKLA~~l~~~-------g~~VllaA~DTFRAaAiEQL~~  188 (340)
T COG0552         141 VILFVGVNGVGKTTTIAKLAKYLKQQ-------GKSVLLAAGDTFRAAAIEQLEV  188 (340)
T ss_pred             EEEEEecCCCchHhHHHHHHHHHHHC-------CCeEEEEecchHHHHHHHHHHH
Confidence            56889999999999999999999877       788888774   3445555443

>PRK09087 hypothetical protein; Validated

Probab=97.77  E-value=2.9e-05  Score=51.11  Aligned_cols=22  Identities=36%  Similarity=0.539  Sum_probs=19.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +.++|.||+|+||||++..++.
T Consensus        45 ~~l~l~G~~GsGKThLl~~~~~   66 (226)
T PRK09087         45 PVVVLAGPVGSGKTHLASIWRE   66 (226)
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            4589999999999999887664

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=97.77  E-value=9.6e-05  Score=49.24  Aligned_cols=49  Identities=27%  Similarity=0.371  Sum_probs=36.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      +..++|.|+||.|||+++..++..+...      .+.++++++..- ..+++..++
T Consensus        19 g~L~vi~a~pg~GKT~~~l~ia~~~a~~------~~~~vly~SlEm-~~~~l~~R~   67 (259)
T PF03796_consen   19 GELTVIAARPGVGKTAFALQIALNAALN------GGYPVLYFSLEM-SEEELAARL   67 (259)
T ss_dssp             T-EEEEEESTTSSHHHHHHHHHHHHHHT------TSSEEEEEESSS--HHHHHHHH
T ss_pred             CcEEEEEecccCCchHHHHHHHHHHHHh------cCCeEEEEcCCC-CHHHHHHHH
Confidence            4588999999999999999999999887      357899998532 233444444

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PRK04040 adenylate kinase; Provisional

Probab=97.77  E-value=2.8e-05  Score=49.86  Aligned_cols=23  Identities=35%  Similarity=0.626  Sum_probs=20.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.|+||+||||++..+...+
T Consensus         4 ~i~v~G~pG~GKtt~~~~l~~~l   26 (188)
T PRK04040          4 VVVVTGVPGVGKTTVLNKALEKL   26 (188)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHh
Confidence            57899999999999999888876

>KOG0346|consensus

Probab=97.76  E-value=0.00015  Score=52.09  Aligned_cols=74  Identities=20%  Similarity=0.193  Sum_probs=56.5

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHH-HHHHHHHHHhchhh-hhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYV-ALRIVEGFLKNKEL-ARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~-~~~~~~~~~~~~~~-~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ..+..|..+|..++.+..++..+.+|+|||.. +.=++..++..... ....+..-++++||+++..|+...+.+.
T Consensus        41 kpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTkEL~qQvy~viekL  116 (569)
T KOG0346|consen   41 KPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTKELAQQVYKVIEKL  116 (569)
T ss_pred             CcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEEEechHHHHHHHHHHHHHH
Confidence            34667899999999999999999999999964 44455666655433 2234568899999999999988877654

>KOG0733|consensus

Probab=97.76  E-value=5.2e-05  Score=56.29  Aligned_cols=24  Identities=38%  Similarity=0.632  Sum_probs=21.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +-+++.||||||||.+|.+++.++
T Consensus       224 rGvLlHGPPGCGKT~lA~AiAgel  247 (802)
T KOG0733|consen  224 RGVLLHGPPGCGKTSLANAIAGEL  247 (802)
T ss_pred             CceeeeCCCCccHHHHHHHHhhhc
Confidence            457999999999999999998877

>PRK00279 adk adenylate kinase; Reviewed

Probab=97.76  E-value=3e-05  Score=50.37  Aligned_cols=23  Identities=43%  Similarity=0.637  Sum_probs=19.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||+||||++..++..+
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~   24 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKY   24 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999988886554

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=97.76  E-value=6.2e-05  Score=49.13  Aligned_cols=41  Identities=22%  Similarity=0.340  Sum_probs=33.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNH   80 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~   80 (97)
                      .+.+.|.|.+|+|||+++..++..+.+.      .+.+++++=|..+
T Consensus        23 ~~H~~I~G~TGsGKS~~~~~ll~~l~~~------~~~~~ii~D~~GE   63 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTVKVLLEELLKK------KGAKVIIFDPHGE   63 (229)
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHHHhc------CCCCEEEEcCCCc
Confidence            4678999999999999999999999843      3667887777554

It contains several conserved aspartates and histidines that could be metal ligands.

>PTZ00088 adenylate kinase 1; Provisional

Probab=97.75  E-value=3.1e-05  Score=51.14  Aligned_cols=23  Identities=26%  Similarity=0.326  Sum_probs=19.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||+||||++..++..+
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~   30 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKE   30 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999998886553

>PRK05748 replicative DNA helicase; Provisional

Probab=97.75  E-value=9.2e-05  Score=53.09  Aligned_cols=50  Identities=22%  Similarity=0.371  Sum_probs=36.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      +..++|.|+||+|||+++..++......      .+.++++++. ....+++..++.
T Consensus       203 G~livIaarpg~GKT~~al~ia~~~a~~------~g~~v~~fSl-Ems~~~l~~R~l  252 (448)
T PRK05748        203 NDLIIVAARPSVGKTAFALNIAQNVATK------TDKNVAIFSL-EMGAESLVMRML  252 (448)
T ss_pred             CceEEEEeCCCCCchHHHHHHHHHHHHh------CCCeEEEEeC-CCCHHHHHHHHH
Confidence            4578999999999999999999887544      2678888774 333555555553

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=97.75  E-value=3.2e-05  Score=55.05  Aligned_cols=24  Identities=29%  Similarity=0.527  Sum_probs=21.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++++.||||||||+++..++..+
T Consensus       109 ~~iLl~Gp~GtGKT~lAr~lA~~l  132 (412)
T PRK05342        109 SNILLIGPTGSGKTLLAQTLARIL  132 (412)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHh
Confidence            579999999999999999997654

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.75  E-value=0.00015  Score=55.90  Aligned_cols=28  Identities=21%  Similarity=0.515  Sum_probs=24.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+.+++||||+|||+++..++..+...
T Consensus       199 ~~n~lL~G~pGvGKT~l~~~la~~i~~~  226 (857)
T PRK10865        199 KNNPVLIGEPGVGKTAIVEGLAQRIING  226 (857)
T ss_pred             cCceEEECCCCCCHHHHHHHHHHHhhcC
Confidence            3589999999999999999999988654

>PRK00625 shikimate kinase; Provisional

Probab=97.74  E-value=3.4e-05  Score=48.88  Aligned_cols=23  Identities=22%  Similarity=0.263  Sum_probs=20.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++++.|.||+|||+++..++..+
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l   24 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFL   24 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999999887664

>cd03114 ArgK-like The function of this protein family is unkown

Probab=97.74  E-value=7.2e-05  Score=46.20  Aligned_cols=25  Identities=24%  Similarity=0.402  Sum_probs=21.5

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +.+.|++|+|||+++..++..+.+.
T Consensus         2 i~~~G~~GsGKTt~~~~l~~~~~~~   26 (148)
T cd03114           2 IGITGVPGAGKSTLIDALITALRAR   26 (148)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHC
Confidence            5688999999999999998887555

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

>PRK06547 hypothetical protein; Provisional

Probab=97.74  E-value=6.9e-05  Score=47.44  Aligned_cols=23  Identities=30%  Similarity=0.423  Sum_probs=19.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.|++|+|||+++..++..+
T Consensus        17 ~i~i~G~~GsGKTt~a~~l~~~~   39 (172)
T PRK06547         17 TVLIDGRSGSGKTTLAGALAART   39 (172)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            56777999999999998887763

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=97.74  E-value=0.00012  Score=54.98  Aligned_cols=46  Identities=22%  Similarity=0.406  Sum_probs=35.7

Q ss_pred             cCCCCCHHHHHHHHHHh--------cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         16 EELGLNTIQFEAYKAAL--------TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~--------~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +++.|.+.....+++..        +++.+|+.||||.|||.++..++..+-+.
T Consensus       324 dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al~Rk  377 (782)
T COG0466         324 DHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKALGRK  377 (782)
T ss_pred             cccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHhCCC
Confidence            55667776666666643        24688999999999999999999988544

>PRK00300 gmk guanylate kinase; Provisional

Probab=97.74  E-value=2.9e-05  Score=49.80  Aligned_cols=26  Identities=23%  Similarity=0.468  Sum_probs=22.2

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..++|.||+|+|||+++..++..+
T Consensus         4 ~g~~i~i~G~sGsGKstl~~~l~~~~   29 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLVKALLERD   29 (205)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            35688999999999999988887764

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=97.74  E-value=4.3e-05  Score=55.02  Aligned_cols=31  Identities=39%  Similarity=0.556  Sum_probs=23.5

Q ss_pred             HHHHHHHHh-cCCceEEeCCCCCchHHHHHHH
Q psy16285         24 QFEAYKAAL-TREFAIIQGPPGTGKTYVALRI   54 (97)
Q Consensus        24 Q~~~i~~~~-~~~~~~v~Gp~GtGKT~~~~~~   54 (97)
                      -+.++.-+. .+.++++.||||||||.++..+
T Consensus       187 AKrAleiAAAGgHnLl~~GpPGtGKTmla~Rl  218 (490)
T COG0606         187 AKRALEIAAAGGHNLLLVGPPGTGKTMLASRL  218 (490)
T ss_pred             HHHHHHHHHhcCCcEEEecCCCCchHHhhhhh
Confidence            344444444 3569999999999999998887

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=97.74  E-value=6.6e-05  Score=52.11  Aligned_cols=34  Identities=18%  Similarity=0.279  Sum_probs=27.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      .+-|.|+||+||||++..++..+...       +.++.+++
T Consensus        58 ~igi~G~~GaGKSTl~~~l~~~l~~~-------g~~v~vi~   91 (332)
T PRK09435         58 RIGITGVPGVGKSTFIEALGMHLIEQ-------GHKVAVLA   91 (332)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-------CCeEEEEE
Confidence            57889999999999999998888654       55666665

>KOG0727|consensus

Probab=97.74  E-value=5.1e-05  Score=51.39  Aligned_cols=22  Identities=41%  Similarity=0.724  Sum_probs=19.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +-+++.||||||||.++.+++.
T Consensus       190 rgvllygppg~gktml~kava~  211 (408)
T KOG0727|consen  190 RGVLLYGPPGTGKTMLAKAVAN  211 (408)
T ss_pred             cceEEeCCCCCcHHHHHHHHhh
Confidence            4688999999999999988854

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=97.74  E-value=3.4e-05  Score=49.37  Aligned_cols=25  Identities=40%  Similarity=0.547  Sum_probs=21.9

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +.|.||+|+||||++..+...+...
T Consensus         2 IgI~G~sgSGKTTla~~L~~~L~~~   26 (194)
T PF00485_consen    2 IGIAGPSGSGKTTLAKRLAQILNKR   26 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCcc
Confidence            5689999999999999998888654

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=97.73  E-value=8.1e-05  Score=46.99  Aligned_cols=26  Identities=27%  Similarity=0.431  Sum_probs=22.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .++|.|++|+||||++..+...+...
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~l~~~   27 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAERLEAR   27 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            36899999999999999998888543

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>TIGR00235 udk uridine kinase

Probab=97.73  E-value=3.1e-05  Score=50.05  Aligned_cols=25  Identities=40%  Similarity=0.437  Sum_probs=21.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+.|.||+|+||||++..+...+
T Consensus         6 g~vi~I~G~sGsGKSTl~~~l~~~l   30 (207)
T TIGR00235         6 GIIIGIGGGSGSGKTTVARKIYEQL   30 (207)
T ss_pred             eEEEEEECCCCCCHHHHHHHHHHHh
Confidence            3467899999999999998887765

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.73  E-value=0.0001  Score=55.72  Aligned_cols=24  Identities=38%  Similarity=0.635  Sum_probs=21.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++..++..+
T Consensus       213 ~giLL~GppGtGKT~laraia~~~  236 (733)
T TIGR01243       213 KGVLLYGPPGTGKTLLAKAVANEA  236 (733)
T ss_pred             ceEEEECCCCCChHHHHHHHHHHh
Confidence            468999999999999999887765

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>KOG1970|consensus

Probab=97.72  E-value=4.1e-05  Score=56.04  Aligned_cols=43  Identities=19%  Similarity=0.312  Sum_probs=29.8

Q ss_pred             CCCCHHHHHHHHHHhc----------CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         18 LGLNTIQFEAYKAALT----------REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~----------~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +.........++.|+.          ++.++|+||+|+||||++..+...+.-
T Consensus        84 LAVHkkKI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkvLskelg~  136 (634)
T KOG1970|consen   84 LAVHKKKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKVLSKELGY  136 (634)
T ss_pred             HhhhHHhHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHHHHHhhCc
Confidence            3344444555555554          357899999999999998888766543

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=97.72  E-value=2.3e-05  Score=55.00  Aligned_cols=26  Identities=42%  Similarity=0.672  Sum_probs=21.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      ++.+++.||||||||.++.+++..+-
T Consensus        50 Gr~iLiaGppGtGKTAlA~~ia~eLG   75 (398)
T PF06068_consen   50 GRAILIAGPPGTGKTALAMAIAKELG   75 (398)
T ss_dssp             T-EEEEEE-TTSSHHHHHHHHHHHCT
T ss_pred             CcEEEEeCCCCCCchHHHHHHHHHhC
Confidence            56789999999999999999998883

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=97.72  E-value=2.4e-05  Score=52.54  Aligned_cols=27  Identities=26%  Similarity=0.334  Sum_probs=23.2

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +++.+.|.||.|+||||++..+...+-
T Consensus        27 ~G~i~~iiGpNG~GKSTLLk~l~g~l~   53 (258)
T COG1120          27 KGEITGILGPNGSGKSTLLKCLAGLLK   53 (258)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            478899999999999999888877663

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=97.72  E-value=3.2e-05  Score=52.27  Aligned_cols=26  Identities=27%  Similarity=0.507  Sum_probs=21.3

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..+++.||+|||||.++...+..+
T Consensus        32 ~~~pvLl~G~~GtGKT~li~~~l~~l   57 (272)
T PF12775_consen   32 NGRPVLLVGPSGTGKTSLIQNFLSSL   57 (272)
T ss_dssp             CTEEEEEESSTTSSHHHHHHHHHHCS
T ss_pred             cCCcEEEECCCCCchhHHHHhhhccC
Confidence            45689999999999999987766543

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.70  E-value=3.7e-05  Score=51.18  Aligned_cols=26  Identities=35%  Similarity=0.420  Sum_probs=21.5

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++.+.|.||+||||||++..++...
T Consensus        28 ~GEfvsilGpSGcGKSTLLriiAGL~   53 (248)
T COG1116          28 KGEFVAILGPSGCGKSTLLRLIAGLE   53 (248)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            47899999999999999977665443

>PRK08506 replicative DNA helicase; Provisional

Probab=97.70  E-value=0.00015  Score=52.52  Aligned_cols=50  Identities=20%  Similarity=0.309  Sum_probs=38.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      +..++|.|+||.|||+++..++..+..+       +.++++.+.- ....++..++..
T Consensus       192 G~LivIaarpg~GKT~fal~ia~~~~~~-------g~~V~~fSlE-Ms~~ql~~Rlla  241 (472)
T PRK08506        192 GDLIIIAARPSMGKTTLCLNMALKALNQ-------DKGVAFFSLE-MPAEQLMLRMLS  241 (472)
T ss_pred             CceEEEEcCCCCChHHHHHHHHHHHHhc-------CCcEEEEeCc-CCHHHHHHHHHH
Confidence            4578999999999999999999887654       6788888753 455666665543

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=97.70  E-value=3.8e-05  Score=53.20  Aligned_cols=27  Identities=26%  Similarity=0.454  Sum_probs=23.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ..++++.||+|||||.+|..++..+.-
T Consensus        97 KSNILLiGPTGsGKTlLAqTLAk~LnV  123 (408)
T COG1219          97 KSNILLIGPTGSGKTLLAQTLAKILNV  123 (408)
T ss_pred             eccEEEECCCCCcHHHHHHHHHHHhCC
Confidence            468999999999999999999887733

>KOG0738|consensus

Probab=97.70  E-value=3.3e-05  Score=54.64  Aligned_cols=24  Identities=38%  Similarity=0.641  Sum_probs=21.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +-+++.||||||||.++.+++...
T Consensus       246 kgvLm~GPPGTGKTlLAKAvATEc  269 (491)
T KOG0738|consen  246 KGVLMVGPPGTGKTLLAKAVATEC  269 (491)
T ss_pred             ceeeeeCCCCCcHHHHHHHHHHhh
Confidence            468999999999999999997765

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=97.70  E-value=6e-05  Score=51.64  Aligned_cols=32  Identities=31%  Similarity=0.474  Sum_probs=25.0

Q ss_pred             HHHHHh-cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         27 AYKAAL-TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        27 ~i~~~~-~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..+. .+.+++|.||+|+||||++.+++..+
T Consensus       136 ~l~~~v~~~~~ili~G~tGsGKTTll~al~~~~  168 (308)
T TIGR02788       136 FLRLAIASRKNIIISGGTGSGKTTFLKSLVDEI  168 (308)
T ss_pred             HHHHHhhCCCEEEEECCCCCCHHHHHHHHHccC
Confidence            344444 46799999999999999998887665

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=97.70  E-value=0.00012  Score=54.63  Aligned_cols=29  Identities=34%  Similarity=0.576  Sum_probs=24.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .++.+++.||||||||+++..++..+...
T Consensus        49 ~~~~~l~~G~~G~GKttla~~l~~~l~~~   77 (637)
T PRK13765         49 QRRHVMMIGSPGTGKSMLAKAMAELLPKE   77 (637)
T ss_pred             hCCeEEEECCCCCcHHHHHHHHHHHcChH
Confidence            46789999999999999999988776433

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=97.70  E-value=0.00014  Score=51.70  Aligned_cols=60  Identities=23%  Similarity=0.363  Sum_probs=47.5

Q ss_pred             HHHHHHHhcC-----CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         25 FEAYKAALTR-----EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        25 ~~~i~~~~~~-----~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..-++.++.+     ..++|-|.||.||||+++.++..+...       . ++|+++ ..+++.|+.-+..+++
T Consensus        79 ~~EldRVLGGG~V~Gs~iLIgGdPGIGKSTLLLQva~~lA~~-------~-~vLYVs-GEES~~QiklRA~RL~  143 (456)
T COG1066          79 IEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKR-------G-KVLYVS-GEESLQQIKLRADRLG  143 (456)
T ss_pred             hHHHHhhhcCCcccccEEEEccCCCCCHHHHHHHHHHHHHhc-------C-cEEEEe-CCcCHHHHHHHHHHhC
Confidence            3345555543     467889999999999999999988666       3 888888 7788999998888886

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=97.69  E-value=0.0001  Score=50.65  Aligned_cols=56  Identities=13%  Similarity=0.132  Sum_probs=33.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChH-HHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNH-ALDQFVEGVL   90 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~-~~~~~~~~l~   90 (97)
                      +..+.|.||||+|||+++..++......... +..+.+++++..... ..+++.+..+
T Consensus       102 g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~-gg~~~~~~yi~te~~f~~~rl~~~~~  158 (317)
T PRK04301        102 QSITEFYGEFGSGKTQICHQLAVNVQLPEEK-GGLEGKAVYIDTEGTFRPERIEQMAE  158 (317)
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHhcccccc-CCCCceEEEEeCCCCcCHHHHHHHHH
Confidence            4577899999999999999998776543110 001246666664331 2344444433

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=97.69  E-value=7.1e-05  Score=50.02  Aligned_cols=29  Identities=28%  Similarity=0.367  Sum_probs=24.4

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ..++..+|.||+|+|||+++..+...+..
T Consensus        14 ~~Gqr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          14 GKGQRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhcccc
Confidence            35789999999999999998888776644

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=97.69  E-value=4.5e-05  Score=48.36  Aligned_cols=25  Identities=32%  Similarity=0.519  Sum_probs=21.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++.+++.||+|+||||++..++..+
T Consensus         3 ge~i~l~G~sGsGKSTl~~~la~~l   27 (176)
T PRK09825          3 GESYILMGVSGSGKSLIGSKIAALF   27 (176)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhc
Confidence            5678999999999999988887654

>PRK08760 replicative DNA helicase; Provisional

Probab=97.69  E-value=0.00014  Score=52.71  Aligned_cols=52  Identities=19%  Similarity=0.252  Sum_probs=37.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +..++|.|+||.|||+++..++..+..+      .+.++++.+. ....+++..++...
T Consensus       229 G~LivIaarPg~GKTafal~iA~~~a~~------~g~~V~~fSl-EMs~~ql~~Rl~a~  280 (476)
T PRK08760        229 TDLIILAARPAMGKTTFALNIAEYAAIK------SKKGVAVFSM-EMSASQLAMRLISS  280 (476)
T ss_pred             CceEEEEeCCCCChhHHHHHHHHHHHHh------cCCceEEEec-cCCHHHHHHHHHHh
Confidence            4578999999999999999999877644      2667888874 23345666665443

>PRK03846 adenylylsulfate kinase; Provisional

Probab=97.69  E-value=9.9e-05  Score=47.39  Aligned_cols=41  Identities=22%  Similarity=0.179  Sum_probs=28.7

Q ss_pred             CCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         20 LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        20 l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+..+.+. ..-.++..+.+.|++|+||||++..+...+...
T Consensus        11 v~~~~~~~-~~~~~~~~i~i~G~~GsGKSTla~~l~~~l~~~   51 (198)
T PRK03846         11 VTKAQREQ-LHGHKGVVLWFTGLSGSGKSTVAGALEEALHEL   51 (198)
T ss_pred             CCHHHHHH-hcCCCCEEEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            44445443 221234578899999999999999998877554

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=97.68  E-value=4.9e-05  Score=47.96  Aligned_cols=25  Identities=20%  Similarity=0.513  Sum_probs=21.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++++.|++|+|||+++..++..+
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l   28 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQL   28 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHc
Confidence            4578999999999999999987664

>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH)

Probab=97.68  E-value=0.00013  Score=43.34  Aligned_cols=34  Identities=26%  Similarity=0.383  Sum_probs=27.2

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +++.|.+|+|||+++..++..+.+.       +.+++++-.
T Consensus         2 i~~~GkgG~GKTt~a~~la~~l~~~-------g~~V~~id~   35 (116)
T cd02034           2 IAITGKGGVGKTTIAALLARYLAEK-------GKPVLAIDA   35 (116)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC-------CCcEEEEEC
Confidence            6899999999999999998887654       556666553

CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.

>PF10412 TrwB_AAD_bind: Type IV secretion-system coupling protein DNA-binding domain; InterPro: IPR019476 The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein

Probab=97.68  E-value=9.6e-05  Score=52.14  Aligned_cols=47  Identities=17%  Similarity=0.279  Sum_probs=33.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVE   87 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~   87 (97)
                      .++++|.|.+|||||+++..++..+...       +.+++|.=++.+-...+.+
T Consensus        15 ~~~~li~G~~GsGKT~~i~~ll~~~~~~-------g~~~iI~D~kg~~~~~f~~   61 (386)
T PF10412_consen   15 NRHILIIGATGSGKTQAIRHLLDQIRAR-------GDRAIIYDPKGEFTERFYR   61 (386)
T ss_dssp             GG-EEEEE-TTSSHHHHHHHHHHHHHHT-------T-EEEEEEETTHHHHHH--
T ss_pred             hCcEEEECCCCCCHHHHHHHHHHHHHHc-------CCEEEEEECCchHHHHhcC
Confidence            4689999999999999989998888776       5677777777666555443

It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells []. This protein forms hexamers from six structurally very similar protomers []. This hexamer contains a central channel running from the cytosolic pole (formed by the all-alpha domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-alpha domain appears to be the DNA-binding domain of the structure. ; PDB: 1E9S_D 1E9R_F 1GKI_B 1GL7_G 1GL6_A.

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=97.68  E-value=0.00012  Score=50.30  Aligned_cols=40  Identities=20%  Similarity=0.292  Sum_probs=30.0

Q ss_pred             CCCHHHHHHHHHHhc-----------CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         19 GLNTIQFEAYKAALT-----------REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~-----------~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.|++.+..+.+           +..+++.|++|+|||+++..++..+
T Consensus       107 ~l~~~~~~~~~~~l~~~~~~~~~~~~~~~I~l~G~~GsGKStvg~~La~~L  157 (309)
T PRK08154        107 QASPAQLARVRDALSGMLGAGRRAARRRRIALIGLRGAGKSTLGRMLAARL  157 (309)
T ss_pred             cCCHHHHHHHHHHHHHHHhhhhhccCCCEEEEECCCCCCHHHHHHHHHHHc
Confidence            456666666665543           3588999999999999998886553

>PF02492 cobW: CobW/HypB/UreG, nucleotide-binding domain; InterPro: IPR003495 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt

Probab=97.68  E-value=9.3e-05  Score=46.84  Aligned_cols=35  Identities=20%  Similarity=0.298  Sum_probs=26.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +.++|.|..|+|||+++..++. ...       .+.++.++..
T Consensus         1 Pv~ii~GfLGsGKTTli~~ll~-~~~-------~~~~~~vI~n   35 (178)
T PF02492_consen    1 PVIIITGFLGSGKTTLINHLLK-RNR-------QGERVAVIVN   35 (178)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHH-HHT-------TTS-EEEEEC
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH-Hhc-------CCceeEEEEc
Confidence            3578999999999999998887 222       3677777764

Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents CobW-like proteins, including P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [], and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site [].; PDB: 2WSM_B 1NIJ_A 2HF9_A 2HF8_B.

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=97.68  E-value=4.7e-05  Score=53.40  Aligned_cols=26  Identities=42%  Similarity=0.603  Sum_probs=23.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      ++-+++.||||||||.+|..+...+-
T Consensus        65 GrgiLi~GppgTGKTAlA~gIa~eLG   90 (450)
T COG1224          65 GRGILIVGPPGTGKTALAMGIARELG   90 (450)
T ss_pred             ccEEEEECCCCCcHHHHHHHHHHHhC
Confidence            45789999999999999999999884

>KOG1533|consensus

Probab=97.68  E-value=5e-05  Score=50.57  Aligned_cols=25  Identities=24%  Similarity=0.448  Sum_probs=19.1

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+|+||||+||||-...+-..+-..
T Consensus         5 qvVIGPPgSGKsTYc~g~~~fls~~   29 (290)
T KOG1533|consen    5 QVVIGPPGSGKSTYCNGMSQFLSAI   29 (290)
T ss_pred             eEEEcCCCCCccchhhhHHHHHHHh
Confidence            4799999999999866665555444

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.68  E-value=0.00021  Score=54.98  Aligned_cols=27  Identities=22%  Similarity=0.489  Sum_probs=24.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.+++||||+|||+++..++..+...
T Consensus       195 ~n~lL~G~pGvGKT~l~~~la~~i~~~  221 (852)
T TIGR03346       195 NNPVLIGEPGVGKTAIVEGLAQRIVNG  221 (852)
T ss_pred             CceEEEcCCCCCHHHHHHHHHHHHhcc
Confidence            588999999999999999998888654

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=97.67  E-value=3.6e-05  Score=52.05  Aligned_cols=23  Identities=26%  Similarity=0.374  Sum_probs=19.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.|+|||||||++..+...+
T Consensus         4 liil~G~pGSGKSTla~~L~~~~   26 (300)
T PHA02530          4 IILTVGVPGSGKSTWAREFAAKN   26 (300)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHC
Confidence            57889999999999999987665

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.67  E-value=0.00013  Score=55.30  Aligned_cols=23  Identities=39%  Similarity=0.611  Sum_probs=20.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.||||||||+++.+++..+
T Consensus       489 giLL~GppGtGKT~lakalA~e~  511 (733)
T TIGR01243       489 GVLLFGPPGTGKTLLAKAVATES  511 (733)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhc
Confidence            57899999999999999998765

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=97.66  E-value=0.00021  Score=48.47  Aligned_cols=27  Identities=37%  Similarity=0.647  Sum_probs=24.3

Q ss_pred             Cc-eEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EF-AIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~-~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +. +++.||||+|||+++..++..+...
T Consensus        24 ~halL~~Gp~G~Gktt~a~~lA~~l~~~   51 (325)
T COG0470          24 PHALLFYGPPGVGKTTAALALAKELLCE   51 (325)
T ss_pred             CceeeeeCCCCCCHHHHHHHHHHHHhCC
Confidence            45 8999999999999999999999854

>KOG0733|consensus

Probab=97.66  E-value=1.6e-05  Score=58.90  Aligned_cols=24  Identities=33%  Similarity=0.570  Sum_probs=20.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .-+++.||||||||.+|.++++..
T Consensus       546 sGvLL~GPPGCGKTLlAKAVANEa  569 (802)
T KOG0733|consen  546 SGVLLCGPPGCGKTLLAKAVANEA  569 (802)
T ss_pred             CceEEeCCCCccHHHHHHHHhhhc
Confidence            357899999999999999997665

>KOG0741|consensus

Probab=97.66  E-value=4.1e-05  Score=56.14  Aligned_cols=26  Identities=38%  Similarity=0.554  Sum_probs=23.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      -+++.||||||||.+|..+...+...
T Consensus       258 GiLLyGPPGTGKTLiARqIGkMLNAr  283 (744)
T KOG0741|consen  258 GILLYGPPGTGKTLIARQIGKMLNAR  283 (744)
T ss_pred             eEEEECCCCCChhHHHHHHHHHhcCC
Confidence            47899999999999999998888665

>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]

Probab=97.66  E-value=0.0003  Score=49.19  Aligned_cols=70  Identities=17%  Similarity=0.129  Sum_probs=58.9

Q ss_pred             CCCCHHHHHHHHHHh----cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         18 LGLNTIQFEAYKAAL----TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~----~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      -+|++.|+.+-..+.    +..-.+|++-+|+|||.++-..++..+.+       +.+|.+.+|.-+-.-++..++...+
T Consensus        96 G~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMif~~i~~al~~-------G~~vciASPRvDVclEl~~Rlk~aF  168 (441)
T COG4098          96 GTLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIFQGIEQALNQ-------GGRVCIASPRVDVCLELYPRLKQAF  168 (441)
T ss_pred             cccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhHHHHHHHHhc-------CCeEEEecCcccchHHHHHHHHHhh
Confidence            357888887655544    46789999999999999999999998887       8899999999988888888888776


Q ss_pred             c
Q psy16285         94 Q   94 (97)
Q Consensus        94 ~   94 (97)
                      .
T Consensus       169 ~  169 (441)
T COG4098         169 S  169 (441)
T ss_pred             c
Confidence            5

>CHL00176 ftsH cell division protein; Validated

Probab=97.66  E-value=5e-05  Score=56.75  Aligned_cols=23  Identities=43%  Similarity=0.637  Sum_probs=20.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.||||||||+++.+++..+
T Consensus       218 gVLL~GPpGTGKT~LAralA~e~  240 (638)
T CHL00176        218 GVLLVGPPGTGKTLLAKAIAGEA  240 (638)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999997654

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=97.65  E-value=0.00011  Score=49.12  Aligned_cols=44  Identities=20%  Similarity=0.293  Sum_probs=31.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHA   81 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~   81 (97)
                      +.++.||||+||||++.-+++.+-..-  ..+.++++.++-.+++.
T Consensus       139 ntLiigpP~~GKTTlLRdiaR~~s~g~--~~~l~kkv~IiDersEI  182 (308)
T COG3854         139 NTLIIGPPQVGKTTLLRDIARLLSDGI--NQFLPKKVGIIDERSEI  182 (308)
T ss_pred             eeEEecCCCCChHHHHHHHHHHhhccc--cccCCceEEEEeccchh
Confidence            689999999999999988887764431  12346677776655543

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=97.65  E-value=4.8e-05  Score=54.17  Aligned_cols=24  Identities=29%  Similarity=0.527  Sum_probs=21.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++++.||||+|||+++..++..+
T Consensus       117 ~~iLL~GP~GsGKT~lAraLA~~l  140 (413)
T TIGR00382       117 SNILLIGPTGSGKTLLAQTLARIL  140 (413)
T ss_pred             ceEEEECCCCcCHHHHHHHHHHhc
Confidence            469999999999999999998665

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=97.65  E-value=2.7e-05  Score=47.20  Aligned_cols=23  Identities=30%  Similarity=0.575  Sum_probs=17.4

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +++.|+||+|||+++..++..+-
T Consensus         2 vLleg~PG~GKT~la~~lA~~~~   24 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARSLG   24 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHHTT
T ss_pred             EeeECCCccHHHHHHHHHHHHcC
Confidence            68999999999999998887763

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.64  E-value=0.00012  Score=51.97  Aligned_cols=29  Identities=28%  Similarity=0.439  Sum_probs=25.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +++..+|.||||+|||+++..+...+..+
T Consensus       168 kGQR~lIvgppGvGKTTLaK~Ian~I~~n  196 (416)
T PRK09376        168 KGQRGLIVAPPKAGKTVLLQNIANSITTN  196 (416)
T ss_pred             cCceEEEeCCCCCChhHHHHHHHHHHHhh
Confidence            46799999999999999999988887664

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.64  E-value=8e-05  Score=53.95  Aligned_cols=26  Identities=31%  Similarity=0.377  Sum_probs=22.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+++.||+|||||+++..++..+...
T Consensus        42 a~Lf~GP~GtGKTTlAriLAk~Lnce   67 (484)
T PRK14956         42 AYIFFGPRGVGKTTIARILAKRLNCE   67 (484)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCcc
Confidence            36999999999999999999887653

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=97.64  E-value=0.00023  Score=50.08  Aligned_cols=56  Identities=23%  Similarity=0.188  Sum_probs=39.7

Q ss_pred             CCCCHHHHHHHHHHhcC--CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         18 LGLNTIQFEAYKAALTR--EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~--~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      -+.+.+|.-|++..++.  +.+.+.|+.|||||-+|.+.+-.....++    .-.++++.-|
T Consensus       227 ~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~----~y~KiiVtRp  284 (436)
T COG1875         227 RPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERK----RYRKIIVTRP  284 (436)
T ss_pred             CcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHh----hhceEEEecC
Confidence            45688999999998865  47888999999999987766544444332    2345555544

>KOG0329|consensus

Probab=97.63  E-value=4.4e-05  Score=51.53  Aligned_cols=70  Identities=20%  Similarity=0.226  Sum_probs=53.5

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHH-HHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYV-ALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~-~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..++.|.+.|..+.-+--++.++-+|-|||.+ ..+.+.++-.-.     +...++++|+|++++.|+.+...+|.
T Consensus        64 hpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~-----g~vsvlvmchtrelafqi~~ey~rfs  134 (387)
T KOG0329|consen   64 HPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVD-----GQVSVLVMCHTRELAFQISKEYERFS  134 (387)
T ss_pred             CchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCC-----CeEEEEEEeccHHHHHHHHHHHHHHH
Confidence            35677888888888888899999999999975 333344432221     24579999999999999999888775

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=97.63  E-value=0.00012  Score=46.46  Aligned_cols=27  Identities=22%  Similarity=0.325  Sum_probs=23.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+.|.|++||||||++..++..+...
T Consensus         7 ~ii~ivG~sgsGKTTLi~~li~~l~~~   33 (173)
T PRK10751          7 PLLAIAAWSGTGKTTLLKKLIPALCAR   33 (173)
T ss_pred             eEEEEECCCCChHHHHHHHHHHHHhhc
Confidence            467899999999999999999887653

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=97.63  E-value=8.1e-05  Score=51.83  Aligned_cols=38  Identities=16%  Similarity=0.376  Sum_probs=30.8

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNH   80 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~   80 (97)
                      .++.|+||+||||++..+...+...      .+.++.+++....
T Consensus         2 ~~l~Gl~GaGKST~~~~l~~~l~~~------~g~~v~~~~~Dd~   39 (340)
T TIGR03575         2 CVLCGLPAAGKSTLARSLSATLRRE------RGWAVAVITYDDI   39 (340)
T ss_pred             eEEECCCCCCHHHHHHHHHHHHHhc------cCCeEEEEccccc
Confidence            5789999999999999999888754      3678888885443

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.

>PRK15453 phosphoribulokinase; Provisional

Probab=97.63  E-value=0.00013  Score=49.68  Aligned_cols=26  Identities=23%  Similarity=0.326  Sum_probs=21.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +..+.|.|+||+||||++..+...+-
T Consensus         5 ~piI~ItG~SGsGKTTva~~l~~if~   30 (290)
T PRK15453          5 HPIIAVTGSSGAGTTTVKRAFEKIFR   30 (290)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHh
Confidence            46789999999999999888876553

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=97.63  E-value=0.00013  Score=49.81  Aligned_cols=26  Identities=19%  Similarity=0.322  Sum_probs=21.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +..+.|.||||+|||+++..++....
T Consensus        95 g~i~ei~G~~g~GKT~l~~~~~~~~~  120 (310)
T TIGR02236        95 QAITEVFGEFGSGKTQICHQLAVNVQ  120 (310)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            34678999999999999998877654

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=97.63  E-value=5e-05  Score=48.16  Aligned_cols=20  Identities=40%  Similarity=0.602  Sum_probs=17.2

Q ss_pred             ceEEeCCCCCchHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      .++|+|.||+||||++..+.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            57899999999999977664

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.62  E-value=0.00023  Score=54.16  Aligned_cols=38  Identities=16%  Similarity=0.329  Sum_probs=28.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +.+.+.||+|+||||++..++..+....     +.++|.+++.
T Consensus       186 ~Vi~lVGpnGvGKTTTiaKLA~~~~~~~-----G~kkV~lit~  223 (767)
T PRK14723        186 GVLALVGPTGVGKTTTTAKLAARCVARE-----GADQLALLTT  223 (767)
T ss_pred             eEEEEECCCCCcHHHHHHHHHhhHHHHc-----CCCeEEEecC
Confidence            4678999999999999999998775431     2356766664

>TIGR00763 lon ATP-dependent protease La

Probab=97.62  E-value=5.8e-05  Score=57.44  Aligned_cols=24  Identities=33%  Similarity=0.641  Sum_probs=22.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.+++.||||||||+++..++..+
T Consensus       348 ~~lll~GppG~GKT~lAk~iA~~l  371 (775)
T TIGR00763       348 PILCLVGPPGVGKTSLGKSIAKAL  371 (775)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999998887

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=97.62  E-value=0.00024  Score=44.83  Aligned_cols=25  Identities=32%  Similarity=0.360  Sum_probs=20.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...++|.|++||||+.+|..+-...
T Consensus        22 ~~pVlI~GE~GtGK~~lA~~IH~~s   46 (168)
T PF00158_consen   22 DLPVLITGETGTGKELLARAIHNNS   46 (168)
T ss_dssp             TS-EEEECSTTSSHHHHHHHHHHCS
T ss_pred             CCCEEEEcCCCCcHHHHHHHHHHhh
Confidence            4689999999999999988886643

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=97.62  E-value=0.00015  Score=51.52  Aligned_cols=45  Identities=20%  Similarity=0.280  Sum_probs=35.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQF   85 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~   85 (97)
                      .++++|.|++|+|||+++..++..+...       +.+++|+=|..+....+
T Consensus        42 ~~h~~i~g~tGsGKt~~i~~l~~~~~~~-------~~~~vi~D~kg~~~~~~   86 (410)
T cd01127          42 EAHTMIIGTTGTGKTTQIRELLASIRAR-------GDRAIIYDPNGGFVSKF   86 (410)
T ss_pred             hccEEEEcCCCCCHHHHHHHHHHHHHhc-------CCCEEEEeCCcchhHhh
Confidence            3588999999999999988888877665       66788888877765544

TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=97.62  E-value=5.3e-05  Score=44.54  Aligned_cols=22  Identities=36%  Similarity=0.590  Sum_probs=19.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      ++.+.+.||+|+|||+++..+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            4678999999999999988765

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>PHA02774 E1; Provisional

Probab=97.62  E-value=0.0001  Score=54.47  Aligned_cols=24  Identities=29%  Similarity=0.652  Sum_probs=22.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++..++..+
T Consensus       435 nciv~~GPP~TGKS~fa~sL~~~L  458 (613)
T PHA02774        435 NCLVIYGPPDTGKSMFCMSLIKFL  458 (613)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999999887

>PRK14526 adenylate kinase; Provisional

Probab=97.61  E-value=6.6e-05  Score=48.98  Aligned_cols=22  Identities=32%  Similarity=0.570  Sum_probs=18.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +++|.||||+||||++..++..
T Consensus         2 ~i~l~G~pGsGKsT~a~~La~~   23 (211)
T PRK14526          2 KLVFLGPPGSGKGTIAKILSNE   23 (211)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999998877643

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=97.61  E-value=7.9e-05  Score=44.86  Aligned_cols=27  Identities=19%  Similarity=0.329  Sum_probs=23.2

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      .+..+++.|+-|+|||+++..++..+-
T Consensus        14 ~g~vi~L~GdLGaGKTtf~r~l~~~lg   40 (123)
T PF02367_consen   14 PGDVILLSGDLGAGKTTFVRGLARALG   40 (123)
T ss_dssp             S-EEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHcC
Confidence            456889999999999999999998883

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=97.61  E-value=0.0002  Score=54.56  Aligned_cols=54  Identities=28%  Similarity=0.381  Sum_probs=45.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ++..+|.+|-|||||+.+..-+...+..      +..++|++++.+..+.++.+++...+
T Consensus        49 ~~V~vVRSpMGTGKTtaLi~wLk~~l~~------~~~~VLvVShRrSL~~sL~~rf~~~~  102 (824)
T PF02399_consen   49 RGVLVVRSPMGTGKTTALIRWLKDALKN------PDKSVLVVSHRRSLTKSLAERFKKAG  102 (824)
T ss_pred             CCeEEEECCCCCCcHHHHHHHHHHhccC------CCCeEEEEEhHHHHHHHHHHHHhhcC
Confidence            4678999999999999766666666544      58899999999999999999997654

It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication

>PRK05595 replicative DNA helicase; Provisional

Probab=97.61  E-value=0.00021  Score=51.28  Aligned_cols=51  Identities=24%  Similarity=0.262  Sum_probs=36.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      +..++|.|+||.|||+++..++..+..+      .+.++++++.. ...+++..++..
T Consensus       201 g~liviaarpg~GKT~~al~ia~~~a~~------~g~~vl~fSlE-ms~~~l~~R~~a  251 (444)
T PRK05595        201 GDMILIAARPSMGKTTFALNIAEYAALR------EGKSVAIFSLE-MSKEQLAYKLLC  251 (444)
T ss_pred             CcEEEEEecCCCChHHHHHHHHHHHHHH------cCCcEEEEecC-CCHHHHHHHHHH
Confidence            4577899999999999999999875433      26788888753 345555555443

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.61  E-value=0.00012  Score=54.75  Aligned_cols=45  Identities=22%  Similarity=0.340  Sum_probs=31.9

Q ss_pred             cCCCCCHHHHHHHHHHhcC--------CceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         16 EELGLNTIQFEAYKAALTR--------EFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~--------~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ..+...+.+.+.+..+...        +.+++.||||+|||+++..++..+..
T Consensus        84 del~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~~  136 (637)
T TIGR00602        84 HELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELGI  136 (637)
T ss_pred             HHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            3455566666666665532        34899999999999998888766543

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=97.61  E-value=0.00028  Score=53.72  Aligned_cols=28  Identities=21%  Similarity=0.384  Sum_probs=24.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+.++.||||+|||+++..++..+...
T Consensus       207 ~~n~LLvGppGvGKT~lae~la~~i~~~  234 (758)
T PRK11034        207 KNNPLLVGESGVGKTAIAEGLAWRIVQG  234 (758)
T ss_pred             CCCeEEECCCCCCHHHHHHHHHHHHHhc
Confidence            3588999999999999999998877654

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.61  E-value=0.00015  Score=52.95  Aligned_cols=27  Identities=26%  Similarity=0.191  Sum_probs=23.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+++.||+|+|||+++..++..+...
T Consensus        44 ~a~Lf~Gp~G~GKTT~ArilAk~Lnc~   70 (507)
T PRK06645         44 GGYLLTGIRGVGKTTSARIIAKAVNCS   70 (507)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhcCc
Confidence            368999999999999999999888653

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=97.60  E-value=7.2e-05  Score=53.45  Aligned_cols=24  Identities=33%  Similarity=0.509  Sum_probs=22.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++++.||||+|||+++..++..+
T Consensus        48 ~~ILLiGppG~GKT~lAraLA~~l   71 (441)
T TIGR00390        48 KNILMIGPTGVGKTEIARRLAKLA   71 (441)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            589999999999999999998876

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>PRK14529 adenylate kinase; Provisional

Probab=97.60  E-value=7.3e-05  Score=49.23  Aligned_cols=23  Identities=26%  Similarity=0.446  Sum_probs=20.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++++.||||+||||.+..++..+
T Consensus         2 ~I~l~G~PGsGK~T~a~~La~~~   24 (223)
T PRK14529          2 NILIFGPNGSGKGTQGALVKKKY   24 (223)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999988887665

>KOG0951|consensus

Probab=97.60  E-value=0.00042  Score=55.02  Aligned_cols=76  Identities=28%  Similarity=0.285  Sum_probs=55.4

Q ss_pred             CCCCHHHHHHHHHHhc-CCceEEeCCCCCchHHHHHHHHHHHHhc-hhhh---hcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         18 LGLNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEGFLKN-KELA---RYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~~~~~~~-~~~~---~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ..|+..|......+.. .+++++.||+|+|||-++..-+-+-+.. .+..   ...+.++.+++|...++.++...+.+.
T Consensus       308 ~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~VgsfSkR  387 (1674)
T KOG0951|consen  308 QSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSFSKR  387 (1674)
T ss_pred             hhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHHHhh
Confidence            3488899988888885 4799999999999999865544333333 2211   114568999999999999998866554


Q ss_pred             c
Q psy16285         93 T   93 (97)
Q Consensus        93 ~   93 (97)
                      .
T Consensus       388 l  388 (1674)
T KOG0951|consen  388 L  388 (1674)
T ss_pred             c
Confidence            3

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=97.60  E-value=6.6e-05  Score=45.72  Aligned_cols=22  Identities=36%  Similarity=0.810  Sum_probs=19.0

Q ss_pred             eEEeCCCCCchHHHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++|.||+|+|||+++..+...+
T Consensus         2 i~i~GpsGsGKstl~~~L~~~~   23 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLEEF   23 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHhcC
Confidence            6789999999999988887654

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>PLN02674 adenylate kinase

Probab=97.59  E-value=6.8e-05  Score=50.01  Aligned_cols=23  Identities=35%  Similarity=0.544  Sum_probs=19.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+++|.||||+||||.+..++..
T Consensus        32 ~~i~l~G~PGsGKgT~a~~La~~   54 (244)
T PLN02674         32 KRLILIGPPGSGKGTQSPIIKDE   54 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Confidence            57899999999999998888653

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=97.59  E-value=0.00028  Score=44.63  Aligned_cols=29  Identities=17%  Similarity=0.259  Sum_probs=24.2

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+..+++.|+||+|||+++..+...+...
T Consensus        17 ~~~~i~i~G~~GsGKstla~~l~~~l~~~   45 (184)
T TIGR00455        17 RGVVIWLTGLSGSGKSTIANALEKKLESK   45 (184)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            34688999999999999999998877543

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>PHA02542 41 41 helicase; Provisional

Probab=97.59  E-value=0.00024  Score=51.48  Aligned_cols=37  Identities=11%  Similarity=0.275  Sum_probs=30.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +..++|.|+||.|||+++..++..+.+.       +.++++++-
T Consensus       190 G~LiiIaarPgmGKTtfalniA~~~a~~-------g~~Vl~fSL  226 (473)
T PHA02542        190 KTLNVLLAGVNVGKSLGLCSLAADYLQQ-------GYNVLYISM  226 (473)
T ss_pred             CcEEEEEcCCCccHHHHHHHHHHHHHhc-------CCcEEEEec
Confidence            4578899999999999999999888644       778888873

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=97.59  E-value=0.00011  Score=50.38  Aligned_cols=45  Identities=18%  Similarity=0.252  Sum_probs=33.8

Q ss_pred             HHHHHHHhc--C--CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         25 FEAYKAALT--R--EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        25 ~~~i~~~~~--~--~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ++.+..+..  +  ..+=|+|+||.||||+.-.++..+.+.       +.+|-|++
T Consensus        38 ~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~l~~~-------G~rVaVlA   86 (323)
T COG1703          38 RELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELRER-------GHRVAVLA   86 (323)
T ss_pred             HHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHHHHHC-------CcEEEEEE
Confidence            445555542  2  356789999999999999999999777       66666665

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=97.58  E-value=0.00036  Score=45.85  Aligned_cols=54  Identities=26%  Similarity=0.465  Sum_probs=45.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccCC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQNT   96 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~~   96 (97)
                      ..++|.|+.|||||.+...++.-++.+       +.++.+++ |...+..++.+..+.+.++
T Consensus        29 sL~lIEGd~~tGKSvLsqr~~YG~L~~-------g~~v~yvs-Te~T~refi~qm~sl~ydv   82 (235)
T COG2874          29 SLILIEGDNGTGKSVLSQRFAYGFLMN-------GYRVTYVS-TELTVREFIKQMESLSYDV   82 (235)
T ss_pred             eEEEEECCCCccHHHHHHHHHHHHHhC-------CceEEEEE-echhHHHHHHHHHhcCCCc
Confidence            467999999999999999999999998       77888888 6667888888887776543

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=97.58  E-value=5.5e-05  Score=45.41  Aligned_cols=26  Identities=27%  Similarity=0.436  Sum_probs=21.7

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.|++|+|||+++..++...
T Consensus        10 ~g~~~~i~G~nGsGKStLl~~l~g~~   35 (137)
T PF00005_consen   10 PGEIVAIVGPNGSGKSTLLKALAGLL   35 (137)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEEccCCCccccceeeecccc
Confidence            46789999999999999988775544

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>PRK00698 tmk thymidylate kinase; Validated

Probab=97.58  E-value=0.00018  Score=45.85  Aligned_cols=28  Identities=25%  Similarity=0.271  Sum_probs=23.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..++|.|+.|+||||++..+...+...
T Consensus         3 ~~~I~ieG~~gsGKsT~~~~L~~~l~~~   30 (205)
T PRK00698          3 GMFITIEGIDGAGKSTQIELLKELLEQQ   30 (205)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            4578999999999999999888877543

>KOG0730|consensus

Probab=97.58  E-value=3.7e-05  Score=57.06  Aligned_cols=59  Identities=19%  Similarity=0.130  Sum_probs=34.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +-+++.||||||||+++.+++...-.+.-....+.--..++-.+..++.+++++.+...
T Consensus       469 kGVLlyGPPGC~KT~lAkalAne~~~nFlsvkgpEL~sk~vGeSEr~ir~iF~kAR~~a  527 (693)
T KOG0730|consen  469 KGVLLYGPPGCGKTLLAKALANEAGMNFLSVKGPELFSKYVGESERAIREVFRKARQVA  527 (693)
T ss_pred             ceEEEECCCCcchHHHHHHHhhhhcCCeeeccCHHHHHHhcCchHHHHHHHHHHHhhcC
Confidence            46899999999999999999877633311000000011123335566666666655543

>KOG0736|consensus

Probab=97.58  E-value=5.3e-05  Score=57.38  Aligned_cols=24  Identities=38%  Similarity=0.616  Sum_probs=20.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .-+++.||||||||.+|.+++..+
T Consensus       706 SGILLYGPPGTGKTLlAKAVATEc  729 (953)
T KOG0736|consen  706 SGILLYGPPGTGKTLLAKAVATEC  729 (953)
T ss_pred             ceeEEECCCCCchHHHHHHHHhhc
Confidence            357899999999999999997654

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=97.58  E-value=0.00012  Score=48.93  Aligned_cols=25  Identities=28%  Similarity=0.379  Sum_probs=21.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      ..+.|.|++|+|||++|..++....
T Consensus        20 ~~v~I~G~~G~GKT~LA~~~~~~~~   44 (287)
T PF00931_consen   20 RVVAIVGMGGIGKTTLARQVARDLR   44 (287)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHCHHH
T ss_pred             EEEEEEcCCcCCcceeeeecccccc
Confidence            4789999999999999999886644

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>PRK14738 gmk guanylate kinase; Provisional

Probab=97.57  E-value=6.9e-05  Score=48.51  Aligned_cols=23  Identities=39%  Similarity=0.642  Sum_probs=19.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +..++|.||+|+|||+++..+..
T Consensus        13 ~~~ivi~GpsG~GK~tl~~~L~~   35 (206)
T PRK14738         13 PLLVVISGPSGVGKDAVLARMRE   35 (206)
T ss_pred             CeEEEEECcCCCCHHHHHHHHHh
Confidence            45788999999999999877754

>TIGR00767 rho transcription termination factor Rho

Probab=97.57  E-value=0.00016  Score=51.42  Aligned_cols=29  Identities=28%  Similarity=0.507  Sum_probs=24.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .++.++|.||||+|||+++..+...+..+
T Consensus       167 ~Gq~~~IvG~~g~GKTtL~~~i~~~I~~n  195 (415)
T TIGR00767       167 KGQRGLIVAPPKAGKTVLLQKIAQAITRN  195 (415)
T ss_pred             CCCEEEEECCCCCChhHHHHHHHHhhccc
Confidence            46789999999999999988888776554

Members of this family differ in the specificity of RNA binding.

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=97.57  E-value=0.00016  Score=50.40  Aligned_cols=39  Identities=21%  Similarity=0.215  Sum_probs=30.7

Q ss_pred             CCHHHHHHHHHHhc-CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         20 LNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        20 l~~~Q~~~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++.+.+.+..+.+ +.+++|.|++|+|||+++..++..+
T Consensus       163 ~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTll~al~~~i  202 (340)
T TIGR03819       163 FPPGVARLLRAIVAARLAFLISGGTGSGKTTLLSALLALV  202 (340)
T ss_pred             CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHccC
Confidence            45666677776664 5699999999999999988887655

Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.

>KOG0734|consensus

Probab=97.57  E-value=9e-05  Score=54.45  Aligned_cols=22  Identities=41%  Similarity=0.715  Sum_probs=19.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +-++++||||||||.++.+++.
T Consensus       338 KGVLLvGPPGTGKTlLARAvAG  359 (752)
T KOG0734|consen  338 KGVLLVGPPGTGKTLLARAVAG  359 (752)
T ss_pred             CceEEeCCCCCchhHHHHHhhc
Confidence            3579999999999999999853

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.57  E-value=0.0002  Score=55.19  Aligned_cols=26  Identities=23%  Similarity=0.396  Sum_probs=23.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+++.||||||||+++..++..++..
T Consensus       600 ~~Lf~Gp~G~GKT~lA~aLa~~l~~~  625 (857)
T PRK10865        600 SFLFLGPTGVGKTELCKALANFMFDS  625 (857)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhhcC
Confidence            57899999999999999999888654

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.57  E-value=0.00038  Score=53.65  Aligned_cols=27  Identities=26%  Similarity=0.330  Sum_probs=23.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.+++||||+|||+++..++..+...
T Consensus       209 ~n~lLvG~pGvGKTal~~~La~~i~~~  235 (852)
T TIGR03345       209 NNPILTGEAGVGKTAVVEGLALRIAAG  235 (852)
T ss_pred             CceeEECCCCCCHHHHHHHHHHHHhhC
Confidence            588999999999999999998887654

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK01184 hypothetical protein; Provisional

Probab=97.56  E-value=7.4e-05  Score=47.22  Aligned_cols=17  Identities=29%  Similarity=0.438  Sum_probs=14.7

Q ss_pred             ceEEeCCCCCchHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVAL   52 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~   52 (97)
                      .++|+||||+||||++.
T Consensus         3 ~i~l~G~~GsGKsT~a~   19 (184)
T PRK01184          3 IIGVVGMPGSGKGEFSK   19 (184)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            46889999999999754

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=97.56  E-value=0.00025  Score=45.37  Aligned_cols=35  Identities=17%  Similarity=0.289  Sum_probs=28.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ..+-++|.+|+||||++.++-..+.+.       +..+.++-
T Consensus        24 ~viW~TGLSGsGKSTiA~ale~~L~~~-------G~~~y~LD   58 (197)
T COG0529          24 AVIWFTGLSGSGKSTIANALEEKLFAK-------GYHVYLLD   58 (197)
T ss_pred             eEEEeecCCCCCHHHHHHHHHHHHHHc-------CCeEEEec
Confidence            367789999999999999999999887       55666554

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.56  E-value=8.1e-05  Score=54.25  Aligned_cols=24  Identities=33%  Similarity=0.376  Sum_probs=21.6

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +++.||||||||+++..++..+..
T Consensus        39 ~Lf~GppGtGKTTlA~~lA~~l~c   62 (504)
T PRK14963         39 YLFSGPRGVGKTTTARLIAMAVNC   62 (504)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhc
Confidence            499999999999999999988864

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=97.56  E-value=0.00017  Score=50.13  Aligned_cols=24  Identities=21%  Similarity=0.263  Sum_probs=21.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.+++.|+||||||+++..+...+
T Consensus        30 ~~vLl~G~pG~gKT~lar~la~ll   53 (334)
T PRK13407         30 GGVLVFGDRGTGKSTAVRALAALL   53 (334)
T ss_pred             CcEEEEcCCCCCHHHHHHHHHHHC
Confidence            589999999999999999887776

>COG3911 Predicted ATPase [General function prediction only]

Probab=97.56  E-value=7.6e-05  Score=46.57  Aligned_cols=23  Identities=30%  Similarity=0.514  Sum_probs=19.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +..++++|.||.|||+++.++..
T Consensus         9 ~~~fIltGgpGaGKTtLL~aLa~   31 (183)
T COG3911           9 HKRFILTGGPGAGKTTLLAALAR   31 (183)
T ss_pred             ceEEEEeCCCCCcHHHHHHHHHH
Confidence            45889999999999999887743

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=97.55  E-value=6.2e-05  Score=54.43  Aligned_cols=23  Identities=39%  Similarity=0.585  Sum_probs=20.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.||||||||.++.+++...
T Consensus       278 giLl~GpPGtGKT~lAkava~~~  300 (494)
T COG0464         278 GVLLYGPPGTGKTLLAKAVALES  300 (494)
T ss_pred             eeEEECCCCCCHHHHHHHHHhhC
Confidence            58999999999999999998744

>PTZ00202 tuzin; Provisional

Probab=97.55  E-value=0.00072  Score=49.05  Aligned_cols=44  Identities=16%  Similarity=0.165  Sum_probs=35.2

Q ss_pred             ccCCCCCHHHHHHHHHHhcC------CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALTR------EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~------~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...+.-++.+..++..+..+      ..++|+|++|+|||+++..++..+
T Consensus       261 ~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l  310 (550)
T PTZ00202        261 IRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKE  310 (550)
T ss_pred             ccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcC
Confidence            45677788899999888752      367899999999999988877544

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=97.55  E-value=0.00033  Score=48.09  Aligned_cols=36  Identities=25%  Similarity=0.346  Sum_probs=29.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +.+++.|.-|+||||++.+++.++-+.       ++++|+++.
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~~~A~~-------G~rtLlvS~   37 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALALALARR-------GKRTLLVST   37 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHT-------TS-EEEEES
T ss_pred             eEEEEecCCCCCcHHHHHHHHHHHhhC-------CCCeeEeec
Confidence            357899999999999999999888776       788888873

...

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=97.55  E-value=0.00011  Score=45.89  Aligned_cols=24  Identities=25%  Similarity=0.483  Sum_probs=20.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++++.|++|+|||+++..++..+
T Consensus         3 ~~i~~~G~~GsGKst~~~~la~~l   26 (171)
T PRK03731          3 QPLFLVGARGCGKTTVGMALAQAL   26 (171)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh
Confidence            357889999999999999987765

>PRK13946 shikimate kinase; Provisional

Probab=97.54  E-value=0.0001  Score=46.88  Aligned_cols=26  Identities=23%  Similarity=0.392  Sum_probs=22.5

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...++++.|++|+|||+++..+...+
T Consensus         9 ~~~~I~l~G~~GsGKsti~~~LA~~L   34 (184)
T PRK13946          9 GKRTVVLVGLMGAGKSTVGRRLATML   34 (184)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHc
Confidence            35689999999999999999987765

>PRK14737 gmk guanylate kinase; Provisional

Probab=97.54  E-value=8.2e-05  Score=47.60  Aligned_cols=25  Identities=24%  Similarity=0.393  Sum_probs=21.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..++|.||+|+|||+++..++...
T Consensus         4 ~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          4 PKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhcC
Confidence            3568999999999999988887653

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=97.54  E-value=0.0001  Score=42.98  Aligned_cols=25  Identities=28%  Similarity=0.446  Sum_probs=19.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .++|.|++|+|||+++..++..-..
T Consensus         1 kI~V~G~~g~GKTsLi~~l~~~~~~   25 (119)
T PF08477_consen    1 KIVVLGDSGVGKTSLIRRLCGGEFP   25 (119)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS--
T ss_pred             CEEEECcCCCCHHHHHHHHhcCCCc
Confidence            3689999999999998888755444

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>KOG0949|consensus

Probab=97.54  E-value=0.00043  Score=53.85  Aligned_cols=73  Identities=22%  Similarity=0.290  Sum_probs=63.4

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .++..+.+|.+.++...+++..+|.+|+-+|||++.-..++..++..     ...-+++++|+..++.|+...+...+
T Consensus       508 ~dF~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~iEKVLRes-----D~~VVIyvaPtKaLVnQvsa~VyaRF  580 (1330)
T KOG0949|consen  508 HDFCPDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAIEKVLRES-----DSDVVIYVAPTKALVNQVSANVYARF  580 (1330)
T ss_pred             hccCCcHHHHHHhhhhhcccceEEEeeccCCceeccHHHHHHHHhhc-----CCCEEEEecchHHHhhhhhHHHHHhh
Confidence            35778999999999999999999999999999999999888888875     46778999999999999887765544

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=97.54  E-value=0.0002  Score=53.13  Aligned_cols=45  Identities=18%  Similarity=0.204  Sum_probs=32.4

Q ss_pred             CCCCCHHHHHHHHHHh--------cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         17 ELGLNTIQFEAYKAAL--------TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~--------~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.+.+.-...+....        +++.+++.||||+|||+++..++..+-+.
T Consensus        78 ~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~le~~  130 (644)
T PRK15455         78 FYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLMERV  130 (644)
T ss_pred             ccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHHHhC
Confidence            3455565555555541        14578999999999999999998877554

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=97.53  E-value=0.0002  Score=48.54  Aligned_cols=26  Identities=31%  Similarity=0.344  Sum_probs=23.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.|.|++||||||++..++..+.+.
T Consensus         3 ~i~i~G~~gSGKTTLi~~Li~~L~~~   28 (274)
T PRK14493          3 VLSIVGYKATGKTTLVERLVDRLSGR   28 (274)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            46789999999999999999999776

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.53  E-value=0.00022  Score=50.92  Aligned_cols=27  Identities=22%  Similarity=0.358  Sum_probs=22.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ++.+.+.||+|+||||++..++..+..
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~~~  217 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARAVI  217 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            457899999999999999988876543

>PRK13975 thymidylate kinase; Provisional

Probab=97.53  E-value=0.00011  Score=46.72  Aligned_cols=24  Identities=33%  Similarity=0.542  Sum_probs=21.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.|++|+||||++..+...+
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~l   26 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEKL   26 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            467899999999999999888776

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	97
2wjv_A	800	Crystal Structure Of The Complex Between Human Nons		1e-08
2gjk_A	624	Structural And Functional Insights Into The Human U		1e-08
2xzo_A	623	Upf1 Helicase - Rna Complex Length = 623		1e-08
2xzl_A	802	Upf1-Rna Complex Length = 802		1e-04
4b3f_X	646	Crystal Structure Of 1ghmbp2 Helicase Length = 646		3e-04
4b3g_A	646	Crystal Structure Of Ighmbp2 Helicase In Complex Wi		3e-04

>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense Mediated Decay Factors Upf1 And Upf2 Length = 800

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 39/70 (55%), Gaps = 6/70 (8%)
Query: 20  LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
           LN  Q  A K  L R  ++IQGPPGTGKT  +  IV        LAR  +GP+L+   +N
Sbjct: 357 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIV------YHLARQGNGPVLVCAPSN 410
Query: 80  HALDQFVEGV 89
            A+DQ  E +
Sbjct: 411 IAVDQLTEKI 420

>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1 Helicase Core Length = 624

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 39/70 (55%), Gaps = 6/70 (8%)
Query: 20  LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
           LN  Q  A K  L R  ++IQGPPGTGKT  +  IV        LAR  +GP+L+   +N
Sbjct: 181 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIV------YHLARQGNGPVLVCAPSN 234
Query: 80  HALDQFVEGV 89
            A+DQ  E +
Sbjct: 235 IAVDQLTEKI 244

>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex Length = 623

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 39/70 (55%), Gaps = 6/70 (8%)
Query: 20  LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
           LN  Q  A K  L R  ++IQGPPGTGKT  +  IV        LAR  +GP+L+   +N
Sbjct: 180 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIV------YHLARQGNGPVLVCAPSN 233
Query: 80  HALDQFVEGV 89
            A+DQ  E +
Sbjct: 234 IAVDQLTEKI 243

>pdb|2XZL|A Chain A, Upf1-Rna Complex Length = 802

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 20  LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
           LN+ Q  A    L R  ++IQGPPGTGKT  +  IV        L++     IL+   +N
Sbjct: 361 LNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIV------YHLSKIHKDRILVCAPSN 414
Query: 80  HALDQF 85
            A+D  
Sbjct: 415 VAVDHL 420

>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase Length = 646

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 30/80 (37%), Positives = 41/80 (51%), Gaps = 10/80 (12%)
Query: 20  LNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY- 77
           L+T Q EA   AL+ +E AII GPPGTGKT   + I+   +K         G  ++ C  
Sbjct: 190 LDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQ--------GLKVLCCAP 241
Query: 78  TNHALDQFVEGVLKYTQNTL 97
           +N A+D  VE +    Q  L
Sbjct: 242 SNIAVDNLVERLALCKQRIL 261

>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna Length = 646

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 30/80 (37%), Positives = 41/80 (51%), Gaps = 10/80 (12%)
Query: 20  LNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY- 77
           L+T Q EA   AL+ +E AII GPPGTGKT   + I+   +K         G  ++ C  
Sbjct: 190 LDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQ--------GLKVLCCAP 241
Query: 78  TNHALDQFVEGVLKYTQNTL 97
           +N A+D  VE +    Q  L
Sbjct: 242 SNIAVDNLVERLALCKQRIL 261

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	97
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	6e-13
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	5e-12
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	7e-11
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	3e-09
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	1e-07
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	5e-07
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	7e-06
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	3e-05
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	5e-05
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	6e-05
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	1e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	5e-04
3b6e_A	216	Interferon-induced helicase C domain-containing P;	6e-04
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	6e-04

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae} Length = 802

 Score = 61.9 bits (150), Expect = 6e-13
 Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 20  LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
           LN+ Q  A    L R  ++IQGPPGTGKT  +  IV        L++     IL+   +N
Sbjct: 361 LNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIV------YHLSKIHKDRILVCAPSN 414

Query: 80  HALDQFVEGVLKYTQNTL 97
            A+D     +       +
Sbjct: 415 VAVDHLAAKLRDLGLKVV 432

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A Length = 800

 Score = 59.2 bits (143), Expect = 5e-12
 Identities = 31/80 (38%), Positives = 41/80 (51%), Gaps = 6/80 (7%)

Query: 13  NVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPI 72
             Q    LN  Q  A K  L R  ++IQGPPGTGKT  +  IV        LAR  +GP+
Sbjct: 350 TAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIV------YHLARQGNGPV 403

Query: 73  LIVCYTNHALDQFVEGVLKY 92
           L+   +N A+DQ  E + + 
Sbjct: 404 LVCAPSNIAVDQLTEKIHQT 423

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A Length = 624

 Score = 56.0 bits (135), Expect = 7e-11
 Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 6/79 (7%)

Query: 19  GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT 78
            LN  Q  A K  L R  ++IQGPPGTGKT  +  IV        LAR  +GP+L+   +
Sbjct: 180 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIV------YHLARQGNGPVLVCAPS 233

Query: 79  NHALDQFVEGVLKYTQNTL 97
           N A+DQ  E + +     +
Sbjct: 234 NIAVDQLTEKIHQTGLKVV 252

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A* Length = 472

 Score = 51.4 bits (123), Expect = 3e-09
 Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 10/70 (14%)

Query: 24  QFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALD 83
           Q +A +  L  +   I  P G+GKT+VA+               +S P LIV  T    +
Sbjct: 98  QEKALERWLVDKRGCIVLPTGSGKTHVAM----------AAINELSTPTLIVVPTLALAE 147

Query: 84  QFVEGVLKYT 93
           Q+ E +  + 
Sbjct: 148 QWKERLGIFG 157

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A* Length = 574

 Score = 46.6 bits (111), Expect = 1e-07
 Identities = 14/73 (19%), Positives = 25/73 (34%), Gaps = 7/73 (9%)

Query: 9   DLSANVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYM 68
           D +   +   GL+  Q             ++ G PGTGK+     +        +LA  +
Sbjct: 179 DWAVPKKARKGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAVA-------DLAESL 231

Query: 69  SGPILIVCYTNHA 81
              + +   T  A
Sbjct: 232 GLEVGLCAPTGKA 244

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19 Length = 237

 Score = 44.7 bits (106), Expect = 5e-07
 Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 10/70 (14%)

Query: 24  QFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALD 83
           Q +A +  L  +   I  P G+GKT+VA+               +S P LIV  T    +
Sbjct: 98  QEKALERWLVDKRGCIVLPTGSGKTHVAMAA----------INELSTPTLIVVPTLALAE 147

Query: 84  QFVEGVLKYT 93
           Q+ E +  + 
Sbjct: 148 QWKERLGIFG 157

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D* Length = 608

 Score = 41.6 bits (98), Expect = 7e-06
 Identities = 14/37 (37%), Positives = 21/37 (56%)

Query: 24  QFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLK 60
           Q  A   ALTR  ++I G PGTGKT    +++   ++
Sbjct: 154 QKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQ 190

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos} Length = 797

 Score = 40.0 bits (92), Expect = 3e-05
 Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 2/69 (2%)

Query: 16  EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIV 75
           E     + Q E  + A+  + A+I  P G+GKT+V++ I E   +N    R     ++ +
Sbjct: 245 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGR--KAKVVFL 302

Query: 76  CYTNHALDQ 84
                  +Q
Sbjct: 303 ATKVPVYEQ 311

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4} Length = 459

 Score = 39.2 bits (91), Expect = 5e-05
 Identities = 13/58 (22%), Positives = 19/58 (32%), Gaps = 7/58 (12%)

Query: 14 VQEELG--LNTIQFEAYKAALT-----REFAIIQGPPGTGKTYVALRIVEGFLKNKEL 64
                  L   Q  A+   +      +    I GP GTG T +   I+E  +   E 
Sbjct: 18 GSHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTKFIIEALISTGET 75

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos} Length = 936

 Score = 39.2 bits (90), Expect = 6e-05
 Identities = 15/48 (31%), Positives = 25/48 (52%)

Query: 16  EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKE 63
           E     + Q E  + A+  + A+I  P G+GKT+V++ I E   +N  
Sbjct: 245 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP 292

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus} Length = 446

 Score = 37.9 bits (87), Expect = 1e-04
 Identities = 12/68 (17%), Positives = 20/68 (29%), Gaps = 12/68 (17%)

Query: 20  LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
           L  +  +      + +  ++ G PG GKT   L  V                 LI+    
Sbjct: 147 LRRLLKDGEPHVSSAKVVLVDGVPGCGKTKEILSRVN------------FEEDLILVPGR 194

Query: 80  HALDQFVE 87
            A +    
Sbjct: 195 QAAEMIRR 202

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 37.9 bits (87), Expect = 2e-04
 Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 11/78 (14%)

Query: 24  QFEAYKAALTR----EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
            +   + AL      +  +I G  G+GKT+VAL +      + ++   M   I    + N
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDV----CLSYKVQCKMDFKIF---WLN 188

Query: 80  HALDQFVEGVLKYTQNTL 97
                  E VL+  Q  L
Sbjct: 189 LKNCNSPETVLEMLQKLL 206

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 37.1 bits (85), Expect = 3e-04
 Identities = 16/115 (13%), Positives = 37/115 (32%), Gaps = 26/115 (22%)

Query: 1   HSSILDAYDLSANV-QEELGLNTI-----QFEAY---KAALTREFAIIQGPPGTGKTYVA 51
           H SI+D Y++      ++L    +         +            + +        ++ 
Sbjct: 446 HRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFR------MVFLD 499

Query: 52  LRIVEGFLKNKELARYMSGPIL-----IVCYTNH------ALDQFVEGVLKYTQN 95
            R +E  +++   A   SG IL     +  Y  +        ++ V  +L +   
Sbjct: 500 FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPK 554

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 36.5 bits (83), Expect = 5e-04
 Identities = 17/48 (35%), Positives = 22/48 (45%)

Query: 13 NVQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLK 60
          N+         Q E    A+  +  II  P G GKT+V+L I E  LK
Sbjct: 7  NLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLK 54

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens} Length = 216

 Score = 35.9 bits (83), Expect = 6e-04
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 24 QFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALD 83
          Q E  + AL  +  II  P G+GKT VA+ I +  L  K+ A    G ++++      ++
Sbjct: 38 QMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASE-PGKVIVLVNKVLLVE 96

Query: 84 Q 84
          Q
Sbjct: 97 Q 97

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A* Length = 556

 Score = 36.5 bits (83), Expect = 6e-04
 Identities = 15/48 (31%), Positives = 25/48 (52%)

Query: 16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKE 63
          E     + Q E  + A+  + A+I  P G+GKT+V++ I E   +N  
Sbjct: 4  ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP 51

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	97
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	99.74
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	99.62
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	99.59
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	99.58
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	99.45
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.42
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	99.41
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.41
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	99.4
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.39
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.38
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.37
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.37
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.37
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.36
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.36
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.35
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.35
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	99.34
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.34
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.33
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.33
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.33
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.33
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.32
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.32
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.3
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.3
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.3
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.3
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.29
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	99.28
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.28
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.28
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.28
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.27
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.27
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.26
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	99.26
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.25
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.23
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.22
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.22
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.22
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.21
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.2
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.2
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.19
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.19
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.18
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.17
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.16
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.15
3h1t_A	590	Type I site-specific restriction-modification syst	99.13
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.13
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.13
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.13
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.12
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.12
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.11
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.09
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.05
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.05
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.05
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.04
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	99.04
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.97
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.91
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.9
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	98.88
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.84
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	98.83
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.83
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.8
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	98.8
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.74
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	98.72
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.72
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	98.69
2qgz_A	308	Helicase loader, putative primosome component; str	98.69
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.69
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	98.69
1yks_A	440	Genome polyprotein [contains: flavivirin protease	98.67
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	98.65
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	98.62
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	98.61
3bos_A	242	Putative DNA replication factor; P-loop containing	98.57
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	98.53
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	98.53
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	98.52
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	98.51
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	98.5
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.48
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.48
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	98.42
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.42
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	98.41
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.41
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	98.39
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	98.39
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.38
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	98.36
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	98.36
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.36
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	98.35
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	98.35
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	98.34
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	98.32
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.32
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	98.31
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	98.31
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.31
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	98.28
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.28
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	98.26
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	98.25
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.25
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.24
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	98.24
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	98.23
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	98.23
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.22
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.22
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	98.21
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	98.21
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	98.2
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	98.2
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	98.2
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.2
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	98.2
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	98.2
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.19
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	98.19
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.19
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.18
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.18
1tue_A	212	Replication protein E1; helicase, replication, E1E	98.17
1p9r_A	418	General secretion pathway protein E; bacterial typ	98.17
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	98.17
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	98.17
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	98.16
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	98.16
2r44_A	331	Uncharacterized protein; putative ATPase, structur	98.16
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	98.15
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.14
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.14
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	98.14
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	98.12
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.12
3co5_A	143	Putative two-component system transcriptional RES	98.12
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	98.11
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.11
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	98.11
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	98.1
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.09
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	98.09
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.08
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	98.08
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.08
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.08
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	98.07
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	98.06
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	98.06
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	98.06
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	98.05
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	98.05
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	98.04
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	98.04
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	98.04
3pvs_A	447	Replication-associated recombination protein A; ma	98.04
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	98.03
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	98.03
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	98.02
2r6a_A	454	DNAB helicase, replicative helicase; replication,	98.02
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	98.02
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	98.01
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	98.01
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	98.01
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	98.0
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	98.0
1u94_A	356	RECA protein, recombinase A; homologous recombinat	98.0
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	98.0
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	98.0
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	97.99
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	97.99
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	97.99
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	97.99
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	97.98
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	97.98
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	97.98
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	97.98
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	97.97
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	97.97
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	97.97
1via_A	175	Shikimate kinase; structural genomics, transferase	97.96
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.96
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	97.96
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.95
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.95
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	97.95
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	97.95
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.95
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	97.94
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.94
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	97.94
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.94
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	97.93
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	97.93
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	97.93
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	97.92
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.92
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	97.92
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	97.92
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	97.92
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	97.92
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	97.92
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.91
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	97.91
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	97.91
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	97.9
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	97.9
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	97.9
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.9
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	97.9
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	97.9
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	97.89
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	97.89
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	97.89
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	97.89
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	97.89
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	97.89
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	97.89
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	97.89
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	97.89
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	97.89
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.89
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	97.88
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	97.88
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.88
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	97.88
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	97.87
2eyu_A	261	Twitching motility protein PILT; pilus retraction	97.87
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	97.87
2fna_A	357	Conserved hypothetical protein; structural genomic	97.87
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	97.86
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	97.86
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	97.86
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	97.86
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	97.85
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	97.85
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	97.85
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	97.85
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	97.85
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	97.85
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	97.84
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	97.84
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	97.83
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	97.83
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	97.83
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	97.82
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	97.81
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	97.81
2og2_A	359	Putative signal recognition particle receptor; nuc	97.8
2ewv_A	372	Twitching motility protein PILT; pilus retraction	97.8
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	97.8
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.79
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	97.79
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	97.79
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	97.79
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	97.78
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	97.78
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	97.78
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	97.78
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	97.78
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	97.78
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	97.78
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	97.77
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	97.77
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	97.77
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	97.77
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	97.77
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	97.76
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	97.76
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	97.75
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	97.75
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	97.74
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	97.74
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.74
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.74
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	97.74
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	97.74
2vli_A	183	Antibiotic resistance protein; transferase, tunica	97.74
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	97.74
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.73
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	97.73
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	97.73
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	97.73
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	97.72
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	97.72
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.72
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	97.72
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	97.71
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	97.71
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	97.71
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	97.71
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	97.7
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	97.7
4a74_A	231	DNA repair and recombination protein RADA; hydrola	97.7
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	97.7
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	97.69
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	97.69
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.69
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	97.69
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	97.68
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	97.67
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	97.67
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.66
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	97.64
3io5_A	333	Recombination and repair protein; storage dimer, i	97.63
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	97.63
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	97.62
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	97.61
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.61
3bs4_A	260	Uncharacterized protein PH0321; structural genomic	97.61
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	97.6
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	97.6
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	97.6
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	97.6
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	97.6
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	97.59
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	97.59
2xxa_A	433	Signal recognition particle protein; protein trans	97.58
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.57
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	97.57
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	97.56
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	97.56
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	97.55
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	97.54
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	97.54
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.53
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	97.53
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	97.52
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	97.52
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	97.52
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	97.51
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	97.5
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	97.5
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	97.5
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	97.5
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	97.5
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	97.49
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	97.49
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	97.48
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	97.48
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	97.48
1b0u_A	262	Histidine permease; ABC transporter, transport pro	97.47
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	97.47
1sgw_A	214	Putative ABC transporter; structural genomics, P p	97.47
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	97.47
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	97.46
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.46
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	97.46
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	97.46
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	97.45
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	97.45
1g6h_A	257	High-affinity branched-chain amino acid transport	97.45
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	97.45
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	97.44
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	97.43
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	97.43
1ji0_A	240	ABC transporter; ATP binding protein, structural g	97.43
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	97.43
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	97.43
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	97.43
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	97.43
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	97.42
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	97.42
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	97.42
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	97.41
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	97.41
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	97.41
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.41
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	97.41
3kta_A	182	Chromosome segregation protein SMC; structural mai	97.4
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	97.4
2ghi_A	260	Transport protein; multidrug resistance protein, M	97.4
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.4
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	97.4
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	97.4
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	97.39
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	97.39
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	97.39
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	97.39
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	97.39
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	97.39
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	97.38
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	97.37
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	97.37
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	97.37
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	97.37
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	97.37
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	97.37
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	97.37
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	97.36
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	97.35
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	97.35
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	97.34
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	97.34
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	97.33
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	97.33
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	97.29
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	97.29
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	97.29
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	97.29
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	97.28
3ice_A	422	Transcription termination factor RHO; transcriptio	97.28
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	97.27
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	97.26
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	97.26
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	97.26
1ihu_A	589	Arsenical pump-driving ATPase; aluminum fluoride,	97.26
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	97.26
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	97.26
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	97.26
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	97.26
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	97.26
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	97.25
3ug7_A	349	Arsenical pump-driving ATPase; tail-anchored, memb	97.24
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	97.23
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	97.21
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	97.21
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	97.2
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	97.2
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	97.19
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	97.19
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	97.19
3bfv_A	271	CAPA1, CAPB2, membrane protein CAPA1, protein tyro	97.18
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	97.18
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.17
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	97.17
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	97.16
3cio_A	299	ETK, tyrosine-protein kinase ETK; WZC, escherichia	97.16
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	97.14
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	97.14
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	97.13
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	97.12
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	97.11
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	97.11
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	97.1
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	97.1
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	97.1
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	97.1
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	97.09
2woo_A	329	ATPase GET3; tail-anchored, membrane protein, targ	97.09
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	97.09
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	97.08
3end_A	307	Light-independent protochlorophyllide reductase ir	97.08
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	97.08
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	97.06
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	97.06
2hf9_A	226	Probable hydrogenase nickel incorporation protein	97.06
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	97.06
3l0o_A	427	Transcription termination factor RHO; helicase, RH	97.05
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	97.04
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	97.04
2wji_A	165	Ferrous iron transport protein B homolog; membrane	97.04
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	97.03
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	97.03
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	97.02
1nrj_B	218	SR-beta, signal recognition particle receptor beta	97.02
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	96.99
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	96.99
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	96.99
2ged_A	193	SR-beta, signal recognition particle receptor beta	96.99
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	96.97
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	96.97
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	96.97
2oze_A	298	ORF delta'; para, walker type atpases, DNA segrega	96.96
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	96.96
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	96.95
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	96.95
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	96.94
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	96.94
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	96.94
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	96.93
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	96.92
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	96.92
1byi_A	224	Dethiobiotin synthase; biotin synthesis, cyclo-lig	96.92
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	96.92
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	96.92
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	96.91
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	96.91
3qkt_A	339	DNA double-strand break repair RAD50 ATPase; RECA-	96.9
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	96.89
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	96.89
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	96.88
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	96.87
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	96.87
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	96.87
2woj_A	354	ATPase GET3; tail-anchored, membrane protein, targ	96.86

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=99.74  E-value=8.7e-18  Score=122.24  Aligned_cols=71  Identities=39%  Similarity=0.481  Sum_probs=64.2

Q ss_pred             CCCCHHHHHHHHHHhc-CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         18 LGLNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      ..||+.|++|+..++. .+..+|+||||||||+++..++.+++..       +.+||+++|||.|++++.++|...+.+
T Consensus       188 ~~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~-------~~~ILv~a~TN~AvD~i~erL~~~~~~  259 (646)
T 4b3f_X          188 TCLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQ-------GLKVLCCAPSNIAVDNLVERLALCKQR  259 (646)
T ss_dssp             TTCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHHHHTTCC
T ss_pred             CCCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHhC-------CCeEEEEcCchHHHHHHHHHHHhcCCc
Confidence            4689999999999886 4688999999999999999999999887       789999999999999999999877654

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=99.62  E-value=3.3e-15  Score=108.51  Aligned_cols=71  Identities=38%  Similarity=0.537  Sum_probs=64.0

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...+++.|.+++..+..++..+|+||||||||+++..++..+...      .+.+|++++|||.|++++.+++.+.+
T Consensus       178 ~~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~~i~~l~~~------~~~~ilv~a~tn~A~~~l~~~l~~~~  248 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ------GNGPVLVCAPSNIAVDQLTEKIHQTG  248 (624)
T ss_dssp             SCCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHHHHHHHHTS------SSCCEEEEESSHHHHHHHHHHHHTTT
T ss_pred             cCCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHHHHHHHHHc------CCCeEEEEeCcHHHHHHHHHHHHhcC
Confidence            346899999999998888899999999999999999999988874      37899999999999999999998764

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.59  E-value=7.5e-15  Score=109.27  Aligned_cols=71  Identities=34%  Similarity=0.419  Sum_probs=63.9

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...|++.|++|+..+..++..+|+||||||||+++..++..+...      .+.+||+++|||.|++++.+++.+.+
T Consensus       358 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i~~l~~~------~~~~ILv~a~tn~A~d~l~~rL~~~g  428 (802)
T 2xzl_A          358 FAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKI------HKDRILVCAPSNVAVDHLAAKLRDLG  428 (802)
T ss_dssp             SCCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHHHHHHHH------HCCCEEEEESSHHHHHHHHHHHHHTT
T ss_pred             cccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhC------CCCeEEEEcCcHHHHHHHHHHHHhhC
Confidence            346899999999999888889999999999999999999888774      37899999999999999999998764

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=99.58  E-value=1.3e-14  Score=107.95  Aligned_cols=72  Identities=38%  Similarity=0.522  Sum_probs=64.5

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ...+++.|.+++..+..++..+|+||||||||+++..++..+...      .+.+|++++|||.|++++.+++.+.+.
T Consensus       354 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~~~i~~l~~~------~~~~ilv~a~tn~A~~~l~~~l~~~g~  425 (800)
T 2wjy_A          354 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ------GNGPVLVCAPSNIAVDQLTEKIHQTGL  425 (800)
T ss_dssp             SCCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHHHHHHHHHTT------CSSCEEEEESSHHHHHHHHHHHHTTTC
T ss_pred             ccCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHHHHHHHHHHc------CCCcEEEEcCcHHHHHHHHHHHHHhCc
Confidence            456899999999999888899999999999999999999988874      378999999999999999999987653

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=99.45  E-value=5.1e-13  Score=96.42  Aligned_cols=66  Identities=18%  Similarity=0.180  Sum_probs=60.0

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      .+.+++.|++++..+..++.++|+||||||||+++..++..+...       +.+|++++||+.++.++.+.+
T Consensus       187 ~~~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~~l~~~l~~~-------g~~Vl~~ApT~~Aa~~L~e~~  252 (574)
T 3e1s_A          187 RKGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAVADLAESL-------GLEVGLCAPTGKAARRLGEVT  252 (574)
T ss_dssp             TTTCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHHHHHHHHHHhc-------CCeEEEecCcHHHHHHhHhhh
Confidence            567899999999999999999999999999999999999888765       789999999999999998754

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=99.42  E-value=1e-12  Score=82.99  Aligned_cols=79  Identities=29%  Similarity=0.379  Sum_probs=64.1

Q ss_pred             cccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHH-HHHHHHhh
Q psy16285         14 VQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQ-FVEGVLKY   92 (97)
Q Consensus        14 ~~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~-~~~~l~~~   92 (97)
                      ....+.+++.|.+++..+.+++++++.+|+|+|||.++...+..++...... ....++++++|+..++.| +.+.+.++
T Consensus        28 ~~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~-~~~~~~lil~p~~~L~~q~~~~~~~~~  106 (216)
T 3b6e_A           28 PEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKA-SEPGKVIVLVNKVLLVEQLFRKEFQPF  106 (216)
T ss_dssp             CSCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHT-TCCCCEEEEESSHHHHHHHHHHTHHHH
T ss_pred             ccCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccc-cCCCcEEEEECHHHHHHHHHHHHHHHH
Confidence            3456789999999999999889999999999999999888777665542211 136799999999999999 77777776


Q ss_pred             c
Q psy16285         93 T   93 (97)
Q Consensus        93 ~   93 (97)
                      .
T Consensus       107 ~  107 (216)
T 3b6e_A          107 L  107 (216)
T ss_dssp             H
T ss_pred             h
Confidence            4

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=99.41  E-value=1.5e-12  Score=91.48  Aligned_cols=69  Identities=22%  Similarity=0.257  Sum_probs=58.6

Q ss_pred             ccCCCCCHHHHHHHHHHhc-----CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALT-----REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~-----~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      ...-.|++.|++++..+..     .+.++|.||||||||+++..++..+...      ...++++++||+.++.++.+++
T Consensus        21 ~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~~~~~~l~~~------~~~~il~~a~T~~Aa~~l~~~~   94 (459)
T 3upu_A           21 MTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTKFIIEALIST------GETGIILAAPTHAAKKILSKLS   94 (459)
T ss_dssp             CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHHHHHHHHHHT------TCCCEEEEESSHHHHHHHHHHH
T ss_pred             CccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHHHHHHHHHHhc------CCceEEEecCcHHHHHHHHhhh
Confidence            3445689999999997653     3489999999999999999999999887      2458999999999999998776

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=99.41  E-value=1.3e-12  Score=86.41  Aligned_cols=71  Identities=21%  Similarity=0.316  Sum_probs=62.5

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         18 LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +.+++.|.+++..+..++..++.+|+|+|||.++..++...+..      ...++++++|++.++.|+.+++.+++.
T Consensus       112 ~~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~------~~~~~lil~Pt~~L~~q~~~~l~~~~~  182 (282)
T 1rif_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN------YEGKILIIVPTTALTTQMADDFVDYRL  182 (282)
T ss_dssp             CCCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHH------CSSEEEEECSSHHHHHHHHHHHHHHTS
T ss_pred             cCccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHc------CCCeEEEEECCHHHHHHHHHHHHHhcc
Confidence            58999999999998888888999999999999988887776655      345899999999999999999999864

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=99.40  E-value=7.4e-13  Score=95.69  Aligned_cols=70  Identities=23%  Similarity=0.258  Sum_probs=59.9

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .|++.|++++.  ...+.++|.|+||||||+++...+.+++.....   ++.+||++++|+.+++++.+++.+..
T Consensus         9 ~Ln~~Q~~av~--~~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~---~~~~iL~ltft~~aa~e~~~rl~~~~   78 (647)
T 3lfu_A            9 SLNDKQREAVA--APRSNLLVLAGAGSGKTRVLVHRIAWLMSVENC---SPYSIMAVTFTNKAAAEMRHRIGQLM   78 (647)
T ss_dssp             TCCHHHHHHHT--CCSSCEEEEECTTSCHHHHHHHHHHHHHHTSCC---CGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHh--CCCCCEEEEECCCCCHHHHHHHHHHHHHHhCCC---ChhhEEEEeccHHHHHHHHHHHHHHh
Confidence            68999999987  346789999999999999999988888876322   35799999999999999999998763

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.39  E-value=4.8e-12  Score=81.42  Aligned_cols=78  Identities=22%  Similarity=0.119  Sum_probs=60.9

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHH-HHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIV-EGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~-~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +...+++.|.+++..+.+++.+++.+|+|+|||......+ ..+.+.. .....+.++++++|+++++.|+.+.+.+++.
T Consensus        44 ~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~-~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  122 (236)
T 2pl3_A           44 QYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQ-WTSTDGLGVLIISPTRELAYQTFEVLRKVGK  122 (236)
T ss_dssp             TCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTT-CCGGGCCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhc-ccccCCceEEEEeCCHHHHHHHHHHHHHHhC
Confidence            3456899999999999999999999999999998755443 3333311 0011367899999999999999999998864

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=99.38  E-value=5.4e-12  Score=79.43  Aligned_cols=78  Identities=22%  Similarity=0.072  Sum_probs=60.9

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +...+++.|.+++..+.+++++++.+|+|+|||..+...+...+.... ....+.++++++|+++++.|+.+.+.++..
T Consensus        20 ~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~-~~~~~~~~lil~P~~~L~~q~~~~~~~~~~   97 (207)
T 2gxq_A           20 GLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQ-ERGRKPRALVLTPTRELALQVASELTAVAP   97 (207)
T ss_dssp             TCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCC-CTTCCCSEEEECSSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhcc-ccCCCCcEEEEECCHHHHHHHHHHHHHHhh
Confidence            345789999999999999999999999999999875544443332110 001367899999999999999999998864

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=99.37  E-value=5.9e-12  Score=80.18  Aligned_cols=72  Identities=19%  Similarity=0.187  Sum_probs=59.7

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+++.|.+++..+.++..+++.+|+|+|||..+...+...+....    ...++++++|+++++.|+.+.++++..
T Consensus        36 ~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~----~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (220)
T 1t6n_A           36 HPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT----GQVSVLVMCHTRELAFQISKEYERFSK  107 (220)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCT----TCCCEEEECSCHHHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccC----CCEEEEEEeCCHHHHHHHHHHHHHHHh
Confidence            489999999999999999999999999999876665555444321    245899999999999999999998853

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=99.37  E-value=5.2e-12  Score=82.11  Aligned_cols=69  Identities=30%  Similarity=0.340  Sum_probs=60.0

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...+.+++.|.+++..+.+++.+++.||+|+|||.++..++..+          +.++++++|+..++.|+.+.+.+++
T Consensus        89 ~~~~~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~----------~~~~liv~P~~~L~~q~~~~~~~~~  157 (237)
T 2fz4_A           89 DAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL----------STPTLIVVPTLALAEQWKERLGIFG  157 (237)
T ss_dssp             CCCCCCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS----------CSCEEEEESSHHHHHHHHHHHGGGC
T ss_pred             cCCCCcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc----------CCCEEEEeCCHHHHHHHHHHHHhCC
Confidence            44578999999999998888889999999999999987776543          5689999999999999999998854

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=99.37  E-value=7.4e-12  Score=79.83  Aligned_cols=73  Identities=18%  Similarity=0.084  Sum_probs=59.2

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHH-HHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVA-LRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~-~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ...+++.|.+++..+.++.++++.+|+|+|||... ..++..+....     .+.++++++|+++++.|+.+.+.++..
T Consensus        34 ~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~-----~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (224)
T 1qde_A           34 FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSV-----KAPQALMLAPTRELALQIQKVVMALAF  107 (224)
T ss_dssp             CCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTC-----CSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccC-----CCceEEEEECCHHHHHHHHHHHHHHhc
Confidence            34689999999999999999999999999999874 33344332221     357999999999999999999988753

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=99.36  E-value=7.6e-12  Score=78.79  Aligned_cols=74  Identities=19%  Similarity=0.069  Sum_probs=59.1

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ...+++.|.+++..+.+++++++.+|+|+|||..+...+........    .+.++++++|+++++.|+.+.+.++..
T Consensus        23 ~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~----~~~~~lil~Pt~~L~~q~~~~~~~~~~   96 (206)
T 1vec_A           23 WEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKK----DNIQAMVIVPTRELALQVSQICIQVSK   96 (206)
T ss_dssp             CCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTS----CSCCEEEECSCHHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccC----CCeeEEEEeCcHHHHHHHHHHHHHHHh
Confidence            34689999999999999999999999999999765544333322211    356899999999999999999988764

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=99.36  E-value=6.9e-12  Score=82.37  Aligned_cols=76  Identities=16%  Similarity=0.127  Sum_probs=59.4

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+++.|.+++..+..++++++.+|+|+|||..+...+...+.........+.++++++|+++++.|+.+.++++..
T Consensus        76 ~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~~~~  151 (262)
T 3ly5_A           76 NMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMT  151 (262)
T ss_dssp             BCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHHHHHHHHHHHHh
Confidence            3899999999999999999999999999998755444333322111111377899999999999999999998764

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=99.35  E-value=1.1e-11  Score=80.11  Aligned_cols=75  Identities=21%  Similarity=0.146  Sum_probs=59.3

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ...+++.|.+++..+.+++.+++.+|+|+|||..+...+...+....   ..+.++++++|+++++.|+.+.+.++..
T Consensus        49 ~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~---~~~~~~lil~Pt~~L~~q~~~~~~~~~~  123 (245)
T 3dkp_A           49 FQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPA---NKGFRALIISPTRELASQIHRELIKISE  123 (245)
T ss_dssp             CCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCC---SSSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcc---cCCceEEEEeCCHHHHHHHHHHHHHHhc
Confidence            34589999999999999999999999999999875444333332210   1356899999999999999999998854

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.35  E-value=5.9e-12  Score=80.29  Aligned_cols=75  Identities=25%  Similarity=0.153  Sum_probs=60.2

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +...+++.|.+++..+.+++++++.+|+|+|||......+...+....    .+.+++|++|+++++.|+.+.++++..
T Consensus        23 g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~----~~~~~lil~Pt~~L~~q~~~~~~~~~~   97 (219)
T 1q0u_A           23 RFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPER----AEVQAVITAPTRELATQIYHETLKITK   97 (219)
T ss_dssp             TCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTS----CSCCEEEECSSHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCc----CCceEEEEcCcHHHHHHHHHHHHHHhh
Confidence            445689999999999999999999999999999875444433333211    357899999999999999999988764

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=99.34  E-value=3.3e-12  Score=92.66  Aligned_cols=69  Identities=28%  Similarity=0.316  Sum_probs=58.6

Q ss_pred             CHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         21 NTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        21 ~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      .+.|++++..+..++.++|+||||||||+++..++..+.....   ..+.++++++||+.++.++.+.+...
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~---~~~~~vll~APTg~AA~~L~e~~~~~  219 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD---GERCRIRLAAPTGKAAARLTESLGKA  219 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS---SCCCCEEEEBSSHHHHHHHHHHHTHH
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh---cCCCeEEEEeCChhHHHHHHHHHHHH
Confidence            6789999999999999999999999999999999888875310   03569999999999999999887653

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=99.34  E-value=5.9e-12  Score=81.36  Aligned_cols=73  Identities=21%  Similarity=0.097  Sum_probs=59.1

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         18 LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ..+++.|.+++..+.++.++++.+|+|+|||..+...+...+....    .+.+++|++|+++++.|+.+.+++++.
T Consensus        51 ~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~----~~~~~lil~Pt~~L~~q~~~~~~~~~~  123 (237)
T 3bor_A           51 EKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEF----KETQALVLAPTRELAQQIQKVILALGD  123 (237)
T ss_dssp             CSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTS----CSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcC----CCceEEEEECcHHHHHHHHHHHHHHhh
Confidence            3489999999999999999999999999999875444443333211    357899999999999999999998864

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=99.33  E-value=1.6e-11  Score=80.15  Aligned_cols=73  Identities=22%  Similarity=0.065  Sum_probs=59.3

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHH-HHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIV-EGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~-~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ...+++.|.+++..+.+++.+++.+|+|+|||..+...+ ..+....     .+.+++|++|+++++.|+.+.++++..
T Consensus        63 ~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~-----~~~~~lil~Ptr~L~~q~~~~~~~~~~  136 (249)
T 3ber_A           63 WTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETP-----QRLFALVLTPTRELAFQISEQFEALGS  136 (249)
T ss_dssp             CCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSC-----CSSCEEEECSSHHHHHHHHHHHHHHHG
T ss_pred             CCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCC-----CCceEEEEeCCHHHHHHHHHHHHHHhc
Confidence            347899999999999999999999999999998754443 3443331     256799999999999999999988753

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.33  E-value=9.9e-12  Score=85.59  Aligned_cols=71  Identities=18%  Similarity=0.098  Sum_probs=60.2

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+.+++.|.+++..+.++.++++.+|||+|||......+.....       .+.+++|++|+++++.|+.+++.++..
T Consensus        19 ~~~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~-------~~~~~lil~Pt~~L~~q~~~~~~~~~~   89 (414)
T 3oiy_A           19 GKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR-------KGKKSALVFPTVTLVKQTLERLQKLAD   89 (414)
T ss_dssp             SSCCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHT-------TTCCEEEEESSHHHHHHHHHHHHHHCC
T ss_pred             CCCCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhc-------CCCEEEEEECCHHHHHHHHHHHHHHcc
Confidence            45788999999999999999999999999999965555444432       378999999999999999999999753

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=99.33  E-value=1.9e-11  Score=78.25  Aligned_cols=77  Identities=22%  Similarity=0.143  Sum_probs=58.7

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhh--hhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKEL--ARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~--~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...+++.|.+++..+.+++++++.+|+|+|||..+...+...+.....  ....+.++++++|+++++.|+.+.++++.
T Consensus        40 ~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  118 (228)
T 3iuy_A           40 ILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYS  118 (228)
T ss_dssp             CCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSSHHHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCCHHHHHHHHHHHHHhc
Confidence            347899999999999999999999999999998754443332221100  01146789999999999999999999874

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=99.33  E-value=1.5e-11  Score=79.07  Aligned_cols=71  Identities=23%  Similarity=0.198  Sum_probs=58.5

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHH-HHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALR-IVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~-~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+++.|.+++..+.++.++++.+|+|+|||..... ++..+....     .+.+++|++|+++++.|+.+.++++..
T Consensus        46 ~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~-----~~~~~lil~Pt~~L~~q~~~~~~~~~~  117 (230)
T 2oxc_A           46 RPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLEN-----LSTQILILAPTREIAVQIHSVITAIGI  117 (230)
T ss_dssp             SCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTS-----CSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcC-----CCceEEEEeCCHHHHHHHHHHHHHHhc
Confidence            48999999999999999999999999999987433 344433321     367999999999999999999998864

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=99.32  E-value=4e-11  Score=77.89  Aligned_cols=78  Identities=22%  Similarity=0.149  Sum_probs=59.7

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhh-----hhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKEL-----ARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~-----~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      ...+++.|.+++..+.+++.+++.+|+|+|||..+...+...+.....     ....+.+++|++|+++++.|+.+.+.+
T Consensus        43 ~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~  122 (253)
T 1wrb_A           43 YQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQK  122 (253)
T ss_dssp             CCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCceEEEEECCHHHHHHHHHHHHH
Confidence            346899999999999999999999999999998755444333322110     001246899999999999999999998


Q ss_pred             hcc
Q psy16285         92 YTQ   94 (97)
Q Consensus        92 ~~~   94 (97)
                      +..
T Consensus       123 ~~~  125 (253)
T 1wrb_A          123 FSL  125 (253)
T ss_dssp             HHT
T ss_pred             Hhc
Confidence            764

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.32  E-value=6.4e-12  Score=88.64  Aligned_cols=71  Identities=21%  Similarity=0.325  Sum_probs=63.1

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .+.+++.|.+++..+..+...++.+|+|+|||.++..++...+..      ...+++|++|+..++.|+.+++.++.
T Consensus       111 ~~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~------~~~~vlvl~P~~~L~~Q~~~~~~~~~  181 (510)
T 2oca_A          111 RIEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN------YEGKILIIVPTTALTTQMADDFVDYR  181 (510)
T ss_dssp             EECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHH------CSSEEEEEESSHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhC------CCCeEEEEECcHHHHHHHHHHHHHhh
Confidence            458999999999999988899999999999999988887777665      34599999999999999999999873

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=99.30  E-value=1.4e-11  Score=84.76  Aligned_cols=72  Identities=24%  Similarity=0.259  Sum_probs=64.0

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +..+.++++|.+++..+..+ ++++.+|+|+|||..+...+...+..      .+.+++|++|+..++.|+.+.+.++.
T Consensus         5 ~~~~~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~------~~~~~liv~P~~~L~~q~~~~~~~~~   76 (494)
T 1wp9_A            5 RDLIQPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTK------YGGKVLMLAPTKPLVLQHAESFRRLF   76 (494)
T ss_dssp             HHHHCCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHH------SCSCEEEECSSHHHHHHHHHHHHHHB
T ss_pred             cCCCCccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhc------CCCeEEEEECCHHHHHHHHHHHHHHh
Confidence            34578999999999999888 89999999999999988887777663      47899999999999999999999986

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.30  E-value=2.7e-11  Score=85.32  Aligned_cols=76  Identities=26%  Similarity=0.281  Sum_probs=63.3

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+.++++|.+++..+..+.++++.+|+|+|||..+...+...+.....  ..+.+++|++|++.++.|+.+.+.+++.
T Consensus         2 ~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~--~~~~~~lil~P~~~L~~q~~~~~~~~~~   77 (555)
T 3tbk_A            2 PLKPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPC--GQKGKVVFFANQIPVYEQQATVFSRYFE   77 (555)
T ss_dssp             CCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS--SCCCCEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhccc--CCCCEEEEEeCCHHHHHHHHHHHHHHhc
Confidence            467899999999999999999999999999999877776666554210  0167899999999999999999998854

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.30  E-value=2e-11  Score=81.95  Aligned_cols=74  Identities=15%  Similarity=0.042  Sum_probs=61.5

Q ss_pred             cCCCCCHHHHHHHHHHhcC-CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTR-EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~-~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +...+++.|.+++..+.++ .++++.+|+|+|||..+...+.......     ++.++++++|++.++.|+.+++.++..
T Consensus        25 g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~-----~~~~~lil~P~~~L~~q~~~~~~~~~~   99 (367)
T 1hv8_A           25 GFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-----NGIEAIILTPTRELAIQVADEIESLKG   99 (367)
T ss_dssp             TCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-----SSCCEEEECSCHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc-----CCCcEEEEcCCHHHHHHHHHHHHHHhC
Confidence            3447899999999998877 6899999999999998766665554432     467999999999999999999998753

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=99.30  E-value=2.6e-11  Score=78.43  Aligned_cols=77  Identities=19%  Similarity=0.099  Sum_probs=59.1

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHH-HHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRI-VEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~-~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...+++.|.+++..+.+++++++.+|+|+|||...... +..+..........+.+++|++|+++++.|+.+.++++.
T Consensus        49 ~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  126 (242)
T 3fe2_A           49 FTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYC  126 (242)
T ss_dssp             CCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEEeCcHHHHHHHHHHHHHHH
Confidence            34589999999999999999999999999999875444 334332211111136789999999999999999988874

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=99.29  E-value=4e-11  Score=79.81  Aligned_cols=69  Identities=14%  Similarity=0.087  Sum_probs=58.2

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +...+++.|.+++..+.+++++++.+|||+|||..+...+..   .       +.++++++|++.++.|+.+.+.++..
T Consensus        13 g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~---~-------~~~~liv~P~~~L~~q~~~~~~~~~~   81 (337)
T 2z0m_A           13 GFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE---L-------GMKSLVVTPTRELTRQVASHIRDIGR   81 (337)
T ss_dssp             TCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHH---H-------TCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHh---h-------cCCEEEEeCCHHHHHHHHHHHHHHhh
Confidence            344689999999999999999999999999999875544332   2       67899999999999999999998753

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19

Probab=99.28  E-value=8.6e-12  Score=91.00  Aligned_cols=70  Identities=23%  Similarity=0.216  Sum_probs=59.6

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .|++.|++++..  ..+.++|.|+||||||+++...+.+++.....   ++.+||++++|+.++.++.+++.+..
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~---~~~~IL~lTfT~~Aa~em~~Rl~~~l   71 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGY---QARHIAAVTFTNKAAREMKERVGQTL   71 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCC---CGGGEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCC---CHHHeEEEeccHHHHHHHHHHHHHHc
Confidence            589999999884  36789999999999999998888888765322   46799999999999999999998764

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.28  E-value=3.4e-11  Score=81.54  Aligned_cols=74  Identities=20%  Similarity=0.087  Sum_probs=60.7

Q ss_pred             cCCCCCHHHHHHHHHHhcC--CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTR--EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~--~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +...+++.|.+++..+..+  +++++.+|+|+|||..+...+...+....    .+.++++++|+..++.|+.+.+.++.
T Consensus        24 ~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~----~~~~~lil~P~~~L~~q~~~~~~~~~   99 (395)
T 3pey_A           24 KFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPED----ASPQAICLAPSRELARQTLEVVQEMG   99 (395)
T ss_dssp             TCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTC----CSCCEEEECSSHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCC----CCccEEEECCCHHHHHHHHHHHHHHh
Confidence            4567899999999999887  89999999999999876655544433211    36789999999999999999999876

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=99.28  E-value=3.2e-11  Score=85.15  Aligned_cols=77  Identities=21%  Similarity=0.247  Sum_probs=61.3

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ..+.++++|.+++..+..+.++++.+|+|+|||..+...+...+.....  ..+.+++|++|+..++.|+.+.+.+++.
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~--~~~~~~lil~P~~~L~~q~~~~~~~~~~   80 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA--GRKAKVVFLATKVPVYEQQKNVFKHHFE   80 (556)
T ss_dssp             ----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS--SCCCCEEEECSSHHHHHHHHHHHHHHHG
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcc--cCCCeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            4578899999999999999999999999999999877776666554210  0167899999999999999999998854

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.28  E-value=3.1e-11  Score=82.36  Aligned_cols=73  Identities=25%  Similarity=0.063  Sum_probs=60.1

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         18 LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ..+++.|.+++..+.++..+++.+|+|+|||..+...+...+....    .+.++++++|+..++.|+.+.++++..
T Consensus        42 ~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~----~~~~~lil~P~~~L~~q~~~~~~~~~~  114 (400)
T 1s2m_A           42 EKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKL----NKIQALIMVPTRELALQTSQVVRTLGK  114 (400)
T ss_dssp             CSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTS----CSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhcc----CCccEEEEcCCHHHHHHHHHHHHHHhc
Confidence            3589999999999999999999999999999876555544443311    356899999999999999999998764

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=99.27  E-value=2.4e-11  Score=84.98  Aligned_cols=69  Identities=30%  Similarity=0.344  Sum_probs=60.5

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ..+.++++|.+++..+..++.+++.+|+|+|||.++...+...          +.+++|++|+..++.|+.+++.+++.
T Consensus        90 ~~~~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~----------~~~~Lvl~P~~~L~~Q~~~~~~~~~~  158 (472)
T 2fwr_A           90 AEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL----------STPTLIVVPTLALAEQWKERLGIFGE  158 (472)
T ss_dssp             CCCCBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH----------CSCEEEEESSHHHHHHHHHHGGGGCG
T ss_pred             CCCCcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc----------CCCEEEEECCHHHHHHHHHHHHhCCC
Confidence            4568999999999999888889999999999999877776654          56899999999999999999998643

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.27  E-value=3.8e-11  Score=81.52  Aligned_cols=72  Identities=19%  Similarity=0.167  Sum_probs=59.5

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         18 LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..+++.|.+++..+..+..+++.+|+|+|||..+...+...+....    ...++++++|++.++.|+.+.+.++.
T Consensus        29 ~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~----~~~~~lil~P~~~L~~q~~~~~~~~~  100 (391)
T 1xti_A           29 EHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT----GQVSVLVMCHTRELAFQISKEYERFS  100 (391)
T ss_dssp             CSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCT----TCCCEEEECSCHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccC----CCeeEEEECCCHHHHHHHHHHHHHHH
Confidence            3489999999999999999999999999999876555554443311    35689999999999999999998875

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=99.26  E-value=3.6e-11  Score=82.36  Aligned_cols=73  Identities=26%  Similarity=0.164  Sum_probs=60.0

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         18 LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ..+++.|.+++..+.+++.+++.+|+|+|||......+...+....    .+.++++++|+++++.|+.+.+.+++.
T Consensus        58 ~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~----~~~~~lil~Pt~~L~~q~~~~~~~~~~  130 (410)
T 2j0s_A           58 EKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV----RETQALILAPTRELAVQIQKGLLALGD  130 (410)
T ss_dssp             CSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTS----CSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhcc----CCceEEEEcCcHHHHHHHHHHHHHHhc
Confidence            3489999999999999999999999999999876655544433211    367999999999999999999998763

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=99.26  E-value=1.7e-11  Score=90.31  Aligned_cols=70  Identities=29%  Similarity=0.305  Sum_probs=59.6

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .|++.|++++..  ..+.++|.|+||||||+++...+.+++.....   ++.+||++++||.|+.++.+++.+..
T Consensus        11 ~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~---~p~~IL~vTFTnkAA~Em~~Rl~~~l   80 (724)
T 1pjr_A           11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHV---APWNILAITFTNKAAREMRERVQSLL   80 (724)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCC---CGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCC---CHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            589999999875  35789999999999999999988888875322   46789999999999999999998763

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.25  E-value=5.2e-11  Score=81.39  Aligned_cols=75  Identities=19%  Similarity=0.069  Sum_probs=61.1

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +...+++.|.+++..+.++..+++.+|+|+|||..+...+...+....    ...++++++|++.++.|+.+.+.+++.
T Consensus        59 ~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~----~~~~~lil~P~~~L~~q~~~~~~~~~~  133 (414)
T 3eiq_A           59 GFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDL----KATQALVLAPTRELAQQIQKVVMALGD  133 (414)
T ss_dssp             TCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTS----CSCCEEEECSSHHHHHHHHHHHHHHGG
T ss_pred             CCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcC----CceeEEEEeChHHHHHHHHHHHHHHhc
Confidence            345689999999999999999999999999999875555444433311    367899999999999999999998863

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.23  E-value=5.3e-11  Score=80.77  Aligned_cols=74  Identities=18%  Similarity=0.036  Sum_probs=59.7

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ...+++.|.+++..+.++..+++.+|+|+|||..+...+...+....    .+.++++++|++.++.|+.+.+.++..
T Consensus        41 ~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~----~~~~~lil~P~~~L~~q~~~~~~~~~~  114 (394)
T 1fuu_A           41 FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSV----KAPQALMLAPTRELALQIQKVVMALAF  114 (394)
T ss_dssp             CCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTC----CSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccC----CCCCEEEEcCCHHHHHHHHHHHHHHhc
Confidence            45789999999999999999999999999999875444433333211    367999999999999999999988753

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=99.22  E-value=9.4e-11  Score=89.82  Aligned_cols=73  Identities=19%  Similarity=0.116  Sum_probs=64.5

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ...+.+++.|.+++..+..+..++|.||||+|||.++...+...+..       +.+++|++|++.++.|+.+++.+++.
T Consensus       180 ~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~-------g~rvlvl~PtraLa~Q~~~~l~~~~~  252 (1108)
T 3l9o_A          180 TYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN-------KQRVIYTSPIKALSNQKYRELLAEFG  252 (1108)
T ss_dssp             CCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHT-------TCEEEEEESSHHHHHHHHHHHHHHTS
T ss_pred             hCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhc-------CCeEEEEcCcHHHHHHHHHHHHHHhC
Confidence            45678999999999999999999999999999999877776666654       78999999999999999999998764

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.22  E-value=1.5e-10  Score=88.13  Aligned_cols=72  Identities=19%  Similarity=0.117  Sum_probs=63.0

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      -.+.+++.|.+++..+.++.+++|.+|||+|||.++...+...+..       +.++++++|++.++.|+.+++.+++.
T Consensus        83 ~~f~L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~-------g~rvL~l~PtkaLa~Q~~~~l~~~~~  154 (1010)
T 2xgj_A           83 YPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN-------KQRVIYTSPIKALSNQKYRELLAEFG  154 (1010)
T ss_dssp             CSSCCCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHT-------TCEEEEEESSHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhcc-------CCeEEEECChHHHHHHHHHHHHHHhC
Confidence            4577999999999999999999999999999999876666655544       68999999999999999999998764

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.22  E-value=1.1e-10  Score=79.71  Aligned_cols=75  Identities=19%  Similarity=0.026  Sum_probs=59.1

Q ss_pred             cCCCCCHHHHHHHHHHhcC--CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTR--EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~--~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +...+++.|.+++..+..+  .++++.+|+|+|||..+...+...+....    ...++++++|+++++.|+.+.+.++.
T Consensus        44 g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~----~~~~~lil~P~~~L~~q~~~~~~~~~  119 (412)
T 3fht_A           44 GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN----KYPQCLCLSPTYELALQTGKVIEQMG  119 (412)
T ss_dssp             TCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTS----CSCCEEEECSSHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcC----CCCCEEEECCCHHHHHHHHHHHHHHH
Confidence            3457899999999999876  89999999999999876444433333211    35589999999999999998888875


Q ss_pred             c
Q psy16285         94 Q   94 (97)
Q Consensus        94 ~   94 (97)
                      .
T Consensus       120 ~  120 (412)
T 3fht_A          120 K  120 (412)
T ss_dssp             T
T ss_pred             h
Confidence            3

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.21  E-value=1.8e-10  Score=83.84  Aligned_cols=78  Identities=26%  Similarity=0.273  Sum_probs=62.7

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+...++++|.+++..+..+.++++.+|+|+|||..+...+...+.....  ..+.+++|++|+..++.|+.+.+.++..
T Consensus         9 ~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~--~~~~~~lvl~Pt~~L~~Q~~~~~~~~~~   86 (696)
T 2ykg_A            9 YSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQ--GQKGKVVFFANQIPVYEQNKSVFSKYFE   86 (696)
T ss_dssp             TC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCT--TCCCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             cCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCcc--CCCCeEEEEECCHHHHHHHHHHHHHHhc
Confidence            35567899999999999999999999999999999877777665544210  0127899999999999999999998863

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=99.20  E-value=3.6e-11  Score=87.49  Aligned_cols=79  Identities=25%  Similarity=0.318  Sum_probs=63.6

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHH-HHHHHhhc
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQF-VEGVLKYT   93 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~-~~~l~~~~   93 (97)
                      ...+.++++|.+++..+..+.+++|.+|+|+|||..+...+..++..... ...+.+++|++|+..++.|+ .+.+++++
T Consensus         3 ~~~~~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~-~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~   81 (699)
T 4gl2_A            3 GAMLQLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKK-ASEPGKVIVLVNKVLLVEQLFRKEFQPFL   81 (699)
T ss_dssp             ----CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHH-HTCCCCBCCEESCSHHHHHHHHHTHHHHH
T ss_pred             CCCCCccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccc-cCCCCeEEEEECCHHHHHHHHHHHHHHHc
Confidence            35678999999999999999999999999999999888887766655321 11237899999999999999 99999887


Q ss_pred             c
Q psy16285         94 Q   94 (97)
Q Consensus        94 ~   94 (97)
                      .
T Consensus        82 ~   82 (699)
T 4gl2_A           82 K   82 (699)
T ss_dssp             T
T ss_pred             C
Confidence            5

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=99.20  E-value=1.9e-10  Score=80.17  Aligned_cols=78  Identities=18%  Similarity=0.087  Sum_probs=60.9

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHH-HHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVAL-RIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~-~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ...+++.|.+++..+.+++.+++.+|+|+|||.... .++..+..........+.+++|++|+++++.|+.+.++++..
T Consensus        76 ~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~  154 (434)
T 2db3_A           76 YKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAF  154 (434)
T ss_dssp             CCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEecCHHHHHHHHHHHHHHhc
Confidence            345899999999999999999999999999998543 345555543211111356899999999999999999998764

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.19  E-value=9.2e-11  Score=89.10  Aligned_cols=73  Identities=16%  Similarity=0.049  Sum_probs=63.2

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .-.+.+++.|.+++..+.+++.+++.+|||+|||.++...+..+...       +.+++|++|+..++.|+.+++.+++.
T Consensus        35 ~~~f~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~-------g~~vlvl~PtraLa~Q~~~~l~~~~~  107 (997)
T 4a4z_A           35 SWPFELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRN-------MTKTIYTSPIKALSNQKFRDFKETFD  107 (997)
T ss_dssp             CCSSCCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHT-------TCEEEEEESCGGGHHHHHHHHHTTC-
T ss_pred             hCCCCCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhc-------CCeEEEEeCCHHHHHHHHHHHHHHcC
Confidence            45678999999999999999999999999999999876666665544       67899999999999999999998753

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=99.19  E-value=1.6e-10  Score=85.72  Aligned_cols=77  Identities=21%  Similarity=0.247  Sum_probs=62.6

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ....++++|.+++..+..+.++++.+|+|+|||.++...+...+.....  ..+.+++|++|+..++.|+.+.+.+++.
T Consensus       245 g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~--~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~  321 (797)
T 4a2q_A          245 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA--GRKAKVVFLATKVPVYEQQKNVFKHHFE  321 (797)
T ss_dssp             ---CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS--SCCCCEEEECSSHHHHHHHHHHHHHHHG
T ss_pred             CCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccc--cCCCeEEEEeCCHHHHHHHHHHHHHhcc
Confidence            3678999999999999999999999999999999877777666554210  0167899999999999999999998864

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.18  E-value=2.3e-10  Score=78.35  Aligned_cols=79  Identities=18%  Similarity=0.091  Sum_probs=59.6

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHH-HHHHHHHhchhh-------------hhcCCCCEEEEeCChHH
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVAL-RIVEGFLKNKEL-------------ARYMSGPILIVCYTNHA   81 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~-~~~~~~~~~~~~-------------~~~~~~~ilv~~~~~~~   81 (97)
                      +...+++.|.+++..+..++.+++.+|||+|||.... .++..+......             ......++++++|++++
T Consensus        34 ~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  113 (417)
T 2i4i_A           34 RYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTREL  113 (417)
T ss_dssp             TCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBTTBSCSBCCSEEEECSSHHH
T ss_pred             CCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccccccccccCCccEEEECCcHHH
Confidence            3457899999999999999999999999999998543 344444432100             00013579999999999


Q ss_pred             HHHHHHHHHhhcc
Q psy16285         82 LDQFVEGVLKYTQ   94 (97)
Q Consensus        82 ~~~~~~~l~~~~~   94 (97)
                      +.|+.+.+.++..
T Consensus       114 ~~q~~~~~~~~~~  126 (417)
T 2i4i_A          114 AVQIYEEARKFSY  126 (417)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhC
Confidence            9999999988753

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=99.17  E-value=2.5e-10  Score=76.39  Aligned_cols=73  Identities=19%  Similarity=0.048  Sum_probs=57.4

Q ss_pred             CCCCCHHHHHHHHHHhcC--CceEEeCCCCCchHHHHH-HHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTR--EFAIIQGPPGTGKTYVAL-RIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~--~~~~v~Gp~GtGKT~~~~-~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...+++.|.+++..+..+  .++++.+|+|||||.... .++..+....     ...+++|++|+++++.|+.+.+.++.
T Consensus       112 ~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~-----~~~~~lil~PtreLa~Q~~~~~~~l~  186 (300)
T 3fmo_B          112 FNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN-----KYPQCLCLSPTYELALQTGKVIEQMG  186 (300)
T ss_dssp             CCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTS-----CSCCEEEECSSHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccC-----CCceEEEEcCcHHHHHHHHHHHHHHH
Confidence            346788899999999876  799999999999998643 4444443321     34589999999999999999988876


Q ss_pred             c
Q psy16285         94 Q   94 (97)
Q Consensus        94 ~   94 (97)
                      .
T Consensus       187 ~  187 (300)
T 3fmo_B          187 K  187 (300)
T ss_dssp             T
T ss_pred             h
Confidence            4

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.16  E-value=2.3e-10  Score=81.55  Aligned_cols=77  Identities=26%  Similarity=0.201  Sum_probs=57.8

Q ss_pred             CCCCCHHHHHHHHHHh--cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAAL--TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~--~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...+++.|.+++..+.  .+..+++.+|||+|||......+...+...........+++|++|+.+++.|+.+.+.++.
T Consensus        92 ~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~La~Q~~~~~~~~~  170 (563)
T 3i5x_A           92 FPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIH  170 (563)
T ss_dssp             CSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHHHHHHHHHHHHHH
Confidence            3458999999999988  5678999999999999865544433333321111123589999999999999999998863

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.15  E-value=2.9e-10  Score=81.60  Aligned_cols=77  Identities=26%  Similarity=0.201  Sum_probs=58.2

Q ss_pred             CCCCCHHHHHHHHHHh--cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAAL--TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~--~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...+++.|.+++..+.  .+..+++.+|||+|||......+...+...........+++|++|+.+++.|+.+.+.++.
T Consensus        41 ~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~La~Q~~~~~~~~~  119 (579)
T 3sqw_A           41 FPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIH  119 (579)
T ss_dssp             CSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHHHHHHHHHHHHHHH
Confidence            3458999999999998  5678999999999999865544433333321111124589999999999999999999864

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.13  E-value=7e-11  Score=84.88  Aligned_cols=79  Identities=22%  Similarity=0.195  Sum_probs=50.6

Q ss_pred             cCCCCCHHHHHHHHHHhc-----CCceEEeCCCCCchHHHHHHHHHHHHhchhh--hhcCCCCEEEEeCChHHHHHHH-H
Q psy16285         16 EELGLNTIQFEAYKAALT-----REFAIIQGPPGTGKTYVALRIVEGFLKNKEL--ARYMSGPILIVCYTNHALDQFV-E   87 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~-----~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~--~~~~~~~ilv~~~~~~~~~~~~-~   87 (97)
                      ....++++|.+++..+..     .+.+++.+|+|+|||.++..++..+....+.  ......++||++|++.++.|+. +
T Consensus       175 ~~~~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~  254 (590)
T 3h1t_A          175 SGYSPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDK  254 (590)
T ss_dssp             ----CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------
T ss_pred             CCCCchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHH
Confidence            456899999999998875     4678999999999999998888888775310  0003689999999999999999 7


Q ss_pred             HHHhhcc
Q psy16285         88 GVLKYTQ   94 (97)
Q Consensus        88 ~l~~~~~   94 (97)
                      .++.++.
T Consensus       255 ~~~~~~~  261 (590)
T 3h1t_A          255 TFTPFGD  261 (590)
T ss_dssp             CCTTTCS
T ss_pred             HHHhcch
Confidence            7766653

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=99.13  E-value=3.2e-10  Score=73.19  Aligned_cols=74  Identities=20%  Similarity=0.210  Sum_probs=57.1

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHH-HHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEG-FLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~-~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .+++.+.|.+++..+.+++.+++.||+|||||+++...+.. ......   ....++++++|++.++.++.+++.+..
T Consensus        59 ~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~---~~~~~~l~~~p~~~la~q~~~~~~~~~  133 (235)
T 3llm_A           59 LLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDR---AAECNIVVTQPRRISAVSVAERVAFER  133 (235)
T ss_dssp             TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTC---GGGCEEEEEESSHHHHHHHHHHHHHTT
T ss_pred             cCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCC---CCceEEEEeccchHHHHHHHHHHHHHh
Confidence            45678889999999999999999999999999865555433 333211   023489999999999999999887654

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=99.13  E-value=3e-10  Score=84.57  Aligned_cols=72  Identities=18%  Similarity=0.065  Sum_probs=61.6

Q ss_pred             cCCCCCHHHHHHHHHHhcC------CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALTR------EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~------~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      ..+.+++.|.+++..+..+      .+.+++||+|+|||.++...+...+..       +.++++++|+..++.|+.+.+
T Consensus       365 lpf~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~-------g~qvlvlaPtr~La~Q~~~~l  437 (780)
T 1gm5_A          365 LPFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA-------GFQTAFMVPTSILAIQHYRRT  437 (780)
T ss_dssp             SSSCCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH-------TSCEEEECSCHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc-------CCeEEEEeCcHHHHHHHHHHH
Confidence            4568999999999988753      488999999999999877776666655       679999999999999999999


Q ss_pred             Hhhcc
Q psy16285         90 LKYTQ   94 (97)
Q Consensus        90 ~~~~~   94 (97)
                      .+++.
T Consensus       438 ~~~~~  442 (780)
T 1gm5_A          438 VESFS  442 (780)
T ss_dssp             HHHHT
T ss_pred             HHHhh
Confidence            98864

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}

Probab=99.12  E-value=2.8e-10  Score=85.94  Aligned_cols=77  Identities=21%  Similarity=0.247  Sum_probs=61.7

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ..+.++++|.+++..+..+.++++.+|+|+|||..+...+...+.....  ..+.+++|++|+..++.|+.+.+.+++.
T Consensus       245 ~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~--~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~  321 (936)
T 4a2w_A          245 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA--GRKAKVVFLATKVPVYEQQKNVFKHHFE  321 (936)
T ss_dssp             ---CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCS--SCCCCEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccc--cCCCeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            4778999999999999999999999999999998877766655544210  0167899999999999999999998864

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.12  E-value=4.1e-10  Score=86.31  Aligned_cols=71  Identities=18%  Similarity=0.086  Sum_probs=61.5

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..+.+++.|.+++..+..+..+++.+|||+|||..+...+......       +.+++|++|+++++.|+.+++.++.
T Consensus        75 ~gf~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~~-------~~~~Lil~PtreLa~Q~~~~l~~l~  145 (1104)
T 4ddu_A           75 FGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARK-------GKKSALVFPTVTLVKQTLERLQKLA  145 (1104)
T ss_dssp             SSSCCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHTT-------TCCEEEEESSHHHHHHHHHHHHTTS
T ss_pred             cCCCCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHhc-------CCeEEEEechHHHHHHHHHHHHHhh
Confidence            3567899999999999999999999999999999666655555533       7899999999999999999999965

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.11  E-value=3.4e-10  Score=82.96  Aligned_cols=70  Identities=24%  Similarity=0.234  Sum_probs=57.3

Q ss_pred             CCCCHHHHHHHHH-HhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         18 LGLNTIQFEAYKA-ALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        18 ~~l~~~Q~~~i~~-~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..+++.|.+++.. +.++++++|.||||+|||+.+...+...+..      .+.++++++|++.++.++.++++++.
T Consensus        29 ~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~------~~~~il~i~P~r~La~q~~~~~~~~~   99 (715)
T 2va8_A           29 KKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLK------NGGKAIYVTPLRALTNEKYLTFKDWE   99 (715)
T ss_dssp             CBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHH------SCSEEEEECSCHHHHHHHHHHHGGGG
T ss_pred             CCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHH------CCCeEEEEeCcHHHHHHHHHHHHHhh
Confidence            3789999999998 5678899999999999999875554433332      26799999999999999999996543

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=99.09  E-value=4.1e-10  Score=78.94  Aligned_cols=72  Identities=19%  Similarity=0.041  Sum_probs=54.6

Q ss_pred             CCCCHHHHHHHHHHhcC--CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         18 LGLNTIQFEAYKAALTR--EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~--~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..+++.|.+++..+..+  .++++.||+|+|||......+...+....    ...+++|++|+++++.|+.+.+.++.
T Consensus       113 ~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~----~~~~~lil~Pt~~La~Q~~~~~~~~~  186 (479)
T 3fmp_B          113 NRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN----KYPQCLCLSPTYELALQTGKVIEQMG  186 (479)
T ss_dssp             CSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTS----CSCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcC----CCCcEEEEeChHHHHHHHHHHHHHHH
Confidence            34666799999999876  79999999999999874443333322211    24489999999999999988877765

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.05  E-value=2.7e-10  Score=83.67  Aligned_cols=69  Identities=22%  Similarity=0.293  Sum_probs=57.8

Q ss_pred             CCCCHHHHHHHHH-HhcCCceEEeCCCCCchHHHH-HHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         18 LGLNTIQFEAYKA-ALTREFAIIQGPPGTGKTYVA-LRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        18 ~~l~~~Q~~~i~~-~~~~~~~~v~Gp~GtGKT~~~-~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..+++.|.+++.. +.+++++++.||||+|||..+ ..++..+...       +.++++++|++.++.++.++++++.
T Consensus        22 ~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~-------~~~~l~i~P~raLa~q~~~~~~~l~   92 (720)
T 2zj8_A           22 ESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ-------GGKAVYIVPLKALAEEKFQEFQDWE   92 (720)
T ss_dssp             CBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH-------CSEEEEECSSGGGHHHHHHHTGGGG
T ss_pred             CCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC-------CCEEEEEcCcHHHHHHHHHHHHHHH
Confidence            3789999999998 678899999999999999987 4444454434       6799999999999999999997553

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=99.05  E-value=2.2e-10  Score=83.93  Aligned_cols=69  Identities=20%  Similarity=0.124  Sum_probs=57.2

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         18 LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..+++.|.+++..+.+++++++.+|||+|||+.+...+...+..       +.++++++|++.++.++.++++++.
T Consensus        24 ~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~-------~~~~l~i~P~r~La~q~~~~~~~~~   92 (702)
T 2p6r_A           24 EELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK-------GGKSLYVVPLRALAGEKYESFKKWE   92 (702)
T ss_dssp             -CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHHTTTT
T ss_pred             CCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh-------CCcEEEEeCcHHHHHHHHHHHHHHH
Confidence            37889999999998889999999999999999875544443333       5799999999999999999996543

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=99.05  E-value=9.4e-10  Score=84.01  Aligned_cols=70  Identities=23%  Similarity=0.151  Sum_probs=59.3

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ++.+ +.|.+++..+..++++++.+|+|+|||..+.-++..+...       +.++++++|+++++.|+.+.+.+++.
T Consensus        55 g~~p-~iQ~~ai~~il~g~dvlv~apTGSGKTl~~lp~l~~~~~~-------~~~~lil~PtreLa~Q~~~~l~~l~~  124 (1054)
T 1gku_B           55 GEPR-AIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK-------GKRCYVIFPTSLLVIQAAETIRKYAE  124 (1054)
T ss_dssp             CSCC-HHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT-------SCCEEEEESCHHHHHHHHHHHHHHHT
T ss_pred             CCCH-HHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHHhhc-------CCeEEEEeccHHHHHHHHHHHHHHHh
Confidence            4457 9999999999999999999999999997555555555443       67999999999999999999998864

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=99.04  E-value=1.4e-09  Score=83.77  Aligned_cols=72  Identities=21%  Similarity=0.124  Sum_probs=59.8

Q ss_pred             cCCCCCHHHHHHHHHHhc----CC--ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALT----RE--FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~----~~--~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      -.+.+++.|.+++..+..    +.  ..++.||+|+|||.++...+..+...       +.+++|++||..++.|+.+.+
T Consensus       600 f~~~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~-------g~~vlvlvPt~~La~Q~~~~~  672 (1151)
T 2eyq_A          600 FPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN-------HKQVAVLVPTTLLAQQHYDNF  672 (1151)
T ss_dssp             CCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT-------TCEEEEECSSHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHh-------CCeEEEEechHHHHHHHHHHH
Confidence            356779999999998875    43  78999999999999877665555444       679999999999999999999


Q ss_pred             Hhhcc
Q psy16285         90 LKYTQ   94 (97)
Q Consensus        90 ~~~~~   94 (97)
                      .+++.
T Consensus       673 ~~~~~  677 (1151)
T 2eyq_A          673 RDRFA  677 (1151)
T ss_dssp             HHHST
T ss_pred             HHHhh
Confidence            87654

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=99.04  E-value=6.1e-10  Score=86.04  Aligned_cols=75  Identities=17%  Similarity=0.206  Sum_probs=58.5

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +....+++.|.++|..  .+++++|.|++|||||+++...+..++..... .....+|+++++|+.++.++.+++.+.
T Consensus         6 ~~~~~~t~eQ~~~i~~--~~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~-~~~~~~il~~Tft~~aa~e~~~ri~~~   80 (1232)
T 3u4q_A            6 PADSTWTDDQWNAIVS--TGQDILVAAAAGSGKTAVLVERMIRKITAEEN-PIDVDRLLVVTFTNASAAEMKHRIAEA   80 (1232)
T ss_dssp             ----CCCHHHHHHHHC--CSSCEEEEECTTCCHHHHHHHHHHHHHSCSSS-CCCGGGEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHhC--CCCCEEEEecCCCcHHHHHHHHHHHHHhcCCC-CCCccceEEEeccHHHHHHHHHHHHHH
Confidence            3567899999999885  37799999999999999988877777665210 013568999999999999999999874

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=98.97  E-value=6.2e-09  Score=73.21  Aligned_cols=73  Identities=18%  Similarity=0.238  Sum_probs=59.7

Q ss_pred             cCCCCCHHHHHHHHHHh----cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         16 EELGLNTIQFEAYKAAL----TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~----~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      -...++++|.+++..+.    .+...++..++|+|||..+..++..+....     ...++||+||+. ++.||.+.+.+
T Consensus        34 ~~~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~~~~~-----~~~~~LIv~P~~-l~~qw~~e~~~  107 (500)
T 1z63_A           34 IKANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKEN-----ELTPSLVICPLS-VLKNWEEELSK  107 (500)
T ss_dssp             CSSCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTT-----CCSSEEEEECST-THHHHHHHHHH
T ss_pred             hhccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHHHhcC-----CCCCEEEEccHH-HHHHHHHHHHH
Confidence            45579999999988763    356788999999999999888888776542     357899999954 78999999999


Q ss_pred             hcc
Q psy16285         92 YTQ   94 (97)
Q Consensus        92 ~~~   94 (97)
                      +..
T Consensus       108 ~~~  110 (500)
T 1z63_A          108 FAP  110 (500)
T ss_dssp             HCT
T ss_pred             HCC
Confidence            864

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}

Probab=98.91  E-value=7.2e-09  Score=78.60  Aligned_cols=72  Identities=19%  Similarity=0.165  Sum_probs=61.2

Q ss_pred             cCCCCCHHHHHHHHHHhcC--CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTR--EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~--~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..+.++++|.+++..+...  ..+++.+++|+|||.++..++..+...+     ...++||+||+ .++.||.+.+.+.+
T Consensus       150 ~~~~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g-----~~~rvLIVvP~-sLl~Qw~~E~~~~f  223 (968)
T 3dmq_A          150 QRTSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSG-----AAERVLIIVPE-TLQHQWLVEMLRRF  223 (968)
T ss_dssp             CSSCCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTS-----SCCCEEEECCT-TTHHHHHHHHHHHS
T ss_pred             CCCCCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhC-----CCCeEEEEeCH-HHHHHHHHHHHHHh
Confidence            4678999999999988763  4789999999999999998888887663     35689999999 88999999996654

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=98.90  E-value=1.7e-08  Score=62.45  Aligned_cols=50  Identities=20%  Similarity=0.149  Sum_probs=38.3

Q ss_pred             CHHHHHHHHHHh---------cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         21 NTIQFEAYKAAL---------TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        21 ~~~Q~~~i~~~~---------~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ++.|.+++..+.         .+..+++.|||||||||++..++..+...      .+..++++.
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~------~g~~~~~~~   74 (180)
T 3ec2_A           16 NVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEK------KGIRGYFFD   74 (180)
T ss_dssp             SHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHH------SCCCCCEEE
T ss_pred             CHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHH------cCCeEEEEE
Confidence            567777777664         25689999999999999999999988744      255666655

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=98.88  E-value=4.6e-09  Score=76.08  Aligned_cols=68  Identities=13%  Similarity=0.191  Sum_probs=56.1

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ...+++.|.+++..+..++.+++.+|||+|||......+  +. .       ..+++|++|+..++.+..+.+.+++.
T Consensus        42 ~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpa--l~-~-------~g~~lVisP~~~L~~q~~~~l~~~gi  109 (591)
T 2v1x_A           42 LEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPA--LC-S-------DGFTLVICPLISLMEDQLMVLKQLGI  109 (591)
T ss_dssp             CCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHH--HT-S-------SSEEEEECSCHHHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHH--HH-c-------CCcEEEEeCHHHHHHHHHHHHHhcCC
Confidence            446889999999999999999999999999997533222  22 2       45899999999999999999998753

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.84  E-value=1.7e-08  Score=73.51  Aligned_cols=69  Identities=20%  Similarity=0.205  Sum_probs=52.1

Q ss_pred             CCCCHHHHHHHHHHh----cCCceEEeCCCCCchHHHHHHH-HHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         18 LGLNTIQFEAYKAAL----TREFAIIQGPPGTGKTYVALRI-VEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~----~~~~~~v~Gp~GtGKT~~~~~~-~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +..++.|.+.+..+.    +++.+++.+|||||||...... +..+...       +.+++|++||+....|+.+.+..+
T Consensus         2 ~~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~-------~~kvli~t~T~~l~~Qi~~el~~l   74 (620)
T 4a15_A            2 YENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSER-------KLKVLYLVRTNSQEEQVIKELRSL   74 (620)
T ss_dssp             ---CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHH-------TCEEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhc-------CCeEEEECCCHHHHHHHHHHHHHH
Confidence            356889998887543    5789999999999999754433 3333332       678999999999999999998876


Q ss_pred             c
Q psy16285         93 T   93 (97)
Q Consensus        93 ~   93 (97)
                      .
T Consensus        75 ~   75 (620)
T 4a15_A           75 S   75 (620)
T ss_dssp             H
T ss_pred             h
Confidence            5

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=98.83  E-value=2.3e-08  Score=79.50  Aligned_cols=72  Identities=17%  Similarity=0.166  Sum_probs=57.8

Q ss_pred             CCCCCHHHHHHHHHHhc-CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ...+++.|.+++..+.. +.+++|.+|||+|||.++...+...+.+.     ++.++++++|+++++.+..+++.+.+
T Consensus       924 f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~-----~~~kavyi~P~raLa~q~~~~~~~~f  996 (1724)
T 4f92_B          924 FPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQS-----SEGRCVYITPMEALAEQVYMDWYEKF  996 (1724)
T ss_dssp             CSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHC-----TTCCEEEECSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhC-----CCCEEEEEcChHHHHHHHHHHHHHHh
Confidence            34589999999999875 56899999999999998765554444332     46789999999999999999987643

>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system, helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP; 2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*

Probab=98.83  E-value=3.6e-09  Score=80.79  Aligned_cols=73  Identities=15%  Similarity=0.115  Sum_probs=58.5

Q ss_pred             CCCCCHHHHHHHHHHhc--------------CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHH
Q psy16285         17 ELGLNTIQFEAYKAALT--------------REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHAL   82 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~--------------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~   82 (97)
                      ...+++.|..++..+..              +...+++.++|||||.++..++..+....     ...++||++|+++++
T Consensus       269 ~~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~~~l~~ll~~~~-----~~~rvLvlvpr~eL~  343 (1038)
T 2w00_A          269 LLVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTSFKAARLATELD-----FIDKVFFVVDRKDLD  343 (1038)
T ss_dssp             EEECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHHHHHHHHHTTCT-----TCCEEEEEECGGGCC
T ss_pred             cccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHHHHHHHHHHhcC-----CCceEEEEeCcHHHH
Confidence            35689999999998764              24689999999999999877664433221     246899999999999


Q ss_pred             HHHHHHHHhhcc
Q psy16285         83 DQFVEGVLKYTQ   94 (97)
Q Consensus        83 ~~~~~~l~~~~~   94 (97)
                      .|+.+.+.++..
T Consensus       344 ~Q~~~~f~~f~~  355 (1038)
T 2w00_A          344 YQTMKEYQRFSP  355 (1038)
T ss_dssp             HHHHHHHHTTST
T ss_pred             HHHHHHHHHhcc
Confidence            999999988764

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.80  E-value=2.8e-08  Score=73.99  Aligned_cols=73  Identities=16%  Similarity=0.247  Sum_probs=60.6

Q ss_pred             CCCCCHHHHHHHHHHh----cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         17 ELGLNTIQFEAYKAAL----TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~----~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ...|+++|.+++..+.    .+.+.+|.-++|.|||..+..++..+.....    ...++||+|| ...+.||.+.+.++
T Consensus       234 ~~~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~----~~~~~LIV~P-~sll~qW~~E~~~~  308 (800)
T 3mwy_W          234 GGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARR----QNGPHIIVVP-LSTMPAWLDTFEKW  308 (800)
T ss_dssp             SSCCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHS----CCSCEEEECC-TTTHHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcC----CCCCEEEEEC-chHHHHHHHHHHHH
Confidence            5689999999998665    5678999999999999998888887765432    3678999999 56799999999998


Q ss_pred             cc
Q psy16285         93 TQ   94 (97)
Q Consensus        93 ~~   94 (97)
                      ..
T Consensus       309 ~p  310 (800)
T 3mwy_W          309 AP  310 (800)
T ss_dssp             ST
T ss_pred             CC
Confidence            74

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=98.80  E-value=8.7e-09  Score=73.55  Aligned_cols=67  Identities=16%  Similarity=0.138  Sum_probs=54.8

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         18 LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ..+++.|.+++..+.+++.+++.+|||+|||.....  -.+. .       ...+++++|+..++.++.+++.+++.
T Consensus        24 ~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~l--p~l~-~-------~g~~lvi~P~~aL~~q~~~~l~~~gi   90 (523)
T 1oyw_A           24 QQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQI--PALL-L-------NGLTVVVSPLISLMKDQVDQLQANGV   90 (523)
T ss_dssp             SSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHH--HHHH-S-------SSEEEEECSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHH--HHHH-h-------CCCEEEECChHHHHHHHHHHHHHcCC
Confidence            467889999999999999999999999999965432  2222 2       45799999999999999999988753

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.74  E-value=4.7e-08  Score=70.03  Aligned_cols=67  Identities=22%  Similarity=0.260  Sum_probs=49.1

Q ss_pred             CCCCCHHHHHHHHHHh----cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         17 ELGLNTIQFEAYKAAL----TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~----~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      .+.+++.|.+++..+.    .++.+++.+|||||||......+  + ..       ..++++++||+.+.+|+.+.+.++
T Consensus         5 ~~~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~--~-~~-------~~~~~~~~~t~~l~~q~~~~~~~l   74 (540)
T 2vl7_A            5 KLQLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLG--M-QL-------KKKVLIFTRTHSQLDSIYKNAKLL   74 (540)
T ss_dssp             ----CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHH--H-HH-------TCEEEEEESCHHHHHHHHHHHGGG
T ss_pred             CCCCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHH--H-hC-------CCcEEEEcCCHHHHHHHHHHHHhc
Confidence            3577889999876543    56799999999999996433222  2 22       578999999999999999998875


Q ss_pred             c
Q psy16285         93 T   93 (97)
Q Consensus        93 ~   93 (97)
                      .
T Consensus        75 ~   75 (540)
T 2vl7_A           75 G   75 (540)
T ss_dssp             T
T ss_pred             C
Confidence            3

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=98.72  E-value=4.8e-08  Score=70.06  Aligned_cols=66  Identities=18%  Similarity=0.240  Sum_probs=51.9

Q ss_pred             CCCCHHHHHHHHHHh----cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         18 LGLNTIQFEAYKAAL----TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~----~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +.+++.|.+.+..+.    .++.+++.+|||||||......+..   .       ..++++++||++...|+.+.+..+.
T Consensus         2 ~~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~---~-------~~~v~i~~pt~~l~~q~~~~~~~l~   71 (551)
T 3crv_A            2 VKLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE---V-------KPKVLFVVRTHNEFYPIYRDLTKIR   71 (551)
T ss_dssp             CSCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH---H-------CSEEEEEESSGGGHHHHHHHHTTCC
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh---C-------CCeEEEEcCCHHHHHHHHHHHHHHh
Confidence            567899999777544    4678999999999998654332222   2       6789999999999999999888764

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=98.72  E-value=8.2e-08  Score=70.02  Aligned_cols=76  Identities=18%  Similarity=0.151  Sum_probs=59.7

Q ss_pred             CCCCHHHHHHHHHHh---------cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         18 LGLNTIQFEAYKAAL---------TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~---------~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      ..|+++|.+++..+.         .+...++.-++|+|||..+..++..+........+...++||+||+ .++.||.+.
T Consensus        54 ~~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E  132 (644)
T 1z3i_X           54 KVLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNE  132 (644)
T ss_dssp             TTCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHH
T ss_pred             hcccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecH-HHHHHHHHH
Confidence            468999999999874         2346788889999999999999888877632211124579999997 789999999


Q ss_pred             HHhhcc
Q psy16285         89 VLKYTQ   94 (97)
Q Consensus        89 l~~~~~   94 (97)
                      +.++..
T Consensus       133 ~~~~~~  138 (644)
T 1z3i_X          133 VGKWLG  138 (644)
T ss_dssp             HHHHHG
T ss_pred             HHHHcC
Confidence            999854

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=98.69  E-value=2.4e-08  Score=69.74  Aligned_cols=50  Identities=24%  Similarity=0.329  Sum_probs=41.6

Q ss_pred             CCceEEeCCCCCchHHHH-HHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVA-LRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~-~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      ++++++.||+|+|||..+ ..++..+...       +.++++++|+..++.|+.+.+.
T Consensus         2 g~~~lv~a~TGsGKT~~~l~~~l~~~~~~-------g~~~lvl~Pt~~La~Q~~~~~~   52 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRVLPQLVREAVKK-------RLRTVILAPTRVVASEMYEALR   52 (431)
T ss_dssp             CCEEEEECCTTSCTTTTHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHTT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHhC-------CCCEEEECcHHHHHHHHHHHhC
Confidence            578999999999999985 5555555544       6799999999999999988775

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=98.69  E-value=1.2e-07  Score=63.75  Aligned_cols=36  Identities=17%  Similarity=0.271  Sum_probs=30.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH-hchhhhhcCCCCEEEEe
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL-KNKELARYMSGPILIVC   76 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~-~~~~~~~~~~~~ilv~~   76 (97)
                      ..++++.||||||||+++.+++..+. ..       +.+++++.
T Consensus       152 ~~~lll~G~~GtGKT~La~aia~~~~~~~-------g~~v~~~~  188 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAMAHELSEKK-------GVSTTLLH  188 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHHHHS-------CCCEEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHhc-------CCcEEEEE
Confidence            46899999999999999999999988 55       66777665

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.69  E-value=1.6e-07  Score=58.79  Aligned_cols=35  Identities=31%  Similarity=0.405  Sum_probs=28.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ..+++.||||||||+++..++..+...       +.+++++.
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~~~-------~~~~~~~~   89 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELAKR-------NVSSLIVY   89 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHTT-------TCCEEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc-------CCeEEEEE
Confidence            679999999999999999999888655       55666554

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=98.69  E-value=1.2e-08  Score=71.69  Aligned_cols=54  Identities=17%  Similarity=0.260  Sum_probs=44.3

Q ss_pred             hcCCceEEeCCCCCchHHH-HHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         32 LTREFAIIQGPPGTGKTYV-ALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~-~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      .+++++++.+|||||||.. +..++..+...       +.+++|++|+++++.|+.+++..+
T Consensus        19 ~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~-------~~~~lvl~Ptr~La~Q~~~~l~g~   73 (459)
T 2z83_A           19 RKRQMTVLDLHPGSGKTRKILPQIIKDAIQQ-------RLRTAVLAPTRVVAAEMAEALRGL   73 (459)
T ss_dssp             STTCEEEECCCTTSCTTTTHHHHHHHHHHHT-------TCCEEEEECSHHHHHHHHHHTTTS
T ss_pred             hcCCcEEEECCCCCCHHHHHHHHHHHHHHhC-------CCcEEEECchHHHHHHHHHHhcCc
Confidence            3567899999999999997 56666666544       689999999999999999988643

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=98.67  E-value=2.1e-08  Score=70.20  Aligned_cols=55  Identities=18%  Similarity=0.175  Sum_probs=44.2

Q ss_pred             hcCCceEEeCCCCCchHHHH-HHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         32 LTREFAIIQGPPGTGKTYVA-LRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~-~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .+++++++.||+|||||..+ ..++..+...       +.++++++|+++++.|+.+.+..+.
T Consensus         6 ~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~-------~~~~lil~Ptr~La~Q~~~~l~~~~   61 (440)
T 1yks_A            6 KKGMTTVLDFHPGAGKTRRFLPQILAECARR-------RLRTLVLAPTRVVLSEMKEAFHGLD   61 (440)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHTTTSC
T ss_pred             hCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc-------CCeEEEEcchHHHHHHHHHHHhcCC
Confidence            35789999999999999975 4455545443       6799999999999999999887543

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=98.65  E-value=1.2e-07  Score=75.45  Aligned_cols=78  Identities=27%  Similarity=0.269  Sum_probs=58.8

Q ss_pred             CCCCCHHHHHHHHHHhc-CCceEEeCCCCCchHHHHHHHH-HHHHhchhh---hhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         17 ELGLNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIV-EGFLKNKEL---ARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~-~~~~~~~~~---~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      ...+++.|.+++..+.. +++++|.+|||+|||.++...+ ..+.+....   ....+.++++++|+++++.+..+.+.+
T Consensus        77 ~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~~  156 (1724)
T 4f92_B           77 FKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGK  156 (1724)
T ss_dssp             CSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHHH
Confidence            44689999999998875 6799999999999999865544 444332110   011356899999999999999999877


Q ss_pred             hcc
Q psy16285         92 YTQ   94 (97)
Q Consensus        92 ~~~   94 (97)
                      .+.
T Consensus       157 ~~~  159 (1724)
T 4f92_B          157 RLA  159 (1724)
T ss_dssp             HHT
T ss_pred             HHh
Confidence            553

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=98.62  E-value=1.8e-08  Score=74.07  Aligned_cols=61  Identities=18%  Similarity=0.266  Sum_probs=47.0

Q ss_pred             HHHHHHh------cCCceEEeCCCCCchHHHH-HHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         26 EAYKAAL------TREFAIIQGPPGTGKTYVA-LRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        26 ~~i~~~~------~~~~~~v~Gp~GtGKT~~~-~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +++..+.      +++++++.||+|+|||..+ ..++..+...       +.++++++|+++++.|+.+.+..+.
T Consensus       227 ~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~-------~~~~lilaPTr~La~Q~~~~l~~~~  294 (673)
T 2wv9_A          227 EPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQK-------RLRTAVLAPTRVVAAEMAEALRGLP  294 (673)
T ss_dssp             ---CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHTTTSC
T ss_pred             cchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhC-------CCcEEEEccHHHHHHHHHHHHhcCC
Confidence            6666555      6789999999999999974 5555555443       6799999999999999999887653

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=98.61  E-value=1.6e-07  Score=69.90  Aligned_cols=67  Identities=13%  Similarity=0.040  Sum_probs=46.9

Q ss_pred             HHHHHHHHHh-cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         23 IQFEAYKAAL-TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        23 ~Q~~~i~~~~-~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .|++++..+. .++.++|.||+|+|||+++..++.......    ..+.++++++|++.++.++.+++.+..
T Consensus        97 ~q~~~i~~~l~~~~~vii~gpTGSGKTtllp~ll~~~~~~~----~~g~~ilvl~P~r~La~q~~~~l~~~~  164 (773)
T 2xau_A           97 AQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPH----LENTQVACTQPRRVAAMSVAQRVAEEM  164 (773)
T ss_dssp             GGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHCGG----GGTCEEEEEESCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHhcccc----CCCceEEecCchHHHHHHHHHHHHHHh
Confidence            4555555555 567899999999999996555433221111    025579999999999999998886654

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=98.57  E-value=6.8e-07  Score=56.66  Aligned_cols=40  Identities=18%  Similarity=0.113  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHhc---CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         22 TIQFEAYKAALT---REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        22 ~~Q~~~i~~~~~---~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ....+.+..+..   +..++|.||||||||+++..++..+...
T Consensus        37 ~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~~~~~~   79 (242)
T 3bos_A           37 DELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANEL   79 (242)
T ss_dssp             HHHHHHHHHHHHTCSCSEEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            445555555443   4689999999999999999998887654

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=98.53  E-value=3.7e-08  Score=69.04  Aligned_cols=59  Identities=22%  Similarity=0.214  Sum_probs=45.5

Q ss_pred             HHHHHhcC-CceEEeCCCCCchHHH-HHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         27 AYKAALTR-EFAIIQGPPGTGKTYV-ALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        27 ~i~~~~~~-~~~~v~Gp~GtGKT~~-~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ++..+.++ ..+++.+|||+|||.. +..++..+...       +.++++++|+++++.|+.+.+..+
T Consensus        11 ~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~-------~~~~lvl~Ptr~La~Q~~~~l~g~   71 (451)
T 2jlq_A           11 VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLR-------RLRTLILAPTRVVAAEMEEALRGL   71 (451)
T ss_dssp             CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhc-------CCcEEEECCCHHHHHHHHHHhcCc
Confidence            45555555 4559999999999994 66666666554       689999999999999999887543

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=98.53  E-value=7.3e-08  Score=70.20  Aligned_cols=58  Identities=24%  Similarity=0.208  Sum_probs=47.8

Q ss_pred             HHHHHhcCCceEEeCCCCCchHHH-HHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         27 AYKAALTREFAIIQGPPGTGKTYV-ALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        27 ~i~~~~~~~~~~v~Gp~GtGKT~~-~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      ++..+.+++.+++.+|||||||.. +..++..+...       +.++++++|+++++.|+.+.+..
T Consensus       179 ~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~-------~~~vLvl~PtreLa~Qi~~~l~~  237 (618)
T 2whx_A          179 DEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKR-------RLRTLILAPTRVVAAEMEEALRG  237 (618)
T ss_dssp             CGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHTTT
T ss_pred             CHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhC-------CCeEEEEcChHHHHHHHHHHhcC
Confidence            466666789999999999999996 46666666554       67999999999999999988753

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=98.52  E-value=1.8e-07  Score=56.74  Aligned_cols=41  Identities=20%  Similarity=0.214  Sum_probs=31.7

Q ss_pred             CCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         20 LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        20 l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.....++..+ .++.+++.||+|+|||+++..++..+...
T Consensus        23 ~n~~~~~~l~~~-~g~~~~l~G~~G~GKTtL~~~i~~~~~~~   63 (149)
T 2kjq_A           23 ENAELVYVLRHK-HGQFIYVWGEEGAGKSHLLQAWVAQALEA   63 (149)
T ss_dssp             CTHHHHHHCCCC-CCSEEEEESSSTTTTCHHHHHHHHHHHTT
T ss_pred             ccHHHHHHHHhc-CCCEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            455555555554 67789999999999999999998887653

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=98.51  E-value=2.4e-07  Score=59.25  Aligned_cols=53  Identities=25%  Similarity=0.359  Sum_probs=39.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .+..++|.||||+|||+++..++..+...       +.++++++... ...++.+++.+++
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~~~-------~~~v~~~~~e~-~~~~~~~~~~~~g   74 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGLKM-------GEPGIYVALEE-HPVQVRQNMAQFG   74 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHHHT-------TCCEEEEESSS-CHHHHHHHHHTTT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhc-------CCeEEEEEccC-CHHHHHHHHHHcC
Confidence            35688999999999999999998887665       66788877433 3466666665443

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=98.50  E-value=7.4e-07  Score=65.38  Aligned_cols=68  Identities=21%  Similarity=0.264  Sum_probs=55.1

Q ss_pred             CCCCCHHHHHHHHHHhc----CC-ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         17 ELGLNTIQFEAYKAALT----RE-FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~----~~-~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      .+.++..|.+++..+..    +. ..++.|.+|+|||+++..++...          ++++||++|+...+.++.+.++.
T Consensus         6 ~~~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~~~~~~----------~~~~lvv~~~~~~A~ql~~el~~   75 (664)
T 1c4o_A            6 GPSPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVIEAL----------GRPALVLAPNKILAAQLAAEFRE   75 (664)
T ss_dssp             SCCCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHH----------TCCEEEEESSHHHHHHHHHHHHH
T ss_pred             CCCCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHHHHHHh----------CCCEEEEecCHHHHHHHHHHHHH
Confidence            45777888888876543    22 46799999999999988776554          45799999999999999999999


Q ss_pred             hcc
Q psy16285         92 YTQ   94 (97)
Q Consensus        92 ~~~   94 (97)
                      |+.
T Consensus        76 ~~~   78 (664)
T 1c4o_A           76 LFP   78 (664)
T ss_dssp             HCT
T ss_pred             HCC
Confidence            974

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.48  E-value=1.8e-07  Score=63.32  Aligned_cols=43  Identities=7%  Similarity=0.105  Sum_probs=32.9

Q ss_pred             CCCHHHHHHHHHHhc-------CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         19 GLNTIQFEAYKAALT-------REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~-------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .-++.|.+.+...+.       +++++|.||||||||+++..++..+...
T Consensus        23 ~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~   72 (318)
T 3te6_A           23 KSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITS   72 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHH
Confidence            345666666654432       4589999999999999999999998764

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=98.48  E-value=1.2e-06  Score=58.53  Aligned_cols=35  Identities=23%  Similarity=0.167  Sum_probs=28.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ..++|.||||||||+++..++..+...       +.+++.+.
T Consensus        38 ~~lll~G~~GtGKT~la~~i~~~~~~~-------~~~~~~i~   72 (324)
T 1l8q_A           38 NPIFIYGSVGTGKTHLLQAAGNEAKKR-------GYRVIYSS   72 (324)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHC-------CCEEEEEE
Confidence            479999999999999999999888665       45666665

>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B*

Probab=98.42  E-value=5.4e-07  Score=69.57  Aligned_cols=59  Identities=19%  Similarity=0.234  Sum_probs=45.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchh-----hhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKE-----LARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~-----~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +..+|.+++|||||+++...+..++....     .......+||++++|+.|+.+|.+|+++..
T Consensus        17 g~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~L   80 (1180)
T 1w36_B           17 GERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNI   80 (1180)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHHH
Confidence            45699999999999987777777664210     000136789999999999999999998753

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=98.42  E-value=2e-06  Score=53.55  Aligned_cols=45  Identities=27%  Similarity=0.440  Sum_probs=33.6

Q ss_pred             CCCCCHHHHHHHHHHhcC---CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         17 ELGLNTIQFEAYKAALTR---EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.-++...+.+..+...   +.++|.||||+|||+++..++..+...
T Consensus        18 ~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~   65 (226)
T 2chg_A           18 EVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGE   65 (226)
T ss_dssp             GCCSCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHHHGG
T ss_pred             HHcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHhcc
Confidence            344456666677666543   369999999999999999998887544

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=98.41  E-value=4.9e-07  Score=57.83  Aligned_cols=53  Identities=17%  Similarity=0.236  Sum_probs=39.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +..++|.|+||+|||+++..++.....+      .+.++++++.. ...+++.+++.+++
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~------~~~~v~~~s~E-~~~~~~~~~~~~~~   82 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEE------YGEPGVFVTLE-ERARDLRREMASFG   82 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHH------HCCCEEEEESS-SCHHHHHHHHHTTT
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHh------cCCCceeeccc-CCHHHHHHHHHHcC
Confidence            4688999999999999999988765544      26778887743 34667777766554

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.41  E-value=2.2e-07  Score=55.80  Aligned_cols=28  Identities=25%  Similarity=0.154  Sum_probs=23.1

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .+.++++.||||||||+++..+......
T Consensus        23 ~~~~vll~G~~GtGKt~lA~~i~~~~~~   50 (145)
T 3n70_A           23 TDIAVWLYGAPGTGRMTGARYLHQFGRN   50 (145)
T ss_dssp             CCSCEEEESSTTSSHHHHHHHHHHSSTT
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHhCCc
Confidence            3568999999999999999988765533

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=98.39  E-value=1.1e-06  Score=55.50  Aligned_cols=51  Identities=25%  Similarity=0.445  Sum_probs=36.3

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      .+..++|.||+|+|||+++..++..+...       +.+++++.... ...++..++..
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~-------~~~v~~~~~~~-~~~~~~~~~~~   72 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFSLHFIAKGLRD-------GDPCIYVTTEE-SRDSIIRQAKQ   72 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHHHHH-------TCCEEEEESSS-CHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHC-------CCeEEEEEccc-CHHHHHHHHHH
Confidence            35688999999999999999998777655       56777776433 23444444443

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=98.39  E-value=2.6e-06  Score=62.43  Aligned_cols=73  Identities=15%  Similarity=0.247  Sum_probs=58.6

Q ss_pred             cccccCCCCCHHHHHHHHHHhc----CC-ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHH
Q psy16285         12 ANVQEELGLNTIQFEAYKAALT----RE-FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFV   86 (97)
Q Consensus        12 ~~~~~~~~l~~~Q~~~i~~~~~----~~-~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~   86 (97)
                      +.....+.++.+|..++..+..    +. ...+.|.+|+|||+++..++...          .+++||++|+...+.++.
T Consensus         5 ~~~~~~~~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~~~~~~----------~~~~lvv~~~~~~A~~l~   74 (661)
T 2d7d_A            5 FELVSKYQPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNLIKEV----------NKPTLVIAHNKTLAGQLY   74 (661)
T ss_dssp             CCCCCSCCCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHH----------CCCEEEECSSHHHHHHHH
T ss_pred             ceeecCCCCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHHHHHHh----------CCCEEEEECCHHHHHHHH
Confidence            4445667888889888886543    22 46789999999999987776554          457999999999999999


Q ss_pred             HHHHhhcc
Q psy16285         87 EGVLKYTQ   94 (97)
Q Consensus        87 ~~l~~~~~   94 (97)
                      +.++.|+.
T Consensus        75 ~el~~~~~   82 (661)
T 2d7d_A           75 SEFKEFFP   82 (661)
T ss_dssp             HHHHHHCT
T ss_pred             HHHHHHcC
Confidence            99999964

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.38  E-value=1.2e-06  Score=53.41  Aligned_cols=43  Identities=16%  Similarity=0.278  Sum_probs=32.5

Q ss_pred             CCCCHHHHHHHHHHhc---CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         18 LGLNTIQFEAYKAALT---REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~---~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +.-++.+.+.+.....   ...++|.||||||||+++..++..+..
T Consensus        24 ~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~   69 (195)
T 1jbk_A           24 VIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIIN   69 (195)
T ss_dssp             CCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             cccchHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            3445666666655543   357899999999999999999988865

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=98.36  E-value=4.3e-07  Score=63.98  Aligned_cols=46  Identities=24%  Similarity=0.257  Sum_probs=38.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +..+|.|+||||||+++...+.            ..++++++||++++++|.+++.+.
T Consensus       162 ~v~~I~G~aGsGKTt~I~~~~~------------~~~~lVlTpT~~aa~~l~~kl~~~  207 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEILSRVN------------FEEDLILVPGRQAAEMIRRRANAS  207 (446)
T ss_dssp             EEEEEEECTTSCHHHHHHHHCC------------TTTCEEEESCHHHHHHHHHHHTTT
T ss_pred             cEEEEEcCCCCCHHHHHHHHhc------------cCCeEEEeCCHHHHHHHHHHhhhc
Confidence            3668999999999999766542            246899999999999999999643

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=98.36  E-value=7.7e-08  Score=70.66  Aligned_cols=62  Identities=16%  Similarity=0.110  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         22 TIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        22 ~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..|.+++..+.+++.+++.||+|+|||+.+..   .+++.       +.++++++|+++++.|+.+++.+..
T Consensus       220 ~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l---~ll~~-------g~~vLVl~PTReLA~Qia~~l~~~~  281 (666)
T 3o8b_A          220 TDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPA---AYAAQ-------GYKVLVLNPSVAATLGFGAYMSKAH  281 (666)
T ss_dssp             CCCCSCCCCCSSCEEEEEECCTTSCTTTHHHH---HHHHT-------TCCEEEEESCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCeEEEEeCCchhHHHHHHH---HHHHC-------CCeEEEEcchHHHHHHHHHHHHHHh
Confidence            33444444434567899999999999965443   23333       6699999999999999999887654

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.36  E-value=1.4e-06  Score=58.84  Aligned_cols=46  Identities=24%  Similarity=0.283  Sum_probs=35.8

Q ss_pred             cCCCCCHHHHHHHHHHh-------cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         16 EELGLNTIQFEAYKAAL-------TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~-------~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+.-++.+.+.+..+.       ....++|.||||||||+++..++..+...
T Consensus        19 ~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~   71 (387)
T 2v1u_A           19 DVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEAR   71 (387)
T ss_dssp             SCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHH
Confidence            45556777877777655       23579999999999999999998887554

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.35  E-value=8.6e-07  Score=62.32  Aligned_cols=24  Identities=42%  Similarity=0.589  Sum_probs=21.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||.++.+++..+
T Consensus       216 rGvLLyGPPGTGKTllAkAiA~e~  239 (434)
T 4b4t_M          216 KGALMYGPPGTGKTLLARACAAQT  239 (434)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             CeeEEECcCCCCHHHHHHHHHHHh
Confidence            468999999999999999998877

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.35  E-value=9e-07  Score=61.71  Aligned_cols=24  Identities=42%  Similarity=0.636  Sum_probs=22.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||.++.+++..+
T Consensus       183 rGvLL~GPPGTGKTllAkAiA~e~  206 (405)
T 4b4t_J          183 KGVILYGPPGTGKTLLARAVAHHT  206 (405)
T ss_dssp             CCEEEESCSSSSHHHHHHHHHHHH
T ss_pred             CceEEeCCCCCCHHHHHHHHHHhh
Confidence            468999999999999999999887

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.34  E-value=1e-06  Score=61.88  Aligned_cols=24  Identities=33%  Similarity=0.607  Sum_probs=21.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +-+++.||||||||.++.+++..+
T Consensus       207 rGiLL~GPPGtGKT~lakAiA~~~  230 (428)
T 4b4t_K          207 RGVLLYGPPGTGKTMLVKAVANST  230 (428)
T ss_dssp             CEEEEESCTTTTHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            358999999999999999999887

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=98.32  E-value=5.5e-06  Score=62.24  Aligned_cols=68  Identities=16%  Similarity=0.003  Sum_probs=53.2

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .+.+.+.|..++..+..+.  +...+||+|||..+..-+. +..-      .+..++|++||+.++.|..+.+..+.
T Consensus        81 G~~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~-l~aL------~g~~vlVltptreLA~qd~e~~~~l~  148 (844)
T 1tf5_A           81 GMFPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVY-LNAL------TGKGVHVVTVNEYLASRDAEQMGKIF  148 (844)
T ss_dssp             SCCCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHH-HHHT------TSSCEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHH-HHHH------cCCCEEEEeCCHHHHHHHHHHHHHHH
Confidence            4578899999999888777  8999999999975443332 1111      36789999999999999988887765

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=98.32  E-value=1.9e-06  Score=55.61  Aligned_cols=24  Identities=38%  Similarity=0.613  Sum_probs=21.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++..++..+
T Consensus        40 ~~vll~G~~GtGKT~la~~la~~~   63 (262)
T 2qz4_A           40 KGALLLGPPGCGKTLLAKAVATEA   63 (262)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999998865

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=98.31  E-value=4e-06  Score=62.98  Aligned_cols=69  Identities=14%  Similarity=-0.028  Sum_probs=52.9

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ++...+.|..++..+..+.  +...++|+|||..+..-+... ..      .+.+++|++||+.++.|..+.+..+..
T Consensus        72 g~~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~-~l------~g~~vlVltPTreLA~Q~~e~~~~l~~  140 (853)
T 2fsf_A           72 GMRHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLN-AL------TGKGVHVVTVNDYLAQRDAENNRPLFE  140 (853)
T ss_dssp             SCCCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHH-HT------TSSCCEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHH-HH------cCCcEEEEcCCHHHHHHHHHHHHHHHH
Confidence            3577899999999887776  899999999997644333211 11      266899999999999999888877653

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.31  E-value=2.7e-06  Score=59.79  Aligned_cols=24  Identities=38%  Similarity=0.549  Sum_probs=21.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .-+++.||||||||.++.+++..+
T Consensus       217 rGvLLyGPPGTGKTlLAkAiA~e~  240 (437)
T 4b4t_I          217 KGVILYGAPGTGKTLLAKAVANQT  240 (437)
T ss_dssp             SEEEEESSTTTTHHHHHHHHHHHH
T ss_pred             CCCceECCCCchHHHHHHHHHHHh
Confidence            468999999999999999999887

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.31  E-value=1.3e-06  Score=53.16  Aligned_cols=43  Identities=19%  Similarity=0.268  Sum_probs=31.8

Q ss_pred             CCCCHHHHHHHHHHhc---CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         18 LGLNTIQFEAYKAALT---REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~---~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +.-++.+.+.+.....   ...++|.||||||||+++..++..+..
T Consensus        24 ~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~~~   69 (187)
T 2p65_A           24 VIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQ   69 (187)
T ss_dssp             CCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHHHHT
T ss_pred             hhcchHHHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            3345555555555443   357899999999999999999988765

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=98.28  E-value=1.8e-06  Score=63.55  Aligned_cols=52  Identities=17%  Similarity=0.243  Sum_probs=39.6

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+++.+++.||||+|||+.+   +..+...        .+.++++|+++++.|+.+++.+.+.
T Consensus       153 l~rk~vlv~apTGSGKT~~a---l~~l~~~--------~~gl~l~PtR~LA~Qi~~~l~~~g~  204 (677)
T 3rc3_A          153 MQRKIIFHSGPTNSGKTYHA---IQKYFSA--------KSGVYCGPLKLLAHEIFEKSNAAGV  204 (677)
T ss_dssp             SCCEEEEEECCTTSSHHHHH---HHHHHHS--------SSEEEEESSHHHHHHHHHHHHHTTC
T ss_pred             cCCCEEEEEcCCCCCHHHHH---HHHHHhc--------CCeEEEeCHHHHHHHHHHHHHhcCC
Confidence            34678999999999999843   2333332        3458899999999999999988653

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=98.28  E-value=4.6e-06  Score=58.47  Aligned_cols=37  Identities=22%  Similarity=0.211  Sum_probs=29.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ..+++.||||+|||+++..++..+....     ++.+++++.
T Consensus       131 ~~lll~Gp~G~GKTtLa~aia~~l~~~~-----~~~~v~~v~  167 (440)
T 2z4s_A          131 NPLFIYGGVGLGKTHLLQSIGNYVVQNE-----PDLRVMYIT  167 (440)
T ss_dssp             CCEEEECSSSSSHHHHHHHHHHHHHHHC-----CSSCEEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhC-----CCCeEEEee
Confidence            4789999999999999999998886652     255666665

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.26  E-value=1.1e-06  Score=61.79  Aligned_cols=24  Identities=38%  Similarity=0.664  Sum_probs=22.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .-+++.||||||||.++.+++..+
T Consensus       216 rGvLL~GPPGtGKTllAkAiA~e~  239 (437)
T 4b4t_L          216 KGVLLYGPPGTGKTLLAKAVAATI  239 (437)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHh
Confidence            468999999999999999999887

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=98.25  E-value=1.5e-06  Score=57.43  Aligned_cols=26  Identities=38%  Similarity=0.525  Sum_probs=23.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++++.||||||||+++..++..+...
T Consensus        69 ~vll~G~~GtGKT~la~~la~~l~~~   94 (309)
T 3syl_A           69 HMSFTGNPGTGKTTVALKMAGLLHRL   94 (309)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            68999999999999999999888664

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=98.25  E-value=2.5e-06  Score=53.61  Aligned_cols=44  Identities=20%  Similarity=0.252  Sum_probs=32.9

Q ss_pred             CCCCCHHHHHHHHHHhc-C---CceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         17 ELGLNTIQFEAYKAALT-R---EFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~-~---~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .+.-++...+.+..+.. +   ..++|.||||+|||+++..++..+..
T Consensus        24 ~~~g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~   71 (250)
T 1njg_A           24 DVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNC   71 (250)
T ss_dssp             GCCSCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHHC
T ss_pred             HHhCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            34556667677766553 2   26899999999999999999887743

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.24  E-value=2.5e-06  Score=55.88  Aligned_cols=24  Identities=38%  Similarity=0.610  Sum_probs=21.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++..++..+
T Consensus        52 ~~~ll~G~~GtGKT~la~~la~~~   75 (285)
T 3h4m_A           52 KGILLYGPPGTGKTLLAKAVATET   75 (285)
T ss_dssp             SEEEEESSSSSSHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHh
Confidence            578999999999999999987665

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=98.24  E-value=1.6e-06  Score=54.25  Aligned_cols=38  Identities=24%  Similarity=0.289  Sum_probs=30.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      +...++.||+|+||||++..++..+...       +.+++++.|.
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~~~~-------g~~v~~~~~~   40 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIYKLG-------KKKVAVFKPK   40 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHT-------TCEEEEEEEC
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHHHC-------CCeEEEEeec
Confidence            4567899999999999998888877655       5677777665

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=98.23  E-value=2.5e-06  Score=57.62  Aligned_cols=24  Identities=38%  Similarity=0.708  Sum_probs=22.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||+||||++..++..+
T Consensus        52 ~~~ll~Gp~G~GKTTLa~~ia~~l   75 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLAHIIASEL   75 (334)
T ss_dssp             CCEEEESSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHh
Confidence            578999999999999999998877

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=98.23  E-value=2.6e-06  Score=57.23  Aligned_cols=50  Identities=20%  Similarity=0.343  Sum_probs=38.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      +..++|.|+||+|||+++..++..+..+       +.++++++.. ....++..++..
T Consensus        68 G~l~li~G~pG~GKTtl~l~ia~~~a~~-------g~~vl~~slE-~s~~~l~~R~~~  117 (315)
T 3bh0_A           68 RNFVLIAARPSMGKTAFALKQAKNMSDN-------DDVVNLHSLE-MGKKENIKRLIV  117 (315)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHTT-------TCEEEEEESS-SCHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHc-------CCeEEEEECC-CCHHHHHHHHHH
Confidence            5688999999999999999998887665       4678888853 445555555543

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.22  E-value=8.6e-06  Score=55.12  Aligned_cols=46  Identities=22%  Similarity=0.270  Sum_probs=34.3

Q ss_pred             cCCCCCHHHHHHHHHHhc-------CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         16 EELGLNTIQFEAYKAALT-------REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~-------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+.-++.+.+.+.....       ...++|.||||||||+++..++..+...
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~   72 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEV   72 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHH
Confidence            455557777766654432       3479999999999999999998887554

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=98.22  E-value=6.7e-06  Score=55.60  Aligned_cols=45  Identities=27%  Similarity=0.330  Sum_probs=33.2

Q ss_pred             cCCCCCHHHHHHHHHHhcC-------C--ceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         16 EELGLNTIQFEAYKAALTR-------E--FAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~-------~--~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ..+.-++.+.+.+..+...       .  .++|.||||||||+++..++..+..
T Consensus        17 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~   70 (389)
T 1fnn_A           17 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKD   70 (389)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTT
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhh
Confidence            4455577776666655431       4  6999999999999999988877643

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=98.21  E-value=2e-06  Score=55.93  Aligned_cols=26  Identities=31%  Similarity=0.296  Sum_probs=22.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      ...++|.||||||||+++..+...+.
T Consensus        29 ~~~vll~G~~GtGKt~la~~i~~~~~   54 (265)
T 2bjv_A           29 DKPVLIIGERGTGKELIASRLHYLSS   54 (265)
T ss_dssp             CSCEEEECCTTSCHHHHHHHHHHTST
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHhcC
Confidence            56899999999999999988877653

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=98.21  E-value=9.2e-07  Score=57.54  Aligned_cols=24  Identities=38%  Similarity=0.614  Sum_probs=21.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus        45 ~~vll~G~~GtGKT~la~~la~~~   68 (268)
T 2r62_A           45 KGVLLVGPPGTGKTLLAKAVAGEA   68 (268)
T ss_dssp             SCCCCBCSSCSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHh
Confidence            468999999999999999998875

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.20  E-value=2.4e-06  Score=60.50  Aligned_cols=24  Identities=38%  Similarity=0.595  Sum_probs=21.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.+++.||||||||.++.+++..+
T Consensus       244 rGILLyGPPGTGKTlLAkAiA~e~  267 (467)
T 4b4t_H          244 KGILLYGPPGTGKTLCARAVANRT  267 (467)
T ss_dssp             SEEEECSCTTSSHHHHHHHHHHHH
T ss_pred             CceEeeCCCCCcHHHHHHHHHhcc
Confidence            468999999999999999999877

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=98.20  E-value=2.1e-06  Score=58.38  Aligned_cols=25  Identities=28%  Similarity=0.527  Sum_probs=22.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...+++.||||||||+++..++..+
T Consensus        51 ~~~vll~GppGtGKT~la~~ia~~~   75 (363)
T 3hws_A           51 KSNILLIGPTGSGKTLLAETLARLL   75 (363)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHc
Confidence            4579999999999999999998765

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=98.20  E-value=8.8e-07  Score=58.95  Aligned_cols=23  Identities=22%  Similarity=0.322  Sum_probs=20.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.||||||||+++.+++..+
T Consensus        38 ~lLl~GppGtGKT~la~aiA~~l   60 (293)
T 3t15_A           38 ILGIWGGKGQGKSFQCELVFRKM   60 (293)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            56788999999999999998877

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=98.20  E-value=3.6e-06  Score=54.98  Aligned_cols=24  Identities=38%  Similarity=0.618  Sum_probs=21.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++..++..+
T Consensus        65 ~~vLl~G~~GtGKT~la~~ia~~~   88 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALAAKIAEES   88 (272)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHh
Confidence            478999999999999999998874

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=98.20  E-value=9.7e-06  Score=61.28  Aligned_cols=68  Identities=13%  Similarity=0.012  Sum_probs=52.0

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ++...+.|..++..+..+.  +...+||+|||.++..-+. +..-      .+..++|++||..++.+..+.+..+.
T Consensus       109 G~rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~-l~aL------~g~~v~VvTpTreLA~Qdae~m~~l~  176 (922)
T 1nkt_A          109 DQRPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAY-LNAL------AGNGVHIVTVNDYLAKRDSEWMGRVH  176 (922)
T ss_dssp             SCCCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHH-HHHT------TTSCEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHH-HHHH------hCCCeEEEeCCHHHHHHHHHHHHHHH
Confidence            4578899999999877766  8999999999976443332 1111      25689999999999998888877765

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=98.20  E-value=2.5e-06  Score=56.21  Aligned_cols=25  Identities=32%  Similarity=0.551  Sum_probs=21.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...+++.||||||||+++..++..+
T Consensus        54 ~~~vll~Gp~GtGKT~la~~la~~~   78 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLARAVATEC   78 (297)
T ss_dssp             CSEEEEESSSSSCHHHHHHHHHHHT
T ss_pred             CCeEEEECcCCCCHHHHHHHHHHHh
Confidence            3578999999999999999987765

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.19  E-value=2.8e-06  Score=60.54  Aligned_cols=43  Identities=28%  Similarity=0.366  Sum_probs=32.5

Q ss_pred             cCCCCCHHHHHHHHHHhcC--------------------CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALTR--------------------EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~--------------------~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+.-++.+.+.+..+...                    ..+++.||||||||+++..++..+
T Consensus        39 ~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l  101 (516)
T 1sxj_A           39 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL  101 (516)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             HHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            3445566677776666532                    578999999999999999988766

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=98.19  E-value=3.3e-06  Score=56.64  Aligned_cols=24  Identities=38%  Similarity=0.689  Sum_probs=21.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus        52 ~~vLl~GppGtGKT~la~aia~~~   75 (322)
T 3eie_A           52 SGILLYGPPGTGKSYLAKAVATEA   75 (322)
T ss_dssp             CEEEEECSSSSCHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHH
Confidence            468999999999999999998765

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=98.19  E-value=4.2e-06  Score=55.57  Aligned_cols=42  Identities=29%  Similarity=0.322  Sum_probs=29.6

Q ss_pred             CCCCCHHHHHHHHHHhc--------CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         17 ELGLNTIQFEAYKAALT--------REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~--------~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+.-.+...+.+..+..        ...++|.||||||||+++..+...+
T Consensus        13 ~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~   62 (324)
T 1hqc_A           13 EYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL   62 (324)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHH
T ss_pred             HhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHh
Confidence            34445555555444332        2579999999999999999998766

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.18  E-value=9.4e-06  Score=61.58  Aligned_cols=70  Identities=16%  Similarity=0.024  Sum_probs=54.5

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ..+...+.|..++..+.++.  +....||+|||.++...+. +..-      .+..++|++||..++.|..+.+..+..
T Consensus        76 lG~~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~-L~aL------~G~qv~VvTPTreLA~Qdae~m~~l~~  145 (997)
T 2ipc_A           76 LGMRHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVA-LNAL------TGKGVHVVTVNDYLARRDAEWMGPVYR  145 (997)
T ss_dssp             TCCCCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHH-HHHT------TCSCCEEEESSHHHHHHHHHHHHHHHH
T ss_pred             hCCCCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHH-HHHH------hCCCEEEEeCCHHHHHHHHHHHHHHHH
Confidence            35577899999999888777  8899999999976443332 1111      267899999999999999998887753

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=98.18  E-value=8.5e-06  Score=53.90  Aligned_cols=43  Identities=23%  Similarity=0.352  Sum_probs=32.0

Q ss_pred             CCCCHHHHHHHHHHhc-C--CceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         18 LGLNTIQFEAYKAALT-R--EFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~-~--~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +.-.+...+.+..+.. +  +.+++.||||+|||+++..++..+..
T Consensus        27 ~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~l~~   72 (327)
T 1iqp_A           27 IVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFG   72 (327)
T ss_dssp             CCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHG
T ss_pred             hhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcC
Confidence            3345666666666553 2  36999999999999999999888754

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=98.17  E-value=1.1e-06  Score=56.39  Aligned_cols=24  Identities=25%  Similarity=0.530  Sum_probs=21.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      .+++.||||||||+++.+++..+.
T Consensus        60 ~ili~GPPGtGKTt~a~ala~~l~   83 (212)
T 1tue_A           60 CLVFCGPANTGKSYFGMSFIHFIQ   83 (212)
T ss_dssp             EEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            589999999999999999988773

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=98.17  E-value=4.3e-06  Score=58.48  Aligned_cols=45  Identities=16%  Similarity=0.431  Sum_probs=34.6

Q ss_pred             cCCCCCHHHHHHHHHHhc--CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         16 EELGLNTIQFEAYKAALT--REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~--~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ..+.+...+...+..+..  ++.++|.||+|+||||++..++..+..
T Consensus       147 ~~Lg~~~~~~~~L~~l~~~~ggii~I~GpnGSGKTTlL~allg~l~~  193 (418)
T 1p9r_A          147 HSLGMTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLYAGLQELNS  193 (418)
T ss_dssp             GGSCCCHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHHHHHHHHCC
T ss_pred             HHcCCCHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHhhcCC
Confidence            445567777777776653  457899999999999999988887643

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=98.17  E-value=5.1e-06  Score=55.68  Aligned_cols=42  Identities=19%  Similarity=0.184  Sum_probs=29.7

Q ss_pred             CCCCCHHHHHHHHHHhc-----C---CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         17 ELGLNTIQFEAYKAALT-----R---EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~-----~---~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+.-.+...+.+..+..     +   ..++|.||||||||+++..++..+
T Consensus        30 ~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~   79 (338)
T 3pfi_A           30 GYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEM   79 (338)
T ss_dssp             GCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHT
T ss_pred             HhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHh
Confidence            34445555555555442     1   479999999999999999986654

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=98.16  E-value=2.8e-06  Score=54.85  Aligned_cols=38  Identities=21%  Similarity=0.136  Sum_probs=31.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      +...++.||+|+||||.+..++..+...       +.+++++.|.
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~~-------g~kVli~~~~   49 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEYA-------DVKYLVFKPK   49 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHT-------TCCEEEEEEC
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHhc-------CCEEEEEEec
Confidence            4577889999999999999998888766       6778887653

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=98.16  E-value=6.4e-06  Score=54.47  Aligned_cols=39  Identities=13%  Similarity=0.152  Sum_probs=31.3

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+..++|.||||+|||+++..++..+...      .+.+++++..
T Consensus        34 ~G~~~~i~G~~G~GKTTl~~~ia~~~~~~------~G~~v~~~~~   72 (296)
T 1cr0_A           34 GGEVIMVTSGSGMGKSTFVRQQALQWGTA------MGKKVGLAML   72 (296)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHHHHHHT------SCCCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHH------cCCeEEEEeC
Confidence            46789999999999999999988877655      2557877764

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=98.16  E-value=1.5e-06  Score=58.29  Aligned_cols=37  Identities=16%  Similarity=0.236  Sum_probs=27.3

Q ss_pred             HHHHHHHHH-HhcCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         22 TIQFEAYKA-ALTREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        22 ~~Q~~~i~~-~~~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +...+.+.. +..+..+++.||||||||+++..++..+
T Consensus        33 ~~~~~~l~~~l~~~~~vll~G~pGtGKT~la~~la~~~   70 (331)
T 2r44_A           33 KYMINRLLIGICTGGHILLEGVPGLAKTLSVNTLAKTM   70 (331)
T ss_dssp             HHHHHHHHHHHHHTCCEEEESCCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCeEEEECCCCCcHHHHHHHHHHHh
Confidence            333344333 3357799999999999999999988755

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=98.15  E-value=2.7e-06  Score=55.97  Aligned_cols=25  Identities=32%  Similarity=0.477  Sum_probs=22.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...+++.||||||||+++..++..+
T Consensus        50 ~~~vll~G~~GtGKT~la~~la~~l   74 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIARRLAKLA   74 (310)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHh
Confidence            4579999999999999999998876

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.14  E-value=4.1e-06  Score=56.41  Aligned_cols=46  Identities=28%  Similarity=0.291  Sum_probs=35.9

Q ss_pred             cCCCCCHHHHHHHHHHhc-------CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         16 EELGLNTIQFEAYKAALT-------REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~-------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+.-++.+.+.+..+..       +..++|.||+|+|||+++..++..+...
T Consensus        20 ~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~   72 (386)
T 2qby_A           20 DELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKK   72 (386)
T ss_dssp             SCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHH
Confidence            455667778777776554       3579999999999999999988877543

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=98.14  E-value=7.6e-06  Score=54.58  Aligned_cols=43  Identities=28%  Similarity=0.405  Sum_probs=31.0

Q ss_pred             cCCCCCHHHHHHHHHHhcC----CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALTR----EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~----~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+...+...+.+..+...    ..+++.||||||||+++..++..+
T Consensus        26 ~~ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l   72 (324)
T 3u61_B           26 DECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDV   72 (324)
T ss_dssp             TTSCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHT
T ss_pred             HHHhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHh
Confidence            4455566777777776643    245667779999999999987765

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=98.14  E-value=5.3e-06  Score=53.73  Aligned_cols=24  Identities=42%  Similarity=0.623  Sum_probs=21.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++..++..+
T Consensus        46 ~~vll~G~~GtGKT~la~~la~~~   69 (257)
T 1lv7_A           46 KGVLMVGPPGTGKTLLAKAIAGEA   69 (257)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEECcCCCCHHHHHHHHHHHc
Confidence            468999999999999999998765

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=98.12  E-value=4.3e-06  Score=54.23  Aligned_cols=34  Identities=24%  Similarity=0.419  Sum_probs=28.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ++++.|+||+||||++..++..+...       +.++++..
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~-------G~~V~v~d   41 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQ-------GVRVMAGV   41 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHC-------CCCEEEEE
Confidence            57899999999999999999999876       66776554

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.12  E-value=4.5e-06  Score=56.15  Aligned_cols=56  Identities=21%  Similarity=0.287  Sum_probs=37.2

Q ss_pred             cccccccCCcccccCCCCCHHHHHHHHHHh-cC---CceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285          3 SILDAYDLSANVQEELGLNTIQFEAYKAAL-TR---EFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus         3 ~~~~~~~~~~~~~~~~~l~~~Q~~~i~~~~-~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .|.+.|.+.  ....+.-++...+.+..+. ..   +.+++.||+|+|||+++..++..+..
T Consensus         3 ~w~~kyrP~--~~~~~vg~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~~la~~l~~   62 (354)
T 1sxj_E            3 LWVDKYRPK--SLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFG   62 (354)
T ss_dssp             -CTTTTCCC--SGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSC
T ss_pred             cchhccCCC--CHHHhcCCHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHHHHHHHHcC
Confidence            345555432  1233445666667777665 32   35899999999999999999887644

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=98.12  E-value=1.5e-06  Score=52.07  Aligned_cols=24  Identities=17%  Similarity=0.134  Sum_probs=20.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ...++++.||||||||+++..+..
T Consensus        26 ~~~~vll~G~~GtGKt~lA~~i~~   49 (143)
T 3co5_A           26 RTSPVFLTGEAGSPFETVARYFHK   49 (143)
T ss_dssp             CSSCEEEEEETTCCHHHHHGGGCC
T ss_pred             CCCcEEEECCCCccHHHHHHHHHH
Confidence            356899999999999999887754

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=98.11  E-value=4.6e-06  Score=53.19  Aligned_cols=37  Identities=30%  Similarity=0.292  Sum_probs=31.8

Q ss_pred             CHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         21 NTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        21 ~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +..|..+++.+..++.+.|.||+|+||||++..++..
T Consensus         9 ~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A            9 TLGQKHYVDAIDTNTIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             SHHHHHHHHHHHHCSEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CHhHHHHHHhccCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4557778888888899999999999999998888766

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.11  E-value=7.9e-06  Score=55.04  Aligned_cols=39  Identities=21%  Similarity=0.389  Sum_probs=28.7

Q ss_pred             CHHHHHHHHHHhc-CC--ceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         21 NTIQFEAYKAALT-RE--FAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        21 ~~~Q~~~i~~~~~-~~--~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      .+...+.+..... ++  .+++.||||||||+++..++..+.
T Consensus        30 ~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~l~   71 (340)
T 1sxj_C           30 QNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIY   71 (340)
T ss_dssp             CHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Confidence            3445555555544 33  389999999999999999988874

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=98.11  E-value=4.1e-06  Score=55.34  Aligned_cols=27  Identities=26%  Similarity=0.439  Sum_probs=23.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+++.||||||||+++..++..+...
T Consensus        48 ~~~ll~G~~GtGKt~la~~la~~~~~~   74 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELAKTLAATLFDT   74 (311)
T ss_dssp             EEEEEESCSSSSHHHHHHHHHHHHHSC
T ss_pred             eEEEEECCCCcCHHHHHHHHHHHHcCC
Confidence            368999999999999999999887554

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=98.10  E-value=1.8e-06  Score=57.52  Aligned_cols=24  Identities=38%  Similarity=0.602  Sum_probs=21.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus        50 ~~vLL~Gp~GtGKT~la~ala~~~   73 (301)
T 3cf0_A           50 KGVLFYGPPGCGKTLLAKAIANEC   73 (301)
T ss_dssp             SEEEEECSSSSSHHHHHHHHHHHT
T ss_pred             ceEEEECCCCcCHHHHHHHHHHHh
Confidence            468999999999999999887654

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=98.09  E-value=1.9e-06  Score=58.04  Aligned_cols=24  Identities=38%  Similarity=0.679  Sum_probs=21.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus        46 ~~iLL~GppGtGKT~la~ala~~~   69 (322)
T 1xwi_A           46 RGILLFGPPGTGKSYLAKAVATEA   69 (322)
T ss_dssp             SEEEEESSSSSCHHHHHHHHHHHT
T ss_pred             ceEEEECCCCccHHHHHHHHHHHc
Confidence            468999999999999999998876

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=98.09  E-value=3.1e-06  Score=53.08  Aligned_cols=26  Identities=19%  Similarity=0.226  Sum_probs=22.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ....++|.||||+||||++..++..+
T Consensus        24 ~~~~i~l~G~~GsGKsTl~~~La~~l   49 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLGKAFARKL   49 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            45689999999999999999887654

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=98.08  E-value=7.8e-06  Score=53.89  Aligned_cols=43  Identities=26%  Similarity=0.425  Sum_probs=32.1

Q ss_pred             CCCCHHHHHHHHHHhcC---CceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         18 LGLNTIQFEAYKAALTR---EFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +.-.+...+.+..+...   +.+++.||||||||+++..++..+..
T Consensus        19 ~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~   64 (319)
T 2chq_A           19 VVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFG   64 (319)
T ss_dssp             SCSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHHHHT
T ss_pred             HhCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHHhcC
Confidence            44456666666665532   35899999999999999999888743

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=98.08  E-value=1e-05  Score=53.11  Aligned_cols=59  Identities=15%  Similarity=0.293  Sum_probs=35.9

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhc---CCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARY---MSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~---~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      .+..++|.||+|+|||+++..++..+.......+.   ...++++++.... .+++..++..+
T Consensus        29 ~G~i~~i~G~~GsGKTtl~~~l~~~~~~g~~~~g~~~~~~~~v~~~~~e~~-~~~~~~r~~~~   90 (279)
T 1nlf_A           29 AGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDP-PTAIHHRLHAL   90 (279)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESSSC-HHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHhcCCCcCCCccCCCccEEEEECCCC-HHHHHHHHHHH
Confidence            46789999999999999999998865431000000   1356777764332 34444444433

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.08  E-value=5.1e-06  Score=55.67  Aligned_cols=38  Identities=29%  Similarity=0.469  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhc-C--CceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         23 IQFEAYKAALT-R--EFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        23 ~Q~~~i~~~~~-~--~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ...+.+..+.. +  +.+++.||||||||+++..++..+..
T Consensus        44 ~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l~~   84 (353)
T 1sxj_D           44 HAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYG   84 (353)
T ss_dssp             TTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            34445555543 3  46899999999999999999888753

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=98.08  E-value=2.4e-06  Score=57.78  Aligned_cols=25  Identities=36%  Similarity=0.636  Sum_probs=22.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      ..+++.||||||||+++..++..+.
T Consensus        71 ~~vLl~GppGtGKT~la~~la~~l~   95 (368)
T 3uk6_A           71 RAVLIAGQPGTGKTAIAMGMAQALG   95 (368)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3789999999999999999998874

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=98.07  E-value=3.1e-06  Score=51.24  Aligned_cols=23  Identities=26%  Similarity=0.433  Sum_probs=20.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||+||||++..+...+
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l   25 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKEL   25 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999999887664

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=98.06  E-value=3.7e-06  Score=57.75  Aligned_cols=37  Identities=24%  Similarity=0.242  Sum_probs=29.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +..+.|.||||+|||+++..++..+...       +.+++++..
T Consensus        61 G~i~~I~GppGsGKSTLal~la~~~~~~-------gg~VlyId~   97 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLALHAIAEAQKM-------GGVAAFIDA   97 (356)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHHHHT-------TCCEEEEES
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhc-------CCeEEEEec
Confidence            3478999999999999999999887654       455655554

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=98.06  E-value=3.3e-06  Score=57.61  Aligned_cols=24  Identities=38%  Similarity=0.689  Sum_probs=21.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus        85 ~~iLL~GppGtGKT~la~ala~~~  108 (355)
T 2qp9_X           85 SGILLYGPPGTGKSYLAKAVATEA  108 (355)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHh
Confidence            368999999999999999998776

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=98.06  E-value=3.7e-06  Score=51.77  Aligned_cols=25  Identities=24%  Similarity=0.192  Sum_probs=21.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...+++.||||+||||++..++..+
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l   29 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLT   29 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            4578999999999999999887665

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=98.05  E-value=2.8e-06  Score=51.98  Aligned_cols=24  Identities=17%  Similarity=0.299  Sum_probs=20.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.|+||+||||++..+...+
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l   27 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            468999999999999999887754

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=98.05  E-value=1.3e-05  Score=55.09  Aligned_cols=24  Identities=33%  Similarity=0.544  Sum_probs=21.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.||||||||+++.+++..+
T Consensus       149 ~~vLL~GppGtGKT~la~aia~~~  172 (389)
T 3vfd_A          149 RGLLLFGPPGNGKTMLAKAVAAES  172 (389)
T ss_dssp             SEEEEESSTTSCHHHHHHHHHHHT
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhh
Confidence            579999999999999999887654

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=98.04  E-value=3.4e-06  Score=59.22  Aligned_cols=24  Identities=46%  Similarity=0.822  Sum_probs=22.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus        64 ~~iLl~GppGtGKT~la~ala~~l   87 (456)
T 2c9o_A           64 RAVLLAGPPGTGKTALALAIAQEL   87 (456)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCcCCHHHHHHHHHHHh
Confidence            479999999999999999999886

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=98.04  E-value=3.5e-06  Score=51.32  Aligned_cols=25  Identities=20%  Similarity=0.513  Sum_probs=20.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+.|.||+|+||||++..+...+
T Consensus         4 ~~~i~l~G~~GsGKSTl~~~La~~l   28 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIGRQLAQQL   28 (173)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHh
Confidence            4578999999999999988876653

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=98.04  E-value=5e-05  Score=54.96  Aligned_cols=74  Identities=12%  Similarity=0.108  Sum_probs=58.4

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ..+.+.+.|...+..+...+..++.+|-|+|||+++...+...+...     ++.++++++++...+..+++.++.+..
T Consensus       160 ~~~~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~-----~~~~i~~va~t~~qA~~~~~~i~~~i~  233 (592)
T 3cpe_A          160 IKVQLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN-----KDKAVGILAHKGSMSAEVLDRTKQAIE  233 (592)
T ss_dssp             BBCCCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTS-----SSCEEEEEESSHHHHHHHHHHHHHHHT
T ss_pred             ccCcCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhC-----CCCeEEEEECCHHHHHHHHHHHHHHHH
Confidence            45789999999998765567889999999999998776655444331     356899999999999999888876643

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.04  E-value=5.9e-06  Score=58.16  Aligned_cols=24  Identities=46%  Similarity=0.555  Sum_probs=21.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++++.||||||||+++..++..+
T Consensus        51 ~~vLL~GppGtGKTtlAr~ia~~~   74 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLAEVIARYA   74 (447)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHh
Confidence            368999999999999999888765

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=98.03  E-value=8e-06  Score=54.62  Aligned_cols=38  Identities=16%  Similarity=0.282  Sum_probs=30.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +..+++.||+|+||||++..++..+...      .+.+++++..
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA~~l~~~------~G~~V~lv~~  142 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLAAISMLE------KHKKIAFITT  142 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHT------TCCCEEEEEC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHh------cCCEEEEEec
Confidence            3478899999999999999999888653      2667777763

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=98.03  E-value=7.7e-06  Score=55.88  Aligned_cols=37  Identities=30%  Similarity=0.310  Sum_probs=29.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +..++|.||||+|||+++..++..+...       +.+++++..
T Consensus        61 G~iv~I~G~pGsGKTtLal~la~~~~~~-------g~~vlyi~~   97 (349)
T 2zr9_A           61 GRVIEIYGPESSGKTTVALHAVANAQAA-------GGIAAFIDA   97 (349)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHT-------TCCEEEEES
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC-------CCeEEEEEC
Confidence            4578999999999999999999887665       556666653

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=98.02  E-value=1.1e-05  Score=56.39  Aligned_cols=49  Identities=22%  Similarity=0.197  Sum_probs=36.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      +..++|.|+||+|||+++..++..+...      .+.++++++.. ....++..++
T Consensus       200 G~l~ii~G~pg~GKT~lal~ia~~~a~~------~g~~vl~~slE-~~~~~l~~R~  248 (444)
T 2q6t_A          200 GSLNIIAARPAMGKTAFALTIAQNAALK------EGVGVGIYSLE-MPAAQLTLRM  248 (444)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHHHT------TCCCEEEEESS-SCHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHh------CCCeEEEEECC-CCHHHHHHHH
Confidence            4678999999999999999999888764      36788888753 2344555554

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=98.02  E-value=9.8e-06  Score=56.88  Aligned_cols=49  Identities=22%  Similarity=0.348  Sum_probs=36.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      +..++|.|+||+|||+++..++..+...      .+.++++++... ...++..++
T Consensus       203 G~liiI~G~pG~GKTtl~l~ia~~~~~~------~g~~Vl~~s~E~-s~~~l~~r~  251 (454)
T 2r6a_A          203 SDLIIVAARPSVGKTAFALNIAQNVATK------TNENVAIFSLEM-SAQQLVMRM  251 (454)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHHHHHH------SSCCEEEEESSS-CHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHh------CCCcEEEEECCC-CHHHHHHHH
Confidence            5688999999999999999999888764      366888888532 234444443

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=98.02  E-value=9.3e-06  Score=55.40  Aligned_cols=49  Identities=18%  Similarity=0.298  Sum_probs=37.7

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      .+..++|.|+||+|||+++..++..+...       +.++++++.. ....++..++
T Consensus        45 ~G~LiiIaG~pG~GKTt~al~ia~~~a~~-------g~~Vl~fSlE-ms~~ql~~Rl   93 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLMMNMVLSALND-------DRGVAVFSLE-MSAEQLALRA   93 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHHT-------TCEEEEEESS-SCHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHc-------CCeEEEEeCC-CCHHHHHHHH
Confidence            35689999999999999999999888765       6788888852 3345555554

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=98.01  E-value=8.1e-06  Score=50.20  Aligned_cols=25  Identities=32%  Similarity=0.523  Sum_probs=21.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .++|.|+||+||||++..+...+-.
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~~   27 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHh
Confidence            4789999999999999998887743

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=98.01  E-value=2.1e-05  Score=53.89  Aligned_cols=29  Identities=21%  Similarity=0.508  Sum_probs=24.7

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .++.++|.||+|+||||++..++..+...
T Consensus       122 ~~g~i~I~GptGSGKTTlL~~l~g~~~~~  150 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTLAAMLDYLNNT  150 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcccCC
Confidence            45689999999999999999888877554

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=98.01  E-value=3.4e-06  Score=54.53  Aligned_cols=23  Identities=35%  Similarity=0.554  Sum_probs=20.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.||||||||+++..++..+
T Consensus        51 g~ll~G~~G~GKTtl~~~i~~~~   73 (254)
T 1ixz_A           51 GVLLVGPPGVGKTHLARAVAGEA   73 (254)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47999999999999999887654

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=98.00  E-value=9.7e-06  Score=50.09  Aligned_cols=28  Identities=32%  Similarity=0.507  Sum_probs=23.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..+++.|++|+||||++..++..+...
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L~~~l~~~   40 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRLADLLQKE   40 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhc
Confidence            3478899999999999999988887543

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=98.00  E-value=3.4e-06  Score=55.72  Aligned_cols=23  Identities=35%  Similarity=0.616  Sum_probs=20.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.||||||||+++..++..+
T Consensus        46 GvlL~Gp~GtGKTtLakala~~~   68 (274)
T 2x8a_A           46 GVLLAGPPGCGKTLLAKAVANES   68 (274)
T ss_dssp             EEEEESSTTSCHHHHHHHHHHHT
T ss_pred             eEEEECCCCCcHHHHHHHHHHHc
Confidence            48999999999999999887754

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=98.00  E-value=1.1e-05  Score=55.40  Aligned_cols=37  Identities=19%  Similarity=0.328  Sum_probs=30.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +..++|.||||+|||+++..++..+...       +.+++++..
T Consensus        63 G~ii~I~G~pGsGKTtLal~la~~~~~~-------g~~vlyid~   99 (356)
T 1u94_A           63 GRIVEIYGPESSGKTTLTLQVIAAAQRE-------GKTCAFIDA   99 (356)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEES
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHC-------CCeEEEEeC
Confidence            4578999999999999999999888765       556777664

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=98.00  E-value=7.3e-06  Score=52.22  Aligned_cols=27  Identities=19%  Similarity=0.117  Sum_probs=22.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +..+.|.||||+|||+++..++.....
T Consensus        24 G~~~~i~G~~GsGKTtl~~~l~~~~~~   50 (243)
T 1n0w_A           24 GSITEMFGEFRTGKTQICHTLAVTCQL   50 (243)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTS
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhC
Confidence            568899999999999999998876433

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=98.00  E-value=5.7e-06  Score=51.85  Aligned_cols=26  Identities=23%  Similarity=0.446  Sum_probs=22.3

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..++|.||+|+||||++..+...+
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            35689999999999999998887665

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=97.99  E-value=5.9e-06  Score=50.82  Aligned_cols=26  Identities=19%  Similarity=0.440  Sum_probs=22.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +..++|.|+||+||||++..+...+-
T Consensus         3 ~~~I~i~G~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            35789999999999999998888764

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=97.99  E-value=7.6e-06  Score=57.51  Aligned_cols=34  Identities=24%  Similarity=0.301  Sum_probs=28.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      .+++.||+|+||||++..++..+...       +.++++++
T Consensus        99 vI~lvG~~GsGKTTt~~kLA~~l~~~-------G~kVllv~  132 (433)
T 3kl4_A           99 IIMLVGVQGSGKTTTAGKLAYFYKKR-------GYKVGLVA  132 (433)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc-------CCeEEEEe
Confidence            67889999999999999999888655       67777766

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=97.99  E-value=6.4e-06  Score=50.60  Aligned_cols=25  Identities=24%  Similarity=0.403  Sum_probs=21.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...+++.|+||+||||++..+...+
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHh
Confidence            4678999999999999999887654

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=97.99  E-value=6.6e-06  Score=57.85  Aligned_cols=48  Identities=21%  Similarity=0.350  Sum_probs=36.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      +..++|.|+||+|||+++..++..+..+       +.++++++.. ...+++..++
T Consensus       197 G~liiIaG~pG~GKTtlal~ia~~~a~~-------g~~vl~fSlE-ms~~ql~~R~  244 (444)
T 3bgw_A          197 RNFVLIAARPSMGKTAFALKQAKNMSDN-------DDVVNLHSLE-MGKKENIKRL  244 (444)
T ss_dssp             SCEEEEEECSSSSHHHHHHHHHHHHHHT-------TCEEEEECSS-SCTTHHHHHH
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHc-------CCEEEEEECC-CCHHHHHHHH
Confidence            4688999999999999999999888776       5678888753 2233444443

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=97.98  E-value=4.5e-06  Score=56.98  Aligned_cols=25  Identities=28%  Similarity=0.591  Sum_probs=22.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...+++.||||||||+++..++..+
T Consensus        72 ~~~ill~Gp~GtGKT~la~~la~~l   96 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQTLAKHL   96 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHh
Confidence            3579999999999999999988766

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=97.98  E-value=1.2e-05  Score=54.76  Aligned_cols=45  Identities=27%  Similarity=0.190  Sum_probs=32.1

Q ss_pred             cCCCCCHHHHHHHHHHh----------cCCceEE--eCCCCCchHHHHHHHHHHHHh
Q psy16285         16 EELGLNTIQFEAYKAAL----------TREFAII--QGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~----------~~~~~~v--~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ..+.-++.+.+.+....          ....++|  .||+|+|||+++..++..+..
T Consensus        22 ~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~   78 (412)
T 1w5s_A           22 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSE   78 (412)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHH
Confidence            34444666666666554          1236788  899999999999999887654

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=97.98  E-value=5e-06  Score=59.37  Aligned_cols=28  Identities=39%  Similarity=0.663  Sum_probs=24.1

Q ss_pred             HhcCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         31 ALTREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        31 ~~~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+.++++.||||||||+++.+++..+
T Consensus        38 l~~~~~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           38 ALSGESVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             HHHTCEEEEECCSSSSHHHHHHHGGGGB
T ss_pred             HhcCCeeEeecCchHHHHHHHHHHHHHH
Confidence            3467899999999999999999987755

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=97.98  E-value=1.1e-05  Score=54.36  Aligned_cols=35  Identities=20%  Similarity=0.377  Sum_probs=28.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ..+++.||+|+||||++..++..+...       +.++++..
T Consensus       105 ~vi~ivG~~GsGKTTl~~~LA~~l~~~-------g~kV~lv~  139 (306)
T 1vma_A          105 FVIMVVGVNGTGKTTSCGKLAKMFVDE-------GKSVVLAA  139 (306)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             eEEEEEcCCCChHHHHHHHHHHHHHhc-------CCEEEEEc
Confidence            367899999999999999998887554       56777665

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=97.97  E-value=3.6e-06  Score=52.04  Aligned_cols=25  Identities=24%  Similarity=0.488  Sum_probs=21.3

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+..++|.||+|+||||++..++..
T Consensus         8 ~g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            8 GGNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhc
Confidence            4568899999999999998888664

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=97.97  E-value=1.9e-05  Score=53.25  Aligned_cols=42  Identities=21%  Similarity=0.264  Sum_probs=30.7

Q ss_pred             CCCCHHHHHHHHHHhc-C---CceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         18 LGLNTIQFEAYKAALT-R---EFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~-~---~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +.-++...+.+..... +   ..+++.||+|+|||+++..++..+.
T Consensus        18 ~vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l~   63 (373)
T 1jr3_A           18 VVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLN   63 (373)
T ss_dssp             SCSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHHS
T ss_pred             ccCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4445666666666553 2   2478999999999999999988774

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=97.97  E-value=7.3e-06  Score=54.89  Aligned_cols=26  Identities=19%  Similarity=0.183  Sum_probs=22.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      ...+++.||||||||+++..++..+.
T Consensus        45 ~~~vLl~G~~GtGKT~la~~la~~~~   70 (350)
T 1g8p_A           45 IGGVLVFGDRGTGKSTAVRALAALLP   70 (350)
T ss_dssp             GCCEEEECCGGGCTTHHHHHHHHHSC
T ss_pred             CceEEEECCCCccHHHHHHHHHHhCc
Confidence            45799999999999999999988764

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=97.96  E-value=6.8e-06  Score=50.32  Aligned_cols=23  Identities=22%  Similarity=0.346  Sum_probs=20.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.|+||+||||++..++..+
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l   28 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDL   28 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHc
Confidence            58899999999999999887765

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=97.96  E-value=1.3e-05  Score=54.56  Aligned_cols=24  Identities=38%  Similarity=0.573  Sum_probs=21.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus       118 ~~vLl~GppGtGKT~la~aia~~~  141 (357)
T 3d8b_A          118 KGILLFGPPGTGKTLIGKCIASQS  141 (357)
T ss_dssp             SEEEEESSTTSSHHHHHHHHHHHT
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHc
Confidence            478999999999999999987654

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=97.96  E-value=7e-06  Score=50.73  Aligned_cols=26  Identities=15%  Similarity=0.381  Sum_probs=22.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..++|.||+|+||||++..+....
T Consensus         4 ~g~~i~i~GpsGsGKSTL~~~L~~~~   29 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIKNTLITKH   29 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            45678999999999999988887654

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=97.95  E-value=1.3e-05  Score=50.50  Aligned_cols=39  Identities=18%  Similarity=0.099  Sum_probs=32.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCCh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN   79 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~   79 (97)
                      +...++.||.|+|||+.+..++..+...       +.+++++.|..
T Consensus         8 g~i~v~~G~mgsGKTT~ll~~a~r~~~~-------g~kV~v~k~~~   46 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELIRRIRRAKIA-------KQKIQVFKPEI   46 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEEEC-
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHC-------CCEEEEEEecc
Confidence            3467899999999999999998888655       78899988754

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=97.95  E-value=1e-05  Score=50.77  Aligned_cols=34  Identities=24%  Similarity=0.224  Sum_probs=27.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +..++|.||||+|||+++..++.   ..       +.+++++..
T Consensus        20 G~~~~i~G~~GsGKTtl~~~l~~---~~-------~~~v~~i~~   53 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLALQTGL---LS-------GKKVAYVDT   53 (220)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHH---HH-------CSEEEEEES
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH---Hc-------CCcEEEEEC
Confidence            46889999999999999998887   22       556777664

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=97.95  E-value=1.9e-05  Score=55.73  Aligned_cols=43  Identities=21%  Similarity=0.357  Sum_probs=31.9

Q ss_pred             CCCHHHHHHHHHHhc---CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         19 GLNTIQFEAYKAALT---REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~---~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .-++...+.+..+..   ..++++.||||||||+++..++..+...
T Consensus       183 iGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT~la~~la~~l~~~  228 (468)
T 3pxg_A          183 IGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINN  228 (468)
T ss_dssp             CCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSS
T ss_pred             cCcHHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhC
Confidence            335555555555542   3588999999999999999999887553

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=97.95  E-value=1e-05  Score=56.97  Aligned_cols=34  Identities=26%  Similarity=0.473  Sum_probs=28.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      .+++.|++|+||||++..++.++.+.       +.++++++
T Consensus       102 vIlivG~~G~GKTTt~~kLA~~l~~~-------G~kVllv~  135 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTVAKLARYFQKR-------GYKVGVVC  135 (443)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTT-------TCCEEEEE
T ss_pred             EEEEECcCCCCHHHHHHHHHHHHHHC-------CCeEEEEe
Confidence            67899999999999999999888665       66777766

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=97.95  E-value=6.7e-06  Score=55.97  Aligned_cols=24  Identities=25%  Similarity=0.367  Sum_probs=21.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +..++|.||||+|||+++..++..
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~  146 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA  146 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh
Confidence            456799999999999999999876

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=97.94  E-value=7.4e-06  Score=51.04  Aligned_cols=26  Identities=31%  Similarity=0.557  Sum_probs=21.9

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..+.|.||+|+||||++..++..+
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhC
Confidence            45688999999999999988887653

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.94  E-value=2.1e-05  Score=63.64  Aligned_cols=39  Identities=18%  Similarity=0.305  Sum_probs=32.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      ++.++++.||||||||+++.+++...+.+       +.+++|+...
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~~~-------G~~v~Fi~~e 1464 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQRE-------GKTCAFIDAE 1464 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTT-------TCCEEEECTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc-------CCcEEEEEcc
Confidence            35689999999999999999999988776       6677777754

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.94  E-value=2.7e-05  Score=51.36  Aligned_cols=43  Identities=23%  Similarity=0.281  Sum_probs=31.8

Q ss_pred             CCCCHHHHHHHHHHhcC---CceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         18 LGLNTIQFEAYKAALTR---EFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +.-++...+.+..+...   +.+++.||||+|||+++..++..+..
T Consensus        23 ~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~   68 (323)
T 1sxj_B           23 IVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLG   68 (323)
T ss_dssp             CCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHG
T ss_pred             HHCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcC
Confidence            33455566666665543   35899999999999999999988754

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=97.94  E-value=9.3e-05  Score=51.30  Aligned_cols=73  Identities=12%  Similarity=0.102  Sum_probs=57.7

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ..+.+.++|...+..+...+..++..+-+.|||+++..++.......     ++.++++++++...+..+++.+..+.
T Consensus       160 ~p~~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~-----~g~~v~~vA~t~~qA~~vf~~i~~mi  232 (385)
T 2o0j_A          160 IKVQLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN-----KDKAVGILAHKGSMSAEVLDRTKQAI  232 (385)
T ss_dssp             EECCCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSS-----SSCEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhC-----CCCeEEEEeCCHHHHHHHHHHHHHHH
Confidence            45789999999998765567789999999999998777765533321     46789999999999888888777654

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=97.93  E-value=6.6e-06  Score=51.57  Aligned_cols=27  Identities=19%  Similarity=0.271  Sum_probs=23.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      .+..+.|.||+|+||||++..++..+.
T Consensus        24 ~g~~i~l~G~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            356889999999999999999888775

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=97.93  E-value=1.5e-05  Score=53.52  Aligned_cols=37  Identities=14%  Similarity=0.226  Sum_probs=28.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +..+.+.||+|+||||++..++..+-..       +.+|++...
T Consensus       102 g~vi~lvG~nGsGKTTll~~Lagll~~~-------~g~V~l~g~  138 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTIAKLGRYYQNL-------GKKVMFCAG  138 (304)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHTT-------TCCEEEECC
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHhc-------CCEEEEEee
Confidence            4578899999999999988888776543       556766653

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=97.93  E-value=6.7e-06  Score=50.11  Aligned_cols=21  Identities=29%  Similarity=0.496  Sum_probs=18.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|+||+||||++..+..
T Consensus         4 ~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEecCCCCCHHHHHHHHHh
Confidence            578999999999999888876

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=97.92  E-value=9.7e-06  Score=49.88  Aligned_cols=24  Identities=29%  Similarity=0.627  Sum_probs=20.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.|+||+||||++..+...+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~l   26 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKAL   26 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHc
Confidence            468899999999999998887654

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=97.92  E-value=1.1e-05  Score=54.40  Aligned_cols=44  Identities=20%  Similarity=0.214  Sum_probs=30.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      +..++|.||||+|||+++..++..+..... ++..+.++++++..
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~-~gg~~~~vlyi~~e  150 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPE-KGGLSGKAVYIDTE  150 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGG-GTCCSCEEEEEESS
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccc-cCCCCCeEEEEECC
Confidence            457899999999999999999877543310 11114567777654

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=97.92  E-value=6e-06  Score=54.20  Aligned_cols=23  Identities=35%  Similarity=0.554  Sum_probs=20.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||||||+++..++..+
T Consensus        75 gvll~Gp~GtGKTtl~~~i~~~~   97 (278)
T 1iy2_A           75 GVLLVGPPGVGKTHLARAVAGEA   97 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT
T ss_pred             eEEEECCCcChHHHHHHHHHHHc
Confidence            47999999999999999887654

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=97.92  E-value=1.5e-05  Score=52.80  Aligned_cols=23  Identities=35%  Similarity=0.404  Sum_probs=20.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.||||||||+++.+++..+
T Consensus       106 ~~~l~GppgtGKt~~a~ala~~~  128 (267)
T 1u0j_A          106 TIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhh
Confidence            58999999999999999988753

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=97.92  E-value=9.3e-06  Score=49.33  Aligned_cols=24  Identities=21%  Similarity=0.342  Sum_probs=21.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++|.|++||||||++..+...+
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~l   31 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLAL   31 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            578999999999999998887765

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=97.92  E-value=7.9e-06  Score=51.50  Aligned_cols=23  Identities=35%  Similarity=0.598  Sum_probs=19.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||+||||++..++..+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999988886654

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=97.92  E-value=1.2e-05  Score=57.08  Aligned_cols=50  Identities=8%  Similarity=0.100  Sum_probs=37.2

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      .+..++|.|+||+|||+++..++..+..+      .+.++++++... ...++..++
T Consensus       241 ~G~l~li~G~pG~GKT~lal~~a~~~a~~------~g~~vl~~s~E~-s~~~l~~r~  290 (503)
T 1q57_A          241 GGEVIMVTSGSGMVMSTFVRQQALQWGTA------MGKKVGLAMLEE-SVEETAEDL  290 (503)
T ss_dssp             TTCEEEEEESSCHHHHHHHHHHHHHHTTT------SCCCEEEEESSS-CHHHHHHHH
T ss_pred             CCeEEEEeecCCCCchHHHHHHHHHHHHh------cCCcEEEEeccC-CHHHHHHHH
Confidence            35678999999999999999999888664      266888888532 344555554

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=97.91  E-value=5.8e-06  Score=57.95  Aligned_cols=24  Identities=38%  Similarity=0.679  Sum_probs=21.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus       168 ~~vLL~GppGtGKT~lA~aia~~~  191 (444)
T 2zan_A          168 RGILLFGPPGTGKSYLAKAVATEA  191 (444)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHc
Confidence            468999999999999999998876

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=97.91  E-value=9.1e-06  Score=50.55  Aligned_cols=23  Identities=48%  Similarity=0.712  Sum_probs=20.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+.|.||+|+||||++..++..+
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l   24 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            46899999999999988887766

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=97.91  E-value=1.6e-05  Score=53.31  Aligned_cols=36  Identities=19%  Similarity=0.270  Sum_probs=28.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ..+.+.||+|+||||++..++..+...       +.+|++...
T Consensus       101 ~vi~lvG~nGsGKTTll~~Lag~l~~~-------~g~V~l~g~  136 (302)
T 3b9q_A          101 AVIMIVGVNGGGKTTSLGKLAHRLKNE-------GTKVLMAAG  136 (302)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHHT-------TCCEEEECC
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHHHc-------CCeEEEEee
Confidence            467899999999999998888777544       567777653

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=97.90  E-value=2.7e-05  Score=48.27  Aligned_cols=37  Identities=16%  Similarity=0.078  Sum_probs=29.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      ..+.|.|++|+||||++..++..+...       +.++.++.+.
T Consensus         5 ~~i~i~G~sGsGKTTl~~~L~~~l~~~-------g~~v~~ik~~   41 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEKWVAAAVRE-------GWRVGTVKHH   41 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHT-------TCCEEEEECC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhhHhc-------CCeeeEEEeC
Confidence            467899999999999999999887654       5566666643

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=97.90  E-value=8.1e-06  Score=49.86  Aligned_cols=25  Identities=24%  Similarity=0.478  Sum_probs=21.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..++|.||+|+||||++..+...+
T Consensus         8 g~~i~l~G~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHhh
Confidence            3578999999999999988887654

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=97.90  E-value=8.7e-06  Score=53.10  Aligned_cols=23  Identities=35%  Similarity=0.590  Sum_probs=20.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.|||||||||++..++..+
T Consensus         3 li~I~G~~GSGKSTla~~La~~~   25 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQET   25 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHhcC
Confidence            46899999999999999998765

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=97.90  E-value=6.9e-06  Score=49.53  Aligned_cols=19  Identities=37%  Similarity=0.625  Sum_probs=17.2

Q ss_pred             ceEEeCCCCCchHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRI   54 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~   54 (97)
                      .++|.||||+||||++..+
T Consensus         3 ~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            5789999999999998877

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=97.90  E-value=8.1e-06  Score=50.35  Aligned_cols=24  Identities=33%  Similarity=0.652  Sum_probs=20.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.|+||+||||++..+...+
T Consensus         6 ~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            6 ALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            467899999999999998887654

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=97.90  E-value=9.7e-06  Score=49.84  Aligned_cols=24  Identities=38%  Similarity=0.667  Sum_probs=20.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.|+||+||||++..+...+
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            468899999999999988887654

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=97.89  E-value=2e-05  Score=51.43  Aligned_cols=27  Identities=30%  Similarity=0.492  Sum_probs=22.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+++.|+||+||||++..+...+...
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~L~~~   31 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKILSKN   31 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHHHhC
Confidence            468899999999999999998876543

>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_B*

Probab=97.89  E-value=1.8e-05  Score=61.05  Aligned_cols=51  Identities=18%  Similarity=0.310  Sum_probs=39.2

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      -+|.|+||||||+++...+.+++.+..    .+.++++++|+..+.. +.+++.+.
T Consensus         4 ~lV~agAGSGKT~~l~~ri~~ll~~~~----~~~~il~lVP~q~TFt-~~~rl~~~   54 (1166)
T 3u4q_B            4 EFLVGRSGSGKTKLIINSIQDELRRAP----FGKPIIFLVPDQMTFL-MEYELAKT   54 (1166)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHHCT----TSSCEEEECCGGGHHH-HHHHHTCC
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHhCC----CCCcEEEEecCcccHH-HHHHHHHh
Confidence            479999999999999998888887632    3689999988776554 55666543

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=97.89  E-value=8e-06  Score=51.31  Aligned_cols=26  Identities=23%  Similarity=0.470  Sum_probs=22.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..++|.||||+||||++..+...+
T Consensus        11 ~~~~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHHC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            35688999999999999998887765

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=97.89  E-value=9.5e-06  Score=51.28  Aligned_cols=26  Identities=23%  Similarity=0.404  Sum_probs=21.9

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..++|.||+|+||||++..++..+
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~~   32 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKDP   32 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHST
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhC
Confidence            35678999999999999988887654

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=97.89  E-value=1.8e-05  Score=53.73  Aligned_cols=36  Identities=17%  Similarity=0.239  Sum_probs=28.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      +..+.+.||+|+||||++..++..+...       +.+|++..
T Consensus       129 g~vi~lvG~nGaGKTTll~~Lag~l~~~-------~g~V~l~g  164 (328)
T 3e70_C          129 PYVIMFVGFNGSGKTTTIAKLANWLKNH-------GFSVVIAA  164 (328)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhc-------CCEEEEEe
Confidence            3478999999999999999888776544       56677665

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=97.89  E-value=1e-05  Score=50.64  Aligned_cols=24  Identities=29%  Similarity=0.437  Sum_probs=20.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.|++|+||||++..+...+
T Consensus        19 ~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999998887665

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=97.89  E-value=1e-05  Score=50.04  Aligned_cols=26  Identities=27%  Similarity=0.553  Sum_probs=22.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +...++|.|+||+||||++..+...+
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHh
Confidence            45678999999999999988887654

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=97.89  E-value=9.1e-06  Score=50.73  Aligned_cols=26  Identities=19%  Similarity=0.212  Sum_probs=22.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +..++|.|+||+||||++..+...+-
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L~~~l~   29 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLLKDWIE   29 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            34688999999999999999888763

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=97.89  E-value=1.2e-05  Score=56.46  Aligned_cols=34  Identities=21%  Similarity=0.294  Sum_probs=28.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      .+++.|++|+||||++..++..+...       +.+++++.
T Consensus       101 vI~ivG~~GvGKTTla~~La~~l~~~-------G~kVllv~  134 (432)
T 2v3c_C          101 VILLVGIQGSGKTTTAAKLARYIQKR-------GLKPALIA  134 (432)
T ss_dssp             CEEEECCSSSSTTHHHHHHHHHHHHH-------HCCEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc-------CCeEEEEe
Confidence            68899999999999999999988765       56777665

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=97.89  E-value=1.2e-05  Score=54.57  Aligned_cols=45  Identities=20%  Similarity=0.162  Sum_probs=30.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCCh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN   79 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~   79 (97)
                      +..++|.||||+|||+++..++........ .+..+.++++++...
T Consensus       122 G~i~~I~G~~GsGKTtla~~la~~~~~~~~-~gg~~~~vlyi~~E~  166 (343)
T 1v5w_A          122 MAITEAFGEFRTGKTQLSHTLCVTAQLPGA-GGYPGGKIIFIDTEN  166 (343)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBT-TTBCCCEEEEEESSS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhcccc-cCCCCCeEEEEECCC
Confidence            347899999999999999998877543210 001245677776543

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=97.88  E-value=1.1e-05  Score=50.02  Aligned_cols=24  Identities=42%  Similarity=0.498  Sum_probs=21.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +..++|+|+|||||||++..+...
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            457899999999999999888776

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=97.88  E-value=1.6e-05  Score=49.19  Aligned_cols=26  Identities=31%  Similarity=0.547  Sum_probs=22.2

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ....++|.|+||+||||++..+...+
T Consensus        11 ~~~~I~l~G~~GsGKsT~a~~L~~~l   36 (199)
T 2bwj_A           11 KCKIIFIIGGPGSGKGTQCEKLVEKY   36 (199)
T ss_dssp             HSCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHh
Confidence            45678999999999999998887664

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=97.88  E-value=2e-05  Score=54.19  Aligned_cols=37  Identities=32%  Similarity=0.366  Sum_probs=29.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +..++|.||||+|||+++..++..+...       +.+++++..
T Consensus        74 G~li~I~G~pGsGKTtlal~la~~~~~~-------g~~vlyi~~  110 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLALAIVAQAQKA-------GGTCAFIDA  110 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHT-------TCCEEEEES
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHHHHC-------CCeEEEEEC
Confidence            4578999999999999999999888665       456666654

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=97.88  E-value=1.9e-05  Score=52.75  Aligned_cols=26  Identities=31%  Similarity=0.367  Sum_probs=22.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      ...++|.||||||||+++..+.....
T Consensus        25 ~~~vLi~Ge~GtGKt~lAr~i~~~~~   50 (304)
T 1ojl_A           25 DATVLIHGDSGTGKELVARALHACSA   50 (304)
T ss_dssp             TSCEEEESCTTSCHHHHHHHHHHHSS
T ss_pred             CCcEEEECCCCchHHHHHHHHHHhCc
Confidence            46899999999999999988877653

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=97.87  E-value=7.6e-06  Score=51.63  Aligned_cols=22  Identities=41%  Similarity=0.566  Sum_probs=18.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +++|.||||+||||++..++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEK   23 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999998888654

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=97.87  E-value=1.7e-05  Score=52.14  Aligned_cols=29  Identities=17%  Similarity=0.414  Sum_probs=24.1

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ..++.+.|.||+|+||||++..++..+..
T Consensus        23 ~~g~~v~i~Gp~GsGKSTll~~l~g~~~~   51 (261)
T 2eyu_A           23 RKMGLILVTGPTGSGKSTTIASMIDYINQ   51 (261)
T ss_dssp             CSSEEEEEECSTTCSHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCccHHHHHHHHHHhCCC
Confidence            35678999999999999998888876643

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=97.87  E-value=1.2e-05  Score=49.54  Aligned_cols=24  Identities=38%  Similarity=0.612  Sum_probs=20.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.|+||+||||++..+...+
T Consensus         4 ~~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            4 LVVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            467899999999999988886654

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=97.87  E-value=3.6e-05  Score=51.19  Aligned_cols=43  Identities=16%  Similarity=0.213  Sum_probs=34.9

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...+.-++.+.+.+.. ...+.++|.||+|+|||+++..++..+
T Consensus        12 ~~~~~gR~~el~~L~~-l~~~~v~i~G~~G~GKT~L~~~~~~~~   54 (357)
T 2fna_A           12 RKDFFDREKEIEKLKG-LRAPITLVLGLRRTGKSSIIKIGINEL   54 (357)
T ss_dssp             GGGSCCCHHHHHHHHH-TCSSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             HHHhcChHHHHHHHHH-hcCCcEEEECCCCCCHHHHHHHHHHhc
Confidence            3456667888888887 765789999999999999998887764

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=97.86  E-value=2.1e-05  Score=57.96  Aligned_cols=61  Identities=16%  Similarity=0.216  Sum_probs=49.5

Q ss_pred             CCCHHHHHHHHHHhc--CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         19 GLNTIQFEAYKAALT--REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~--~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      .++..|.+++.....  .+..+|+|+.|.|||+++-..+..+.          .+++|++|+..++..+.+-.
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a~~~----------~~~~vtAP~~~a~~~l~~~~  237 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLISRIA----------GRAIVTAPAKASTDVLAQFA  237 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHHHSS----------SCEEEECSSCCSCHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHHHHH----------hCcEEECCCHHHHHHHHHHh
Confidence            568899999998776  56789999999999988777776652          34799999999998877654

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=97.86  E-value=1e-05  Score=50.43  Aligned_cols=26  Identities=35%  Similarity=0.526  Sum_probs=22.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..+.|.||+|+||||++..+...+
T Consensus         5 ~g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            5 KGLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            45688999999999999988877655

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=97.86  E-value=1.2e-05  Score=51.28  Aligned_cols=23  Identities=35%  Similarity=0.603  Sum_probs=19.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.||||+||+|.+..++..+
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~   24 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEK   24 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            36889999999999988886554

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=97.86  E-value=1.4e-05  Score=48.44  Aligned_cols=24  Identities=25%  Similarity=0.374  Sum_probs=20.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.|+||+||||++..+...+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~l   26 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARAL   26 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            368899999999999998887654

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=97.85  E-value=1.4e-05  Score=50.22  Aligned_cols=25  Identities=20%  Similarity=0.507  Sum_probs=21.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+.|.||+|+||||++..+....
T Consensus         4 g~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            4 PRPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             -CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            5678999999999999988887754

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=97.85  E-value=1e-05  Score=51.00  Aligned_cols=26  Identities=23%  Similarity=0.577  Sum_probs=22.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +..+.|.||+|+||||++..+...+-
T Consensus        22 g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           22 RQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            35788999999999999888877764

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=97.85  E-value=2.3e-05  Score=52.94  Aligned_cols=35  Identities=23%  Similarity=0.337  Sum_probs=28.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ..+++.||+|+||||++..++..+...       +.+++++.
T Consensus       106 ~vI~ivG~~G~GKTT~~~~LA~~l~~~-------g~kVllid  140 (320)
T 1zu4_A          106 NIFMLVGVNGTGKTTSLAKMANYYAEL-------GYKVLIAA  140 (320)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHC-------CCeEEEEe
Confidence            467899999999999999998887654       66777765

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=97.85  E-value=1.3e-05  Score=49.75  Aligned_cols=23  Identities=26%  Similarity=0.385  Sum_probs=20.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.|++|+||||++..+...+
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l   24 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKL   24 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHhc
Confidence            47899999999999999888765

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=97.85  E-value=1.5e-05  Score=50.54  Aligned_cols=25  Identities=36%  Similarity=0.571  Sum_probs=21.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+++.|+||+||||++..++..+
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~l   28 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQERF   28 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc
Confidence            3468999999999999998887654

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=97.84  E-value=1.3e-05  Score=50.06  Aligned_cols=24  Identities=33%  Similarity=0.660  Sum_probs=20.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.|+||+||||++..+...+
T Consensus        21 ~~I~l~G~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           21 MRVLLLGPPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            368899999999999988887654

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=97.84  E-value=1.5e-05  Score=51.40  Aligned_cols=25  Identities=48%  Similarity=0.755  Sum_probs=21.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...++|.||+|+||||++..++..+
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999998887443

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=97.83  E-value=1.2e-05  Score=51.62  Aligned_cols=24  Identities=29%  Similarity=0.601  Sum_probs=20.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.++|.||||+||+|.+..++..+
T Consensus        30 kiI~llGpPGsGKgTqa~~L~~~~   53 (217)
T 3umf_A           30 KVIFVLGGPGSGKGTQCEKLVQKF   53 (217)
T ss_dssp             EEEEEECCTTCCHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHH
Confidence            467889999999999988886554

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=97.83  E-value=1.4e-05  Score=50.05  Aligned_cols=27  Identities=22%  Similarity=0.341  Sum_probs=22.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +..++|.|++|+||||++..+...+-.
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l~~   36 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYLKN   36 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            457899999999999999988877643

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=97.83  E-value=3.2e-05  Score=48.38  Aligned_cols=28  Identities=18%  Similarity=0.372  Sum_probs=23.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..++|.|++|+||||++..+...+-..
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l~~~   36 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEALCAA   36 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            4578999999999999999988877443

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=97.82  E-value=3.4e-05  Score=47.42  Aligned_cols=25  Identities=28%  Similarity=0.389  Sum_probs=21.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .++|.|++|+||||++..+...+..
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~~   26 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLKQ   26 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4689999999999999988887643

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=97.81  E-value=1.4e-05  Score=50.70  Aligned_cols=24  Identities=25%  Similarity=0.338  Sum_probs=21.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.||||+||||++..++..+
T Consensus         6 ~~I~l~G~~GsGKsT~~~~La~~l   29 (222)
T 1zak_A            6 LKVMISGAPASGKGTQCELIKTKY   29 (222)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999887765

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=97.81  E-value=1.7e-05  Score=49.96  Aligned_cols=28  Identities=25%  Similarity=0.417  Sum_probs=22.8

Q ss_pred             HhcCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         31 ALTREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        31 ~~~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..++.+.|.||+|+||||++..++..+
T Consensus        17 i~~Gei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           17 AAVGRVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             --CCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3567899999999999999988887665

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=97.80  E-value=2.8e-05  Score=53.39  Aligned_cols=36  Identities=19%  Similarity=0.270  Sum_probs=28.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ..+.+.||+|+||||++..++..+...       +.+|++...
T Consensus       158 ~vi~lvG~nGsGKTTll~~Lag~l~~~-------~G~V~l~g~  193 (359)
T 2og2_A          158 AVIMIVGVNGGGKTTSLGKLAHRLKNE-------GTKVLMAAG  193 (359)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHHT-------TCCEEEECC
T ss_pred             eEEEEEcCCCChHHHHHHHHHhhcccc-------CCEEEEecc
Confidence            467899999999999998888877544       567777653

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=97.80  E-value=2.3e-05  Score=53.87  Aligned_cols=29  Identities=17%  Similarity=0.445  Sum_probs=24.3

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .++.++|.||+|+||||++..++..+...
T Consensus       135 ~g~~i~ivG~~GsGKTTll~~l~~~~~~~  163 (372)
T 2ewv_A          135 KMGLILVTGPTGSGKSTTIASMIDYINQT  163 (372)
T ss_dssp             SSEEEEEECSSSSSHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhcCcC
Confidence            45689999999999999999988876543

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=97.80  E-value=1.6e-05  Score=57.17  Aligned_cols=25  Identities=36%  Similarity=0.643  Sum_probs=22.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+++.||||||||+++..++..+
T Consensus       108 g~~vll~Gp~GtGKTtlar~ia~~l  132 (543)
T 3m6a_A          108 GPILCLAGPPGVGKTSLAKSIAKSL  132 (543)
T ss_dssp             SCEEEEESSSSSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhc
Confidence            4579999999999999999998877

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.79  E-value=4.6e-05  Score=56.46  Aligned_cols=43  Identities=19%  Similarity=0.342  Sum_probs=32.2

Q ss_pred             CCCCHHHHHHHHHHhc---CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         18 LGLNTIQFEAYKAALT---REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~---~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +.-++...+.+..+..   ..++++.||||||||+++..++..+..
T Consensus       182 iiG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~la~~la~~l~~  227 (758)
T 3pxi_A          182 VIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIIN  227 (758)
T ss_dssp             CCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHS
T ss_pred             ccCchHHHHHHHHHHhCCCCCCeEEECCCCCCHHHHHHHHHHHHhc
Confidence            3345556655555542   358999999999999999999988754

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=97.79  E-value=1.5e-05  Score=48.92  Aligned_cols=23  Identities=35%  Similarity=0.627  Sum_probs=19.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.|+||+||||++..+...+
T Consensus         8 ~I~l~G~~GsGKsT~~~~L~~~l   30 (194)
T 1qf9_A            8 VVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            67899999999999988887654

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=97.79  E-value=2e-05  Score=49.85  Aligned_cols=24  Identities=29%  Similarity=0.556  Sum_probs=20.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+.|.||+|+||||++..+...+
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~   29 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEAL   29 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            468899999999999988887654

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=97.79  E-value=1e-05  Score=49.99  Aligned_cols=22  Identities=36%  Similarity=0.690  Sum_probs=19.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ..++|.||+|+||||++..++.
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhc
Confidence            3578999999999999888865

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=97.78  E-value=1.8e-05  Score=56.22  Aligned_cols=24  Identities=38%  Similarity=0.600  Sum_probs=21.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus        50 ~gvLL~GppGtGKT~Laraia~~~   73 (476)
T 2ce7_A           50 KGILLVGPPGTGKTLLARAVAGEA   73 (476)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHc
Confidence            358999999999999999998765

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=97.78  E-value=4.1e-05  Score=46.96  Aligned_cols=26  Identities=27%  Similarity=0.363  Sum_probs=22.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +..+++.|++|+||||++..+...+.
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~l~   30 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEYLV   30 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHh
Confidence            45788999999999999988887763

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=97.78  E-value=2e-05  Score=49.94  Aligned_cols=23  Identities=30%  Similarity=0.612  Sum_probs=18.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++|+||||||+.+..++...
T Consensus         7 i~l~tG~pGsGKT~~a~~~~~~~   29 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKMVSMMAND   29 (199)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHH
Confidence            56899999999999987765554

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=97.78  E-value=1.9e-05  Score=50.63  Aligned_cols=24  Identities=38%  Similarity=0.697  Sum_probs=21.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++++.|+||+||||++..++..+
T Consensus        17 ~~I~l~G~~GsGKsT~a~~La~~l   40 (233)
T 1ak2_A           17 VRAVLLGPPGAGKGTQAPKLAKNF   40 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999887665

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=97.78  E-value=1.8e-05  Score=51.18  Aligned_cols=24  Identities=29%  Similarity=0.461  Sum_probs=20.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.||||+||||++..+...+
T Consensus        30 ~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           30 GRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            368999999999999998887654

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=97.78  E-value=2e-05  Score=47.61  Aligned_cols=23  Identities=17%  Similarity=0.143  Sum_probs=19.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.|+||+||||++..+...+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l   24 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSL   24 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999988887654

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=97.78  E-value=2.2e-05  Score=49.32  Aligned_cols=24  Identities=29%  Similarity=0.620  Sum_probs=20.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.++|.||+|+|||+++..++...
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~   25 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC
Confidence            468999999999999988776654

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=97.77  E-value=6.5e-05  Score=50.25  Aligned_cols=35  Identities=26%  Similarity=0.242  Sum_probs=28.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+++.|++|+||||++..++..+...       +.+++++..
T Consensus       100 vi~i~G~~G~GKTT~~~~la~~~~~~-------g~~v~l~~~  134 (297)
T 1j8m_F          100 VIMLVGVQGTGKTTTAGKLAYFYKKK-------GFKVGLVGA  134 (297)
T ss_dssp             EEEEECSSCSSTTHHHHHHHHHHHHT-------TCCEEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-------CCeEEEEec
Confidence            56789999999999999998887654       667777664

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=97.77  E-value=5.9e-05  Score=53.83  Aligned_cols=52  Identities=23%  Similarity=0.414  Sum_probs=36.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      .+..++|.||+|+|||+++..++......       +.+++++++... ..++..+..++
T Consensus       280 ~G~i~~i~G~~GsGKSTLl~~l~g~~~~~-------G~~vi~~~~ee~-~~~l~~~~~~~  331 (525)
T 1tf7_A          280 KDSIILATGATGTGKTLLVSRFVENACAN-------KERAILFAYEES-RAQLLRNAYSW  331 (525)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHHHTT-------TCCEEEEESSSC-HHHHHHHHHTT
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHhC-------CCCEEEEEEeCC-HHHHHHHHHHc
Confidence            35688999999999999999888776543       556766665432 34555555443

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=97.77  E-value=2e-05  Score=50.25  Aligned_cols=26  Identities=27%  Similarity=0.468  Sum_probs=22.5

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..+.|.||+|+||||++..++...
T Consensus        22 ~G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           22 NIYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            46789999999999999988887754

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=97.77  E-value=1.4e-05  Score=53.16  Aligned_cols=23  Identities=35%  Similarity=0.518  Sum_probs=19.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||+||||++..+...+
T Consensus        35 livl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           35 AFLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             EEEEECCTTSCTHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999988887654

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=97.77  E-value=4.6e-05  Score=52.32  Aligned_cols=41  Identities=20%  Similarity=0.255  Sum_probs=33.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNH   80 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~   80 (97)
                      .+++++|.||+|+|||+++..++..+...       +.+++++=|.++
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~~~~~-------~~~~~~~D~~~~   74 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLREYMQ-------GSRVIIIDPERE   74 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHHHTT-------TCCEEEEESSCC
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHHHHHC-------CCEEEEEeCCcC
Confidence            46789999999999999999998887654       567777766543

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=97.76  E-value=1.8e-05  Score=50.00  Aligned_cols=23  Identities=35%  Similarity=0.423  Sum_probs=19.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++|.|+||+||||++..+...+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKY   24 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999998887654

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=97.76  E-value=7.6e-05  Score=49.57  Aligned_cols=43  Identities=12%  Similarity=0.161  Sum_probs=33.7

Q ss_pred             ccCCCCCHHHHHHHHHHhc-CCceEEeCCCCCchHHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALT-REFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~-~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      ...+.-++.+.+.+..+.. ++.++|.||+|+|||+++..++..
T Consensus        11 ~~~~~gR~~el~~L~~~l~~~~~v~i~G~~G~GKT~Ll~~~~~~   54 (350)
T 2qen_A           11 REDIFDREEESRKLEESLENYPLTLLLGIRRVGKSSLLRAFLNE   54 (350)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             hHhcCChHHHHHHHHHHHhcCCeEEEECCCcCCHHHHHHHHHHH
Confidence            3456667888888777664 578999999999999998887654

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=97.75  E-value=6e-05  Score=47.51  Aligned_cols=38  Identities=11%  Similarity=0.163  Sum_probs=27.7

Q ss_pred             CHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         21 NTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        21 ~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      ...++.... ...+..+++.|++|+||||++..+...+-
T Consensus        13 ~~~~r~~~~-~~~~~~i~~~G~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           13 TRSERTELR-NQRGLTIWLTGLSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             CHHHHHHHH-TSSCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CHHHhhccc-CCCCCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            444444422 23456788999999999999998888775

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=97.75  E-value=3.4e-05  Score=55.17  Aligned_cols=39  Identities=21%  Similarity=0.118  Sum_probs=29.5

Q ss_pred             CCHHHHHHHHHHh-cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         20 LNTIQFEAYKAAL-TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        20 l~~~Q~~~i~~~~-~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++......+.... .+.+++|.||+|+||||++..++..+
T Consensus       245 ~~~~~l~~l~~~v~~g~~i~I~GptGSGKTTlL~aL~~~i  284 (511)
T 2oap_1          245 VPSGVLAYLWLAIEHKFSAIVVGETASGKTTTLNAIMMFI  284 (511)
T ss_dssp             SCHHHHHHHHHHHHTTCCEEEEESTTSSHHHHHHHHGGGS
T ss_pred             CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            4555556666544 45689999999999999988877655

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=97.74  E-value=6.2e-05  Score=47.77  Aligned_cols=38  Identities=21%  Similarity=0.260  Sum_probs=33.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      .+.++|.+++|.||||.+..++..+...       +.+|+|+.+-
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~-------G~rV~~vQF~   65 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGH-------GKNVGVVQFI   65 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHT-------TCCEEEEESS
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHC-------CCeEEEEEee
Confidence            5789999999999999999999999887       8899999653

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=97.74  E-value=4.1e-05  Score=48.04  Aligned_cols=27  Identities=22%  Similarity=0.235  Sum_probs=22.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+.|.||+|+||||++..+...+...
T Consensus        23 ~~i~i~G~~GsGKstl~~~l~~~~~~~   49 (201)
T 1rz3_A           23 LVLGIDGLSRSGKTTLANQLSQTLREQ   49 (201)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhc
Confidence            468899999999999988887766443

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=97.74  E-value=0.00016  Score=54.31  Aligned_cols=41  Identities=20%  Similarity=0.314  Sum_probs=30.2

Q ss_pred             CCHHHHHHHHHHhc---CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         20 LNTIQFEAYKAALT---REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        20 l~~~Q~~~i~~~~~---~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      -++.....+..+..   ..++++.||||||||+++..++..+..
T Consensus       174 Gr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la~~la~~l~~  217 (854)
T 1qvr_A          174 GRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVK  217 (854)
T ss_dssp             SCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhc
Confidence            34445444444442   347899999999999999999998865

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=97.74  E-value=4e-05  Score=51.68  Aligned_cols=26  Identities=23%  Similarity=0.324  Sum_probs=23.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+++.||+|+|||+++..++..+...
T Consensus        26 a~L~~G~~G~GKt~~a~~la~~l~~~   51 (334)
T 1a5t_A           26 ALLIQALPGMGDDALIYALSRYLLCQ   51 (334)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTCS
T ss_pred             eEEEECCCCchHHHHHHHHHHHHhCC
Confidence            48999999999999999999988654

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=97.74  E-value=2.4e-05  Score=49.93  Aligned_cols=23  Identities=26%  Similarity=0.442  Sum_probs=19.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.|+||+||||++..+...+
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~l   24 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKY   24 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999988887665

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=97.74  E-value=1.6e-05  Score=49.50  Aligned_cols=25  Identities=24%  Similarity=0.442  Sum_probs=21.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..++|.|++|+||||++..+...+
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHTS
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4578999999999999988887765

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=97.74  E-value=1.3e-05  Score=49.15  Aligned_cols=25  Identities=36%  Similarity=0.470  Sum_probs=16.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...++|.|+||+||||++..+...+
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~l   29 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHERL   29 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhc
Confidence            3468899999999999988886654

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=97.74  E-value=1.7e-05  Score=50.49  Aligned_cols=25  Identities=44%  Similarity=0.618  Sum_probs=20.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...++|.|+||+||||++..++..+
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc
Confidence            3578999999999999988887543

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=97.73  E-value=2.6e-05  Score=58.48  Aligned_cols=24  Identities=38%  Similarity=0.602  Sum_probs=20.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||.++.+++..+
T Consensus       512 ~gvLl~GPPGtGKT~lAkaiA~e~  535 (806)
T 3cf2_A          512 KGVLFYGPPGCGKTLLAKAIANEC  535 (806)
T ss_dssp             SCCEEESSTTSSHHHHHHHHHHTT
T ss_pred             ceEEEecCCCCCchHHHHHHHHHh
Confidence            358999999999999999997765

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=97.73  E-value=2.6e-05  Score=49.40  Aligned_cols=24  Identities=29%  Similarity=0.434  Sum_probs=20.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.|+||+||||++..++..+
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l   29 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEY   29 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            468899999999999998887655

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=97.73  E-value=4.2e-05  Score=54.69  Aligned_cols=35  Identities=17%  Similarity=0.338  Sum_probs=28.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ..+.|.||+|+||||++..++..+...       +.+|++..
T Consensus       294 eVI~LVGpNGSGKTTLl~~LAgll~~~-------~G~V~l~g  328 (503)
T 2yhs_A          294 FVILMVGVNGVGKTTTIGKLARQFEQQ-------GKSVMLAA  328 (503)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHT-------TCCEEEEC
T ss_pred             eEEEEECCCcccHHHHHHHHHHHhhhc-------CCeEEEec
Confidence            468899999999999988888776443       67788763

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=97.73  E-value=2.7e-05  Score=49.37  Aligned_cols=26  Identities=15%  Similarity=0.356  Sum_probs=22.2

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..++|.||+|+|||+++..++...
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~~   43 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQN   43 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhhC
Confidence            46788999999999999988887654

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=97.72  E-value=2.2e-05  Score=55.36  Aligned_cols=24  Identities=33%  Similarity=0.509  Sum_probs=21.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++++.||||||||+++..++..+
T Consensus        51 ~~iLl~GppGtGKT~lar~lA~~l   74 (444)
T 1g41_A           51 KNILMIGPTGVGKTEIARRLAKLA   74 (444)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHc
Confidence            579999999999999999988776

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=97.72  E-value=2.2e-05  Score=52.58  Aligned_cols=25  Identities=20%  Similarity=0.280  Sum_probs=21.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..++|.||||+|||+++..++...
T Consensus        98 g~i~~i~G~~gsGKT~la~~la~~~  122 (322)
T 2i1q_A           98 QSVTEFAGVFGSGKTQIMHQSCVNL  122 (322)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3578999999999999999988764

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.72  E-value=3.8e-05  Score=56.85  Aligned_cols=26  Identities=35%  Similarity=0.529  Sum_probs=23.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++++.||||||||+++.+++..+...
T Consensus       523 ~~Ll~Gp~GtGKT~lA~ala~~l~~~  548 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELARALAESIFGD  548 (758)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcCC
Confidence            59999999999999999999888543

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=97.72  E-value=2.9e-05  Score=49.78  Aligned_cols=26  Identities=19%  Similarity=0.411  Sum_probs=22.1

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..++|.||+|+||||++..++...
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g~~   40 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLKTQ   40 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhccC
Confidence            46789999999999999988877654

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=97.71  E-value=0.00012  Score=52.43  Aligned_cols=35  Identities=17%  Similarity=0.355  Sum_probs=29.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+++.|+||+||||++..++..+...       +.++++++.
T Consensus       103 vI~ivG~~GvGKTTl~~kLA~~l~~~-------G~kVllVd~  137 (504)
T 2j37_W          103 VIMFVGLQGSGKTTTCSKLAYYYQRK-------GWKTCLICA  137 (504)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhC-------CCeEEEEec
Confidence            57889999999999999999888655       667777664

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=97.71  E-value=5.1e-05  Score=51.50  Aligned_cols=28  Identities=21%  Similarity=0.138  Sum_probs=23.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..+.|.||||+||||++..++..+...
T Consensus        55 g~~v~i~G~~GaGKSTLl~~l~g~~~~~   82 (337)
T 2qm8_A           55 AIRVGITGVPGVGKSTTIDALGSLLTAA   82 (337)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhhhhC
Confidence            4578999999999999999888776543

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=97.71  E-value=3.5e-05  Score=48.38  Aligned_cols=25  Identities=32%  Similarity=0.577  Sum_probs=21.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +.+.+.||+|+||||++..++..+.
T Consensus         2 ~~i~i~G~nG~GKTTll~~l~g~~~   26 (189)
T 2i3b_A            2 RHVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCChHHHHHHHHHhhcc
Confidence            5688999999999999888887765

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=97.71  E-value=1.5e-05  Score=48.88  Aligned_cols=21  Identities=24%  Similarity=0.509  Sum_probs=18.2

Q ss_pred             cCCceEEeCCCCCchHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALR   53 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~   53 (97)
                      .++.+.+.||+|+||||++..
T Consensus         8 ~gei~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHH
Confidence            356789999999999999883

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=97.70  E-value=7.6e-05  Score=46.35  Aligned_cols=27  Identities=19%  Similarity=0.288  Sum_probs=22.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +.++|.|++|+||||++..++..+...
T Consensus         7 ~~i~i~G~sGsGKTTl~~~l~~~l~~~   33 (174)
T 1np6_A            7 PLLAFAAWSGTGKTTLLKKLIPALCAR   33 (174)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhcccc
Confidence            568899999999999999998876543

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=97.70  E-value=2.1e-05  Score=49.08  Aligned_cols=22  Identities=27%  Similarity=0.528  Sum_probs=19.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++|.|++|+||||++..+...
T Consensus        17 ~I~l~G~~GsGKsT~~~~L~~~   38 (203)
T 1ukz_A           17 VIFVLGGPGAGKGTQCEKLVKD   38 (203)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6789999999999998888654

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=97.70  E-value=1.9e-05  Score=49.84  Aligned_cols=27  Identities=22%  Similarity=0.223  Sum_probs=22.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ++.+.|.||+|+||||++..++..+..
T Consensus        25 G~~~~l~G~nGsGKSTll~~l~g~~~~   51 (231)
T 4a74_A           25 QAITEVFGEFGSGKTQLAHTLAVMVQL   51 (231)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhc
Confidence            568899999999999999888875543

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=97.70  E-value=2.7e-05  Score=55.40  Aligned_cols=24  Identities=38%  Similarity=0.629  Sum_probs=20.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.||||||||+++.+++..+
T Consensus       239 ~~vLL~GppGtGKT~lAraia~~~  262 (489)
T 3hu3_A          239 RGILLYGPPGTGKTLIARAVANET  262 (489)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             CcEEEECcCCCCHHHHHHHHHHHh
Confidence            468999999999999999886653

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=97.69  E-value=2.4e-05  Score=49.08  Aligned_cols=25  Identities=24%  Similarity=0.235  Sum_probs=21.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+.|.||+|+||||++..+...+
T Consensus         6 ~~~i~i~G~~GsGKSTl~~~l~~~~   30 (211)
T 3asz_A            6 PFVIGIAGGTASGKTTLAQALARTL   30 (211)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHh
Confidence            4578899999999999988887765

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=97.69  E-value=6.8e-05  Score=52.06  Aligned_cols=43  Identities=21%  Similarity=0.281  Sum_probs=35.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALD   83 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~   83 (97)
                      ..+++|.|+||+|||+++..++..++..       +.+++|+=|..+...
T Consensus        53 ~~h~~i~G~tGsGKs~~~~~li~~~~~~-------g~~viv~Dpkge~~~   95 (437)
T 1e9r_A           53 PRHLLVNGATGTGKSVLLRELAYTGLLR-------GDRMVIVDPNGDMLS   95 (437)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHHT-------TCEEEEEEETTHHHH
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHHHHC-------CCcEEEEeCCCchhH
Confidence            3578999999999999988888888776       667888888777654

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=97.69  E-value=9e-05  Score=54.79  Aligned_cols=40  Identities=20%  Similarity=0.298  Sum_probs=30.5

Q ss_pred             CHHHHHHHHHHhc---CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         21 NTIQFEAYKAALT---REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        21 ~~~Q~~~i~~~~~---~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ++.+.+.+..+..   ..++++.||||||||+++..++..+..
T Consensus       191 r~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~la~~la~~l~~  233 (758)
T 1r6b_X          191 REKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQ  233 (758)
T ss_dssp             CHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHHHHHHHHHHHh
Confidence            5555555555443   358999999999999999999988754

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=97.69  E-value=4.3e-05  Score=50.03  Aligned_cols=25  Identities=24%  Similarity=0.289  Sum_probs=22.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..++|.|++|+||||++..++..+
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~~l   72 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMARSL   72 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhc
Confidence            7899999999999999988887644

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=97.68  E-value=6.4e-05  Score=51.21  Aligned_cols=35  Identities=17%  Similarity=0.263  Sum_probs=28.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+.|.|+||+|||+++..++..+...       +.+++++..
T Consensus        81 ~I~i~G~~G~GKSTl~~~L~~~l~~~-------g~kV~vi~~  115 (355)
T 3p32_A           81 RVGITGVPGVGKSTAIEALGMHLIER-------GHRVAVLAV  115 (355)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTT-------TCCEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhC-------CCceEEEec
Confidence            68899999999999999999887655       566666653

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=97.67  E-value=2.3e-05  Score=55.97  Aligned_cols=23  Identities=35%  Similarity=0.554  Sum_probs=20.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||||||+++.+++..+
T Consensus        66 GvLL~GppGtGKTtLaraIa~~~   88 (499)
T 2dhr_A           66 GVLLVGPPGVGKTHLARAVAGEA   88 (499)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47999999999999999987654

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=97.67  E-value=1.7e-05  Score=51.60  Aligned_cols=23  Identities=26%  Similarity=0.398  Sum_probs=20.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.|+||+||||++..+...+
T Consensus        34 ~i~l~G~~GsGKSTla~~L~~~l   56 (253)
T 2p5t_B           34 AILLGGQSGAGKTTIHRIKQKEF   56 (253)
T ss_dssp             EEEEESCGGGTTHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            67899999999999998887765

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=97.66  E-value=8.6e-05  Score=47.70  Aligned_cols=39  Identities=15%  Similarity=0.026  Sum_probs=31.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNH   80 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~   80 (97)
                      ...+++||.|+|||+.+..++..+...       +++++++.|...
T Consensus        29 ~l~vitG~MgsGKTT~lL~~a~r~~~~-------g~kVli~k~~~d   67 (214)
T 2j9r_A           29 WIEVICGSMFSGKSEELIRRVRRTQFA-------KQHAIVFKPCID   67 (214)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHHHT-------TCCEEEEECC--
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHC-------CCEEEEEEeccC
Confidence            456789999999999999998888666       789999987543

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=97.64  E-value=2e-05  Score=50.31  Aligned_cols=25  Identities=28%  Similarity=0.466  Sum_probs=15.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHH-HHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIV-EGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~-~~~   58 (97)
                      +..+.|.||+|+||||++..++ ..+
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC---
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            5678999999999999988887 543

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=97.63  E-value=3.9e-05  Score=52.22  Aligned_cols=26  Identities=23%  Similarity=0.548  Sum_probs=22.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.|.||||+|||+++..++..+.+.
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~   55 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQ   55 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            67999999999999999998887654

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=97.63  E-value=6.7e-05  Score=54.40  Aligned_cols=34  Identities=29%  Similarity=0.517  Sum_probs=26.2

Q ss_pred             HHHHHHHh-cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         25 FEAYKAAL-TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        25 ~~~i~~~~-~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+.+.... .+..+++.||||||||+++..++..+
T Consensus        50 l~~l~~~i~~g~~vll~Gp~GtGKTtlar~ia~~l   84 (604)
T 3k1j_A           50 VEVIKTAANQKRHVLLIGEPGTGKSMLGQAMAELL   84 (604)
T ss_dssp             HHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHTS
T ss_pred             HhhccccccCCCEEEEEeCCCCCHHHHHHHHhccC
Confidence            33444433 46799999999999999999888765

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=97.62  E-value=3.6e-05  Score=48.15  Aligned_cols=21  Identities=29%  Similarity=0.387  Sum_probs=18.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+.|.||+|+||||++..+..
T Consensus         4 ~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999888754

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=97.61  E-value=9e-05  Score=50.49  Aligned_cols=27  Identities=22%  Similarity=0.276  Sum_probs=22.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+.|.|+||+||||++..++..+...
T Consensus        75 ~~v~lvG~pgaGKSTLln~L~~~~~~~  101 (349)
T 2www_A           75 FRVGLSGPPGAGKSTFIEYFGKMLTER  101 (349)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHhhhc
Confidence            468899999999999999998876544

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=97.61  E-value=2e-05  Score=59.11  Aligned_cols=24  Identities=38%  Similarity=0.629  Sum_probs=20.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus       239 ~GILL~GPPGTGKT~LAraiA~el  262 (806)
T 3cf2_A          239 RGILLYGPPGTGKTLIARAVANET  262 (806)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHTTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh
Confidence            358999999999999999887554

>3bs4_A Uncharacterized protein PH0321; structural genomics, unknown function, PSI-2, protein struct initiative; 1.60A {Pyrococcus horikoshii}

Probab=97.61  E-value=6.1e-05  Score=49.69  Aligned_cols=53  Identities=9%  Similarity=0.109  Sum_probs=42.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      ..++|.|+||+|||+++...+...+++       +.++++++. .+...++.++.+.++-+
T Consensus        22 s~~li~g~p~~~~~~l~~qfl~~g~~~-------Ge~~~~~~~-~e~~~~l~~~~~~~G~d   74 (260)
T 3bs4_A           22 LILIHEEDASSRGKDILFYILSRKLKS-------DNLVGMFSI-SYPLQLIIRILSRFGVD   74 (260)
T ss_dssp             EEEEEECSGGGCHHHHHHHHHHHHHHT-------TCEEEEEEC-SSCHHHHHHHHHHTTCC
T ss_pred             cEEEEEeCCCccHHHHHHHHHHHHHHC-------CCcEEEEEE-eCCHHHHHHHHHHcCCC
Confidence            467888999999999999998888877       778888885 55577888888777643

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=97.60  E-value=5.1e-05  Score=51.08  Aligned_cols=26  Identities=23%  Similarity=0.488  Sum_probs=22.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..++..+
T Consensus       125 ~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          125 KKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             TCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            36788999999999999988887765

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=97.60  E-value=9e-05  Score=49.45  Aligned_cols=36  Identities=22%  Similarity=0.291  Sum_probs=28.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ..+.+.|++|+||||++..++..+...       +.++++...
T Consensus        99 ~~i~i~g~~G~GKTT~~~~la~~~~~~-------~~~v~l~~~  134 (295)
T 1ls1_A           99 NLWFLVGLQGSGKTTTAAKLALYYKGK-------GRRPLLVAA  134 (295)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHHHHHT-------TCCEEEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc-------CCeEEEecC
Confidence            467788999999999999998887554       667777653

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=97.60  E-value=3.8e-05  Score=47.91  Aligned_cols=21  Identities=33%  Similarity=0.287  Sum_probs=18.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+.|.|++|+||||++..+..
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHH
Confidence            478999999999999888765

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=97.60  E-value=3.7e-05  Score=47.00  Aligned_cols=26  Identities=23%  Similarity=0.454  Sum_probs=22.8

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..+.+.||.|+||||++..++..+
T Consensus        32 ~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           32 KAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            35688999999999999999888877

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=97.60  E-value=4.5e-05  Score=49.58  Aligned_cols=23  Identities=26%  Similarity=0.527  Sum_probs=20.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +..+.|.||+|+||||++..++.
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~   49 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAE   49 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46789999999999999988873

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=97.59  E-value=0.00015  Score=46.26  Aligned_cols=29  Identities=28%  Similarity=0.440  Sum_probs=24.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++..+++.|++|+||||.+..+...+...
T Consensus         5 ~g~~i~~eG~~gsGKsT~~~~l~~~l~~~   33 (213)
T 4edh_A            5 TGLFVTLEGPEGAGKSTNRDYLAERLRER   33 (213)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHTT
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            45578899999999999999988887554

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=97.58  E-value=0.00012  Score=51.47  Aligned_cols=36  Identities=19%  Similarity=0.282  Sum_probs=29.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+++.|++|+||||++..++..+...      .+.+++++..
T Consensus       102 vI~ivG~~GvGKTT~a~~LA~~l~~~------~G~kVllvd~  137 (433)
T 2xxa_A          102 VVLMAGLQGAGKTTSVGKLGKFLREK------HKKKVLVVSA  137 (433)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT------SCCCEEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHh------cCCeEEEEec
Confidence            56778999999999999999888664      2677877664

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=97.57  E-value=7.7e-05  Score=56.02  Aligned_cols=26  Identities=27%  Similarity=0.466  Sum_probs=23.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+++.||||||||+++..+...+...
T Consensus       590 ~vLl~Gp~GtGKT~lA~~la~~~~~~  615 (854)
T 1qvr_A          590 SFLFLGPTGVGKTELAKTLAATLFDT  615 (854)
T ss_dssp             EEEEBSCSSSSHHHHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcCC
Confidence            68999999999999999999888654

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=97.57  E-value=5.3e-05  Score=51.86  Aligned_cols=26  Identities=19%  Similarity=0.440  Sum_probs=22.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..++|.||+|+||||++..++..+
T Consensus       174 ~G~~i~ivG~sGsGKSTll~~l~~~~  199 (361)
T 2gza_A          174 LERVIVVAGETGSGKTTLMKALMQEI  199 (361)
T ss_dssp             TTCCEEEEESSSSCHHHHHHHHHTTS
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHhcC
Confidence            46799999999999999988887654

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=97.56  E-value=0.0001  Score=47.50  Aligned_cols=34  Identities=18%  Similarity=0.200  Sum_probs=28.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ..+++.|.+|+||||++..++..+. .       +.+++++.
T Consensus        15 ~i~~~~GkgGvGKTTl~~~La~~l~-~-------g~~v~vvd   48 (262)
T 1yrb_A           15 MIVVFVGTAGSGKTTLTGEFGRYLE-D-------NYKVAYVN   48 (262)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHT-T-------TSCEEEEE
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHH-C-------CCeEEEEe
Confidence            4678899999999999999998886 5       56777665

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=97.56  E-value=5.6e-05  Score=48.62  Aligned_cols=26  Identities=31%  Similarity=0.584  Sum_probs=22.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +..+++.||+|+||||++..+...+-
T Consensus        26 g~~i~i~G~~GsGKsT~~~~l~~~l~   51 (229)
T 4eaq_A           26 SAFITFEGPEGSGKTTVINEVYHRLV   51 (229)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            45788999999999999988888763

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=97.55  E-value=4.5e-05  Score=49.34  Aligned_cols=25  Identities=36%  Similarity=0.417  Sum_probs=20.8

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        30 ~Ge~~~iiG~nGsGKSTLl~~l~Gl   54 (235)
T 3tif_A           30 EGEFVSIMGPSGSGKSTMLNIIGCL   54 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcC
Confidence            3678999999999999998777543

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=97.54  E-value=4.5e-05  Score=51.75  Aligned_cols=23  Identities=26%  Similarity=0.567  Sum_probs=20.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||+|||+++..++..+
T Consensus         7 ~i~i~GptGsGKTtla~~La~~l   29 (323)
T 3crm_A            7 AIFLMGPTAAGKTDLAMALADAL   29 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            68899999999999999998765

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=97.54  E-value=2.2e-05  Score=49.16  Aligned_cols=25  Identities=24%  Similarity=0.438  Sum_probs=21.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .++|.|++|+||||++..+...+-.
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~~   26 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFRA   26 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHHE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            4689999999999999998887743

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.53  E-value=0.00011  Score=59.53  Aligned_cols=39  Identities=18%  Similarity=0.305  Sum_probs=33.5

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      .+.++++.||||||||+++..++...++.       +.++++++..
T Consensus      1080 ~g~~vll~G~~GtGKT~la~~~~~ea~k~-------Ge~~~Fit~e 1118 (2050)
T 3cmu_A         1080 MGRIVEIYGPESSGKTTLTLQVIAAAQRE-------GKTCAFIDAE 1118 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTT-------TCCEEEECTT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHc-------CCeEEEEEcc
Confidence            45789999999999999999999999877       6778887743

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=97.53  E-value=2.7e-05  Score=53.19  Aligned_cols=24  Identities=25%  Similarity=0.645  Sum_probs=21.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.||+|+|||+++..++..+
T Consensus        41 ~lIvI~GPTgsGKTtLa~~LA~~l   64 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLSIDLAAHF   64 (339)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTTS
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHC
Confidence            478999999999999999998776

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=97.52  E-value=7.4e-05  Score=48.51  Aligned_cols=25  Identities=28%  Similarity=0.541  Sum_probs=20.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...+.|.||+|+||||++..++..+
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~l   33 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARAL   33 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3478999999999999998887554

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=97.52  E-value=3.3e-05  Score=52.35  Aligned_cols=26  Identities=31%  Similarity=0.331  Sum_probs=22.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..++..+
T Consensus       170 ~g~~v~i~G~~GsGKTTll~~l~g~~  195 (330)
T 2pt7_A          170 IGKNVIVCGGTGSGKTTYIKSIMEFI  195 (330)
T ss_dssp             HTCCEEEEESTTSCHHHHHHHGGGGS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            57899999999999999988877654

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=97.52  E-value=8e-05  Score=51.47  Aligned_cols=25  Identities=28%  Similarity=0.519  Sum_probs=21.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..++|.||||+||||++..++...
T Consensus       169 ~~~i~l~G~~GsGKSTl~~~l~~~~  193 (377)
T 1svm_A          169 KRYWLFKGPIDSGKTTLAAALLELC  193 (377)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhc
Confidence            4688999999999999998888653

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=97.51  E-value=7.9e-05  Score=46.33  Aligned_cols=23  Identities=35%  Similarity=0.658  Sum_probs=19.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+.|.|++|+||||++..+...+
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~l   26 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAAL   26 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            67899999999999988886643

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=97.50  E-value=7e-05  Score=50.41  Aligned_cols=27  Identities=15%  Similarity=0.095  Sum_probs=21.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +..+.|.||+|+||||++..+...+-.
T Consensus        90 g~ivgI~G~sGsGKSTL~~~L~gll~~  116 (312)
T 3aez_A           90 PFIIGVAGSVAVGKSTTARVLQALLAR  116 (312)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCchHHHHHHHHHhhccc
Confidence            447889999999999998877766643

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=97.50  E-value=7e-05  Score=48.29  Aligned_cols=25  Identities=24%  Similarity=0.299  Sum_probs=21.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+.|.||+|+||||++..+...+
T Consensus        25 g~iigI~G~~GsGKSTl~k~L~~~l   49 (245)
T 2jeo_A           25 PFLIGVSGGTASGKSTVCEKIMELL   49 (245)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHh
Confidence            4478899999999999988877655

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=97.50  E-value=0.00014  Score=51.05  Aligned_cols=35  Identities=23%  Similarity=0.291  Sum_probs=28.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+++.|++|+||||++..++..+...       +.+++++..
T Consensus       100 vi~i~G~~GsGKTT~~~~LA~~l~~~-------g~~Vllvd~  134 (425)
T 2ffh_A          100 LWFLVGLQGSGKTTTAAKLALYYKGK-------GRRPLLVAA  134 (425)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTT-------TCCEEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc-------CCeEEEeec
Confidence            57788999999999999998888654       667777663

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=97.50  E-value=5.1e-05  Score=48.69  Aligned_cols=25  Identities=28%  Similarity=0.340  Sum_probs=20.7

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        29 ~Ge~~~iiG~nGsGKSTLl~~l~Gl   53 (224)
T 2pcj_A           29 KGEFVSIIGASGSGKSTLLYILGLL   53 (224)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3678899999999999998777543

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=97.49  E-value=0.00025  Score=50.56  Aligned_cols=28  Identities=25%  Similarity=0.585  Sum_probs=22.5

Q ss_pred             cCCceEEeCCCCCchHHHHHHH-HHHHHh
Q psy16285         33 TREFAIIQGPPGTGKTYVALRI-VEGFLK   60 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~-~~~~~~   60 (97)
                      .+..+.|.||+|+||||++..+ +..+..
T Consensus        38 ~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~~   66 (525)
T 1tf7_A           38 IGRSTLVSGTSGTGKTLFSIQFLYNGIIE   66 (525)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHh
Confidence            4678999999999999998886 345544

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=97.49  E-value=6.6e-05  Score=48.62  Aligned_cols=23  Identities=26%  Similarity=0.416  Sum_probs=20.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+.|.|++||||||++..+...+
T Consensus        24 iI~I~G~~GSGKST~a~~L~~~l   46 (252)
T 1uj2_A           24 LIGVSGGTASGKSSVCAKIVQLL   46 (252)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999988887754

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=97.48  E-value=7.3e-05  Score=49.28  Aligned_cols=22  Identities=27%  Similarity=0.457  Sum_probs=19.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+++.|+||+||||++..+...
T Consensus         4 ~I~l~G~~GsGKST~a~~L~~~   25 (301)
T 1ltq_A            4 IILTIGCPGSGKSTWAREFIAK   25 (301)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            5789999999999998888763

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=97.48  E-value=6.2e-05  Score=48.71  Aligned_cols=26  Identities=15%  Similarity=0.325  Sum_probs=21.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..++..+
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           30 EGALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            36789999999999999988776544

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=97.48  E-value=0.00013  Score=48.79  Aligned_cols=24  Identities=21%  Similarity=0.165  Sum_probs=20.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+.|.||+|+||||++..+...+
T Consensus        81 ~iigI~G~~GsGKSTl~~~L~~~l  104 (308)
T 1sq5_A           81 YIISIAGSVAVGKSTTARVLQALL  104 (308)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Confidence            477899999999999988777665

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=97.47  E-value=6.6e-05  Score=49.30  Aligned_cols=25  Identities=24%  Similarity=0.199  Sum_probs=20.9

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        31 ~Ge~~~liG~nGsGKSTLlk~l~Gl   55 (262)
T 1b0u_A           31 AGDVISIIGSSGSGKSTFLRCINFL   55 (262)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3678899999999999998877544

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=97.47  E-value=0.00032  Score=45.55  Aligned_cols=29  Identities=31%  Similarity=0.540  Sum_probs=24.9

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++..+++.|++|+||||.+..+...+...
T Consensus        26 ~~~~i~~eG~~GsGKsT~~~~l~~~l~~~   54 (236)
T 3lv8_A           26 NAKFIVIEGLEGAGKSTAIQVVVETLQQN   54 (236)
T ss_dssp             CCCEEEEEESTTSCHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            45678999999999999999998888655

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=97.47  E-value=7.2e-05  Score=47.86  Aligned_cols=26  Identities=27%  Similarity=0.367  Sum_probs=21.5

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..++..+
T Consensus        34 ~Ge~~~iiG~NGsGKSTLlk~l~Gl~   59 (214)
T 1sgw_A           34 KGNVVNFHGPNGIGKTTLLKTISTYL   59 (214)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            46789999999999999988775543

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=97.47  E-value=5.2e-05  Score=51.45  Aligned_cols=24  Identities=25%  Similarity=0.505  Sum_probs=21.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.||+|+|||+++..++..+
T Consensus         4 ~~i~i~GptgsGKt~la~~La~~~   27 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLAKRL   27 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHTT
T ss_pred             cEEEEECCCcCCHHHHHHHHHHhC
Confidence            467899999999999999998765

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=97.46  E-value=6e-05  Score=47.20  Aligned_cols=24  Identities=25%  Similarity=0.261  Sum_probs=20.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+.|.|++|+||||++..+...+
T Consensus        22 ~~i~i~G~~GsGKSTl~~~L~~~~   45 (207)
T 2qt1_A           22 FIIGISGVTNSGKTTLAKNLQKHL   45 (207)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTTS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            467899999999999988877643

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=97.46  E-value=8.2e-05  Score=54.99  Aligned_cols=23  Identities=30%  Similarity=0.606  Sum_probs=21.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++++.||||||||+++..++..+
T Consensus       490 ~~ll~G~~GtGKT~la~~la~~l  512 (758)
T 1r6b_X          490 SFLFAGPTGVGKTEVTVQLSKAL  512 (758)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHHh
Confidence            68999999999999999998877

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=97.46  E-value=6.8e-05  Score=49.70  Aligned_cols=25  Identities=24%  Similarity=0.222  Sum_probs=21.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        33 ~Ge~~~iiGpnGsGKSTLl~~l~Gl   57 (275)
T 3gfo_A           33 RGEVTAILGGNGVGKSTLFQNFNGI   57 (275)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcC
Confidence            3678999999999999998877543

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=97.46  E-value=0.00019  Score=45.46  Aligned_cols=38  Identities=26%  Similarity=0.375  Sum_probs=29.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      +...++.||.|+|||+-+...+......       +++++++.|.
T Consensus        20 g~l~fiyG~MgsGKTt~Ll~~i~n~~~~-------~~kvl~~kp~   57 (195)
T 1w4r_A           20 GQIQVILGPMFSGKSTELMRRVRRFQIA-------QYKCLVIKYA   57 (195)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHHT-------TCCEEEEEET
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHc-------CCeEEEEccc
Confidence            4578999999999997666666666555       6789988875

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=97.45  E-value=9e-05  Score=48.27  Aligned_cols=25  Identities=24%  Similarity=0.440  Sum_probs=21.5

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        28 ~Ge~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           28 KGEVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3678999999999999998887764

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=97.45  E-value=6.8e-05  Score=47.85  Aligned_cols=25  Identities=32%  Similarity=0.373  Sum_probs=20.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..++|.||||+|||+++..++...
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g   58 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRG   58 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhC
Confidence            3467999999999999998887654

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=97.45  E-value=7.2e-05  Score=48.94  Aligned_cols=25  Identities=28%  Similarity=0.430  Sum_probs=21.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        32 ~Ge~~~liG~nGsGKSTLlk~l~Gl   56 (257)
T 1g6h_A           32 KGDVTLIIGPNGSGKSTLINVITGF   56 (257)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3678999999999999998877544

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=97.45  E-value=8.1e-05  Score=46.11  Aligned_cols=22  Identities=32%  Similarity=0.320  Sum_probs=18.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ..+.|.|++||||||++..+..
T Consensus         9 ~~I~i~G~~GsGKST~~~~La~   30 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAALLRS   30 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3678999999999999888764

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=97.44  E-value=9.7e-05  Score=48.63  Aligned_cols=25  Identities=28%  Similarity=0.502  Sum_probs=21.5

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        45 ~Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           45 PGEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3678999999999999998887765

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=97.43  E-value=8e-05  Score=47.94  Aligned_cols=26  Identities=23%  Similarity=0.460  Sum_probs=21.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||.|+||||++..++..+
T Consensus        33 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   58 (229)
T 2pze_A           33 RGQLLAVAGSTGAGKTSLLMMIMGEL   58 (229)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            36789999999999999988776544

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=97.43  E-value=0.00014  Score=50.63  Aligned_cols=27  Identities=15%  Similarity=0.092  Sum_probs=21.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +..+.|.||||+|||+++..++.....
T Consensus       178 Gei~~I~G~sGsGKTTLl~~la~~~~~  204 (400)
T 3lda_A          178 GSITELFGEFRTGKSQLCHTLAVTCQI  204 (400)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTS
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHhcc
Confidence            468899999999999999877655443

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=97.43  E-value=7.8e-05  Score=48.30  Aligned_cols=25  Identities=24%  Similarity=0.275  Sum_probs=21.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        31 ~Ge~~~l~G~nGsGKSTLl~~l~Gl   55 (240)
T 1ji0_A           31 RGQIVTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3678999999999999998877544

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=97.43  E-value=0.0004  Score=44.34  Aligned_cols=28  Identities=29%  Similarity=0.438  Sum_probs=24.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..+++.|++|+||||.+..+...+...
T Consensus         3 g~~i~~eG~~gsGKsT~~~~l~~~l~~~   30 (213)
T 4tmk_A            3 SKYIVIEGLEGAGKTTARNVVVETLEQL   30 (213)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            4578899999999999999998888655

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=97.43  E-value=7.9e-05  Score=48.54  Aligned_cols=25  Identities=28%  Similarity=0.259  Sum_probs=21.1

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        34 ~Ge~~~i~G~nGsGKSTLl~~l~Gl   58 (247)
T 2ff7_A           34 QGEVIGIVGRSGSGKSTLTKLIQRF   58 (247)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3678999999999999998877554

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=97.43  E-value=0.00019  Score=48.64  Aligned_cols=28  Identities=18%  Similarity=0.208  Sum_probs=23.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ...+.+.|+||+||||++..++..+...
T Consensus        56 ~~~i~i~G~~g~GKSTl~~~l~~~~~~~   83 (341)
T 2p67_A           56 TLRLGVTGTPGAGKSTFLEAFGMLLIRE   83 (341)
T ss_dssp             SEEEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHHHhc
Confidence            3478899999999999999988776543

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=97.43  E-value=0.00042  Score=49.65  Aligned_cols=25  Identities=24%  Similarity=0.515  Sum_probs=21.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      ..+++.|.||+||||++..++..+-
T Consensus        36 ~lIvlvGlpGSGKSTia~~La~~L~   60 (520)
T 2axn_A           36 TVIVMVGLPARGKTYISKKLTRYLN   60 (520)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3678999999999999999987763

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=97.42  E-value=8.2e-05  Score=49.00  Aligned_cols=24  Identities=25%  Similarity=0.378  Sum_probs=20.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      ++.+.|.||+|+||||++..++..
T Consensus        50 Gei~~liG~NGsGKSTLlk~l~Gl   73 (263)
T 2olj_A           50 GEVVVVIGPSGSGKSTFLRCLNLL   73 (263)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEEcCCCCcHHHHHHHHHcC
Confidence            678899999999999998877544

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=97.42  E-value=8.2e-05  Score=49.00  Aligned_cols=25  Identities=28%  Similarity=0.417  Sum_probs=21.1

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        36 ~Ge~~~liG~nGsGKSTLl~~l~Gl   60 (266)
T 4g1u_C           36 SGEMVAIIGPNGAGKSTLLRLLTGY   60 (266)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcC
Confidence            3678999999999999998877543

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=97.42  E-value=8.8e-05  Score=50.68  Aligned_cols=24  Identities=29%  Similarity=0.628  Sum_probs=21.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.||+|+|||+++..++..+
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l   31 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKF   31 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHc
Confidence            367899999999999999998876

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=97.41  E-value=9e-05  Score=50.95  Aligned_cols=26  Identities=27%  Similarity=0.240  Sum_probs=21.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..++...
T Consensus        29 ~Ge~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           29 PGEILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCchHHHHHHHHhcCC
Confidence            36789999999999999987776543

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=97.41  E-value=6.7e-05  Score=47.00  Aligned_cols=45  Identities=13%  Similarity=0.237  Sum_probs=27.7

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ++|+|++|||||+.+..++..           +.++++++.....-+++.+++..+
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~-----------~~~~~yiaT~~~~d~e~~~rI~~h   46 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD-----------APQVLYIATSQILDDEMAARIQHH   46 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS-----------CSSEEEEECCCC------CHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHhc-----------CCCeEEEecCCCCCHHHHHHHHHH
Confidence            689999999999998877533           235667775443345666666554

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=97.41  E-value=0.00013  Score=46.73  Aligned_cols=26  Identities=35%  Similarity=0.480  Sum_probs=21.2

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..+.|.|++|+||||++..+...+
T Consensus        15 ~~~~i~i~G~~gsGKst~~~~l~~~l   40 (236)
T 1q3t_A           15 KTIQIAIDGPASSGKSTVAKIIAKDF   40 (236)
T ss_dssp             CCCEEEEECSSCSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            34578999999999999988876543

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=97.41  E-value=0.00021  Score=57.26  Aligned_cols=36  Identities=19%  Similarity=0.357  Sum_probs=29.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      +..++|.||||+|||+++..++..+...       +.++++++
T Consensus       732 G~lVlI~G~PG~GKTtLal~lA~~aa~~-------g~~VlyiS  767 (1706)
T 3cmw_A          732 GRIVEIYGPESSGKTTLTLQVIAAAQRE-------GKTCAFID  767 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEC
T ss_pred             CceEEEECCCCCCcHHHHHHHHHHHHHc-------CCCeEEEe
Confidence            4578999999999999999999988765       45666655

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=97.41  E-value=0.00013  Score=45.88  Aligned_cols=23  Identities=26%  Similarity=0.254  Sum_probs=19.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      ..+.|+|++||||||++..+...
T Consensus        13 ~iIgltG~~GSGKSTva~~L~~~   35 (192)
T 2grj_A           13 MVIGVTGKIGTGKSTVCEILKNK   35 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            46789999999999998888765

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=97.40  E-value=0.0001  Score=45.15  Aligned_cols=25  Identities=28%  Similarity=0.465  Sum_probs=21.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+..+|.||+|+|||+++.++...+
T Consensus        26 ~g~~~i~G~NGsGKStll~ai~~~l   50 (182)
T 3kta_A           26 KGFTAIVGANGSGKSNIGDAILFVL   50 (182)
T ss_dssp             SSEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHH
Confidence            3578999999999999988876654

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=97.40  E-value=9.1e-05  Score=48.57  Aligned_cols=25  Identities=32%  Similarity=0.284  Sum_probs=21.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        40 ~Gei~~l~G~NGsGKSTLlk~l~Gl   64 (256)
T 1vpl_A           40 EGEIFGLIGPNGAGKTTTLRIISTL   64 (256)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcC
Confidence            3678999999999999998877544

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=97.40  E-value=8.9e-05  Score=48.63  Aligned_cols=26  Identities=19%  Similarity=0.328  Sum_probs=21.7

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..++..+
T Consensus        45 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   70 (260)
T 2ghi_A           45 SGTTCALVGHTGSGKSTIAKLLYRFY   70 (260)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhccC
Confidence            36789999999999999988876543

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=97.40  E-value=0.00022  Score=57.16  Aligned_cols=38  Identities=18%  Similarity=0.318  Sum_probs=31.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      +..++|.||||||||+++..++...+..       +.++++++..
T Consensus        34 G~i~lI~G~pGsGKT~LAlqla~~~~~~-------G~~vlYI~te   71 (1706)
T 3cmw_A           34 GRIVEIYGPESSGKTTLTLQVIAAAQRE-------GKTCAFIDAE   71 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEECTT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhC-------CCceEEEEec
Confidence            5689999999999999999999888766       6677777753

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=97.40  E-value=9.3e-05  Score=48.34  Aligned_cols=26  Identities=27%  Similarity=0.414  Sum_probs=21.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..++..+
T Consensus        25 ~Ge~~~liG~NGsGKSTLlk~l~Gl~   50 (249)
T 2qi9_C           25 AGEILHLVGPNGAGKSTLLARMAGMT   50 (249)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            36788999999999999988776543

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=97.40  E-value=8.6e-05  Score=49.90  Aligned_cols=23  Identities=26%  Similarity=0.426  Sum_probs=19.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +.++|+|+.|+||||++..+...
T Consensus         5 ~v~~i~G~~GaGKTTll~~l~~~   27 (318)
T 1nij_A            5 AVTLLTGFLGAGKTTLLRHILNE   27 (318)
T ss_dssp             EEEEEEESSSSSCHHHHHHHHHS
T ss_pred             cEEEEEecCCCCHHHHHHHHHhh
Confidence            46789999999999998887764

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=97.39  E-value=9.4e-05  Score=50.08  Aligned_cols=24  Identities=25%  Similarity=0.476  Sum_probs=20.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++|.||+|+|||+++..++..+
T Consensus        11 ~~i~i~GptgsGKt~la~~La~~~   34 (316)
T 3foz_A           11 KAIFLMGPTASGKTALAIELRKIL   34 (316)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             cEEEEECCCccCHHHHHHHHHHhC
Confidence            357899999999999999998765

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=97.39  E-value=0.00028  Score=47.80  Aligned_cols=23  Identities=17%  Similarity=0.150  Sum_probs=19.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+.|.||+|+||||++..+...+
T Consensus        94 iigI~GpsGSGKSTl~~~L~~ll  116 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTSRVLKALL  116 (321)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57889999999999987776655

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=97.39  E-value=9.1e-05  Score=48.88  Aligned_cols=25  Identities=28%  Similarity=0.434  Sum_probs=21.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        44 ~Ge~~~i~G~nGsGKSTLlk~l~Gl   68 (271)
T 2ixe_A           44 PGKVTALVGPNGSGKSTVAALLQNL   68 (271)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3678999999999999998877544

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=97.39  E-value=7.6e-05  Score=48.41  Aligned_cols=26  Identities=19%  Similarity=0.360  Sum_probs=21.3

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..++..+
T Consensus        27 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (243)
T 1mv5_A           27 PNSIIAFAGPSGGGKSTIFSLLERFY   52 (243)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            35688999999999999988776543

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=97.39  E-value=9.6e-05  Score=49.03  Aligned_cols=26  Identities=23%  Similarity=0.116  Sum_probs=21.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..++..+
T Consensus        46 ~Ge~~~liG~NGsGKSTLlk~l~Gl~   71 (279)
T 2ihy_A           46 KGDKWILYGLNGAGKTTLLNILNAYE   71 (279)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            36788999999999999988775443

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=97.39  E-value=0.00012  Score=50.32  Aligned_cols=26  Identities=31%  Similarity=0.341  Sum_probs=21.5

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..++...
T Consensus        40 ~Ge~~~llGpnGsGKSTLLr~iaGl~   65 (355)
T 1z47_A           40 EGEMVGLLGPSGSGKTTILRLIAGLE   65 (355)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            36789999999999999988776443

>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency decline, ATP-binding, DNA DAMA repair, DNA-binding, helicase, hydrolase; 1.95A {Escherichia coli} PDB: 2b2n_A* 4dfc_A

Probab=97.38  E-value=0.00052  Score=48.85  Aligned_cols=51  Identities=14%  Similarity=0.287  Sum_probs=43.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +....+.|.+|+|||.++..++...          ++++++++++...+.++.+.++.|..
T Consensus        14 ~~~~~l~g~~gs~ka~~~a~l~~~~----------~~p~lvv~~~~~~A~~l~~~l~~~~~   64 (483)
T 3hjh_A           14 GEQRLLGELTGAACATLVAEIAERH----------AGPVVLIAPDMQNALRLHDEISQFTD   64 (483)
T ss_dssp             TCEEEEECCCTTHHHHHHHHHHHHS----------SSCEEEEESSHHHHHHHHHHHHHTCS
T ss_pred             CCeEEEeCCCchHHHHHHHHHHHHh----------CCCEEEEeCCHHHHHHHHHHHHhhCC
Confidence            4578999999999999977776432          66899999999999999999998864

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=97.37  E-value=0.00013  Score=48.63  Aligned_cols=25  Identities=28%  Similarity=0.809  Sum_probs=21.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .+.|.||+|+||||++..+...+-.
T Consensus        33 ii~I~G~sGsGKSTla~~L~~~l~~   57 (290)
T 1odf_A           33 FIFFSGPQGSGKSFTSIQIYNHLME   57 (290)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhhh
Confidence            5789999999999998888777754

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=97.37  E-value=0.00012  Score=47.50  Aligned_cols=24  Identities=25%  Similarity=0.516  Sum_probs=20.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.+.|.||+|+||||++..++..+
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl~   48 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCC
Confidence            678899999999999988776543

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=97.37  E-value=0.00013  Score=45.99  Aligned_cols=22  Identities=27%  Similarity=0.400  Sum_probs=18.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ..+.|.|++|+||||++..+..
T Consensus         5 ~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            5 YIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3678999999999999888754

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=97.37  E-value=0.00013  Score=50.59  Aligned_cols=26  Identities=31%  Similarity=0.437  Sum_probs=21.5

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..++...
T Consensus        28 ~Ge~~~llGpsGsGKSTLLr~iaGl~   53 (381)
T 3rlf_A           28 EGEFVVFVGPSGCGKSTLLRMIAGLE   53 (381)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHHcCC
Confidence            36789999999999999987776543

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=97.37  E-value=6.4e-05  Score=54.59  Aligned_cols=23  Identities=30%  Similarity=0.342  Sum_probs=20.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++++.||||||||+++..++..+
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~~  351 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRVA  351 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTTC
T ss_pred             ceEEECCCchHHHHHHHHHHHhC
Confidence            79999999999999998887654

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=97.37  E-value=0.00013  Score=50.20  Aligned_cols=26  Identities=35%  Similarity=0.578  Sum_probs=21.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..++...
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (359)
T 2yyz_A           28 DGEFVALLGPSGCGKTTTLLMLAGIY   53 (359)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHHCCC
Confidence            36789999999999999987776543

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=97.37  E-value=0.00013  Score=50.19  Aligned_cols=26  Identities=31%  Similarity=0.586  Sum_probs=21.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..++...
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (362)
T 2it1_A           28 DGEFMALLGPSGSGKSTLLYTIAGIY   53 (362)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCchHHHHHHHHhcCC
Confidence            36788999999999999988776543

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=97.36  E-value=0.00011  Score=48.35  Aligned_cols=25  Identities=20%  Similarity=0.323  Sum_probs=20.9

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        32 ~Ge~~~liG~nGsGKSTLl~~i~Gl   56 (266)
T 2yz2_A           32 EGECLLVAGNTGSGKSTLLQIVAGL   56 (266)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCC
Confidence            3678899999999999998877544

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=97.35  E-value=0.00014  Score=50.24  Aligned_cols=25  Identities=36%  Similarity=0.502  Sum_probs=21.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        36 ~Ge~~~llGpnGsGKSTLLr~iaGl   60 (372)
T 1v43_A           36 DGEFLVLLGPSGCGKTTTLRMIAGL   60 (372)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcC
Confidence            3678999999999999998777644

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=97.35  E-value=0.00014  Score=50.21  Aligned_cols=25  Identities=40%  Similarity=0.521  Sum_probs=21.1

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl   52 (372)
T 1g29_1           28 DGEFMILLGPSGCGKTTTLRMIAGL   52 (372)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCcHHHHHHHHHHcC
Confidence            3678999999999999998777644

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=97.34  E-value=0.00054  Score=48.97  Aligned_cols=42  Identities=21%  Similarity=0.266  Sum_probs=32.7

Q ss_pred             cCCCCCHHHHHHHHHHhc-----CCceEEeCCCCCchHHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALT-----REFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~-----~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      ..+.-++...+.+.....     .+.+.|.||+|.|||+++..++..
T Consensus       124 ~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  170 (591)
T 1z6t_A          124 VVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRD  170 (591)
T ss_dssp             SSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             CeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhc
Confidence            445567888888887764     347899999999999999887654

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=97.34  E-value=0.00012  Score=47.94  Aligned_cols=26  Identities=15%  Similarity=0.218  Sum_probs=21.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..++..+
T Consensus        30 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~   55 (253)
T 2nq2_C           30 KGDILAVLGQNGCGKSTLLDLLLGIH   55 (253)
T ss_dssp             TTCEEEEECCSSSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            36788999999999999987776543

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=97.33  E-value=7.6e-05  Score=46.20  Aligned_cols=27  Identities=22%  Similarity=0.268  Sum_probs=22.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +.+.|.|++|+||||++..++..+-..
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~~~   29 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILRER   29 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhhhc
Confidence            457899999999999988888776543

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=97.33  E-value=0.00014  Score=51.49  Aligned_cols=29  Identities=28%  Similarity=0.226  Sum_probs=24.1

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .++.+.|.||+|+||||++..++..+...
T Consensus       137 ~Ge~v~IvGpnGsGKSTLlr~L~Gl~~p~  165 (460)
T 2npi_A          137 EGPRVVIVGGSQTGKTSLSRTLCSYALKF  165 (460)
T ss_dssp             SCCCEEEEESTTSSHHHHHHHHHHTTHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCccccc
Confidence            46799999999999999988887766444

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=97.29  E-value=0.00017  Score=47.59  Aligned_cols=25  Identities=16%  Similarity=0.324  Sum_probs=20.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ++.|.||+|+||||++..++.....
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~~~   28 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQVS   28 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCC
Confidence            4689999999999998888766533

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=97.29  E-value=0.00011  Score=50.22  Aligned_cols=25  Identities=36%  Similarity=0.510  Sum_probs=21.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        25 ~Ge~~~llGpnGsGKSTLLr~iaGl   49 (348)
T 3d31_A           25 SGEYFVILGPTGAGKTLFLELIAGF   49 (348)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCccHHHHHHHHHcC
Confidence            3678999999999999998777644

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=97.29  E-value=0.0002  Score=49.27  Aligned_cols=25  Identities=28%  Similarity=0.521  Sum_probs=21.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ++++.||+|+|||+++..++..+-.
T Consensus        26 ~i~l~G~~G~GKTTl~~~la~~l~~   50 (359)
T 2ga8_A           26 CVILVGSPGSGKSTIAEELCQIINE   50 (359)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHHhCC
Confidence            4899999999999999888776643

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=97.29  E-value=0.00032  Score=48.17  Aligned_cols=31  Identities=26%  Similarity=0.356  Sum_probs=24.3

Q ss_pred             HHHHhcCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         28 YKAALTREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        28 i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.....+..+.|.||+|+||||++..++...
T Consensus       209 L~~~~~G~~~~lvG~sG~GKSTLln~L~g~~  239 (358)
T 2rcn_A          209 LEEALTGRISIFAGQSGVGKSSLLNALLGLQ  239 (358)
T ss_dssp             HHHHHTTSEEEEECCTTSSHHHHHHHHHCCS
T ss_pred             HHHhcCCCEEEEECCCCccHHHHHHHHhccc
Confidence            3344567789999999999999988876543

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=97.28  E-value=0.00051  Score=44.32  Aligned_cols=28  Identities=21%  Similarity=0.324  Sum_probs=20.7

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ++..+++.||+|+||||.+..+...+..
T Consensus        24 ~g~~I~~eG~~GsGKsT~~~~l~~~l~~   51 (227)
T 3v9p_A           24 RGKFITFEGIDGAGKTTHLQWFCDRLQE   51 (227)
T ss_dssp             CCCEEEEECCC---CHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            4567899999999999999988887744

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=97.28  E-value=0.00082  Score=47.02  Aligned_cols=40  Identities=23%  Similarity=0.318  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHh---cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         22 TIQFEAYKAAL---TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        22 ~~Q~~~i~~~~---~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +.-..+|+...   +++...|.||+|+|||+++..++..+.++
T Consensus       159 ~tGiraID~~~pi~rGQr~~IvG~sG~GKTtLl~~Iar~i~~~  201 (422)
T 3ice_A          159 DLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYN  201 (422)
T ss_dssp             HHHHHHHHHHSCCBTTCEEEEECCSSSSHHHHHHHHHHHHHHH
T ss_pred             cccceeeeeeeeecCCcEEEEecCCCCChhHHHHHHHHHHhhc
Confidence            44455666544   47899999999999999998888777654

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=97.27  E-value=0.00015  Score=47.75  Aligned_cols=25  Identities=40%  Similarity=0.470  Sum_probs=21.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++.+.|.||+|+||||++..++..+
T Consensus        30 Ge~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEEECCCCCCHHHHHHHHhCCC
Confidence            5688999999999999988887655

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=97.26  E-value=0.00034  Score=46.70  Aligned_cols=28  Identities=29%  Similarity=0.487  Sum_probs=22.5

Q ss_pred             HHHHhcCCceEEeCCCCCchHHHHHHHH
Q psy16285         28 YKAALTREFAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        28 i~~~~~~~~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      +.....+....+.||+|+||||++..+.
T Consensus       159 L~~~l~G~i~~l~G~sG~GKSTLln~l~  186 (302)
T 2yv5_A          159 LVDYLEGFICILAGPSGVGKSSILSRLT  186 (302)
T ss_dssp             HHHHTTTCEEEEECSTTSSHHHHHHHHH
T ss_pred             HHhhccCcEEEEECCCCCCHHHHHHHHH
Confidence            3333456788999999999999988887

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=97.26  E-value=0.00025  Score=47.15  Aligned_cols=25  Identities=20%  Similarity=0.307  Sum_probs=18.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      ..+.|.||+|+||||++..+...+-
T Consensus         6 ~iIgItG~sGSGKSTva~~L~~~lg   30 (290)
T 1a7j_A            6 PIISVTGSSGAGTSTVKHTFDQIFR   30 (290)
T ss_dssp             CEEEEESCC---CCTHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4678999999999999988877654

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=97.26  E-value=0.00019  Score=50.17  Aligned_cols=23  Identities=26%  Similarity=0.680  Sum_probs=20.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||+|+|||+++..++..+
T Consensus         4 ~i~i~GptgsGKttla~~La~~~   26 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLSIQLAQKF   26 (409)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHH
T ss_pred             EEEEECcchhhHHHHHHHHHHHC
Confidence            57899999999999999998876

>1ihu_A Arsenical pump-driving ATPase; aluminum fluoride, ADP, ARSA ATPase, ATP binding site, hydro; HET: ADP; 2.15A {Escherichia coli} SCOP: c.37.1.10 c.37.1.10 PDB: 1f48_A* 1ii0_A* 1ii9_A*

Probab=97.26  E-value=0.00048  Score=49.65  Aligned_cols=37  Identities=19%  Similarity=0.329  Sum_probs=30.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ...+++.|.+|+||||++..++..+.+.       +++++++..
T Consensus         8 ~~i~~~sgkGGvGKTT~a~~lA~~lA~~-------G~rVLlvd~   44 (589)
T 1ihu_A            8 PPYLFFTGKGGVGKTSISCATAIRLAEQ-------GKRVLLVST   44 (589)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEEC
T ss_pred             CEEEEEeCCCcCHHHHHHHHHHHHHHHC-------CCcEEEEEC
Confidence            3567889999999999999999998776       678888653

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=97.26  E-value=0.00011  Score=51.10  Aligned_cols=22  Identities=27%  Similarity=0.416  Sum_probs=19.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ..+++.|+||+||||++..++.
T Consensus       259 ~lIil~G~pGSGKSTla~~L~~  280 (416)
T 3zvl_A          259 EVVVAVGFPGAGKSTFIQEHLV  280 (416)
T ss_dssp             CEEEEESCTTSSHHHHHHHHTG
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            4678999999999999988753

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=97.26  E-value=0.00013  Score=49.69  Aligned_cols=25  Identities=24%  Similarity=0.290  Sum_probs=21.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+.|.||||+|||+++..++..+
T Consensus       131 G~i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          131 QAITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4578999999999999988887765

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=97.26  E-value=0.00023  Score=42.85  Aligned_cols=26  Identities=27%  Similarity=0.471  Sum_probs=21.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      .+..+|.||+|+|||+++.++...+.
T Consensus        23 ~g~~~I~G~NGsGKStil~Ai~~~l~   48 (149)
T 1f2t_A           23 EGINLIIGQNGSGKSSLLDAILVGLY   48 (149)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHc
Confidence            45789999999999999888876653

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=97.26  E-value=0.00017  Score=50.02  Aligned_cols=25  Identities=16%  Similarity=0.194  Sum_probs=21.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        46 ~Ge~~~llGpsGsGKSTLLr~iaGl   70 (390)
T 3gd7_A           46 PGQRVGLLGRTGSGKSTLLSAFLRL   70 (390)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCC
Confidence            3678999999999999998877654

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=97.26  E-value=0.00022  Score=51.53  Aligned_cols=29  Identities=17%  Similarity=0.271  Sum_probs=24.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++..+.|.|++|+||||++..++..+...
T Consensus       368 ~G~iI~LiG~sGSGKSTLar~La~~L~~~  396 (552)
T 3cr8_A          368 QGFTVFFTGLSGAGKSTLARALAARLMEM  396 (552)
T ss_dssp             SCEEEEEEESSCHHHHHHHHHHHHHHHTT
T ss_pred             cceEEEEECCCCChHHHHHHHHHHhhccc
Confidence            35678999999999999999888877543

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=97.25  E-value=0.00014  Score=49.62  Aligned_cols=25  Identities=20%  Similarity=0.333  Sum_probs=21.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+.|.||+|+||||++..++..+
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~  194 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVF  194 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHT
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHh
Confidence            4578999999999999988887664

>3ug7_A Arsenical pump-driving ATPase; tail-anchored, membrane protein, targeting factor, ATP-bindi TRC40, ARSA, nucleotide-binding; HET: ADP; 2.90A {Methanocaldococcus jannaschii} PDB: 3ug6_A*

Probab=97.24  E-value=0.00048  Score=46.87  Aligned_cols=34  Identities=21%  Similarity=0.295  Sum_probs=28.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      .+++.|..|+||||++..++..+.+.       +++++++.
T Consensus        28 i~v~sgKGGvGKTTvA~~LA~~lA~~-------G~rVLlvD   61 (349)
T 3ug7_A           28 YIMFGGKGGVGKTTMSAATGVYLAEK-------GLKVVIVS   61 (349)
T ss_dssp             EEEEECSSSTTHHHHHHHHHHHHHHS-------SCCEEEEE
T ss_pred             EEEEeCCCCccHHHHHHHHHHHHHHC-------CCeEEEEe
Confidence            56778999999999999999988766       77888777

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=97.23  E-value=0.00046  Score=46.39  Aligned_cols=35  Identities=23%  Similarity=0.364  Sum_probs=29.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .+++.|..|+||||++..++..+.+.       +++++++..
T Consensus        16 i~v~sgKGGvGKTTvA~~LA~~lA~~-------G~rVLlvD~   50 (324)
T 3zq6_A           16 FVFIGGKGGVGKTTISAATALWMARS-------GKKTLVIST   50 (324)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT-------TCCEEEEEC
T ss_pred             EEEEeCCCCchHHHHHHHHHHHHHHC-------CCcEEEEeC
Confidence            56778999999999999999988766       778887764

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=97.21  E-value=0.00019  Score=47.45  Aligned_cols=20  Identities=35%  Similarity=0.486  Sum_probs=18.0

Q ss_pred             ceEEeCCCCCchHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      .+.|.|++|+||||++..+.
T Consensus        77 iI~I~G~~GSGKSTva~~La   96 (281)
T 2f6r_A           77 VLGLTGISGSGKSSVAQRLK   96 (281)
T ss_dssp             EEEEEECTTSCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            57899999999999988876

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=97.21  E-value=0.00017  Score=48.12  Aligned_cols=25  Identities=24%  Similarity=0.481  Sum_probs=20.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++.+.|.||.|+||||++..++..+
T Consensus        64 Ge~~~i~G~NGsGKSTLlk~l~Gl~   88 (290)
T 2bbs_A           64 GQLLAVAGSTGAGKTSLLMMIMGEL   88 (290)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCC
Confidence            5678999999999999988776544

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=97.20  E-value=0.00054  Score=44.14  Aligned_cols=27  Identities=26%  Similarity=0.335  Sum_probs=23.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +..+++.|++|+||||++..+...+..
T Consensus        21 ~~~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           21 SMFITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            447788999999999999999988866

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=97.20  E-value=0.00029  Score=44.27  Aligned_cols=23  Identities=26%  Similarity=0.465  Sum_probs=19.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      ..+.|.|++|+|||+++..+...
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~   26 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASE   26 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            46889999999999998887654

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=97.19  E-value=0.00012  Score=50.21  Aligned_cols=25  Identities=36%  Similarity=0.287  Sum_probs=21.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        30 ~Ge~~~llGpnGsGKSTLLr~iaGl   54 (353)
T 1oxx_K           30 NGERFGILGPSGAGKTTFMRIIAGL   54 (353)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCC
Confidence            3678999999999999998877654

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=97.19  E-value=0.00027  Score=43.76  Aligned_cols=22  Identities=23%  Similarity=0.434  Sum_probs=19.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++|.|++|+|||+++..++..
T Consensus         7 kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            7 KVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5789999999999998888764

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=97.19  E-value=0.00082  Score=47.78  Aligned_cols=29  Identities=17%  Similarity=0.251  Sum_probs=25.1

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +++..++.||+|+|||+++..++.....+
T Consensus       150 kGq~~~i~G~sGvGKTtL~~~l~~~~~~~  178 (473)
T 1sky_E          150 KGGKIGLFGGAGVGKTVLIQELIHNIAQE  178 (473)
T ss_dssp             TTCEEEEECCSSSCHHHHHHHHHHHHHHH
T ss_pred             cCCEEEEECCCCCCccHHHHHHHhhhhhc
Confidence            57899999999999999999988776554

>3bfv_A CAPA1, CAPB2, membrane protein CAPA1, protein tyrosine kinase; chimerical protein, P-loop protein, capsule biogenesis/degradation; HET: ADP; 1.80A {Staphylococcus aureus} PDB: 2ved_A*

Probab=97.18  E-value=0.00073  Score=44.45  Aligned_cols=35  Identities=26%  Similarity=0.419  Sum_probs=27.7

Q ss_pred             CceEEeCC-CCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         35 EFAIIQGP-PGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        35 ~~~~v~Gp-~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      +.++|.++ +|.|||+++..++..+.+.       +++++++-
T Consensus        83 kvI~vts~kgG~GKTt~a~nLA~~lA~~-------G~rVLLID  118 (271)
T 3bfv_A           83 QSIVITSEAPGAGKSTIAANLAVAYAQA-------GYKTLIVD  118 (271)
T ss_dssp             CEEEEECSSTTSSHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHHhC-------CCeEEEEe
Confidence            35667765 7999999999999988765       77888764

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=97.18  E-value=0.00028  Score=48.67  Aligned_cols=24  Identities=17%  Similarity=0.216  Sum_probs=20.3

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++.+.|.||+|+||||++..+..
T Consensus        53 ~Gei~~IiGpnGaGKSTLlr~i~G   76 (366)
T 3tui_C           53 AGQIYGVIGASGAGKSTLIRCVNL   76 (366)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCCEEEEEcCCCchHHHHHHHHhc
Confidence            367899999999999999777654

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=97.17  E-value=0.00044  Score=46.35  Aligned_cols=24  Identities=21%  Similarity=0.083  Sum_probs=20.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.+++.||||+|||+++..++..+
T Consensus        19 ~~~Lf~Gp~G~GKtt~a~~la~~~   42 (305)
T 2gno_A           19 ISILINGEDLSYPREVSLELPEYV   42 (305)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhC
Confidence            468999999999999999988753

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=97.17  E-value=0.0014  Score=41.14  Aligned_cols=33  Identities=15%  Similarity=0.232  Sum_probs=26.3

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      +++.|+-|+||||.+..+...+...       +.+++++.
T Consensus         3 I~~EG~DGsGKsTq~~~L~~~L~~~-------g~~v~~tr   35 (197)
T 3hjn_A            3 ITFEGIDGSGKSTQIQLLAQYLEKR-------GKKVILKR   35 (197)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC-------CCcEEEEE
Confidence            5688999999999999888888665       55665554

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=97.16  E-value=0.00048  Score=45.91  Aligned_cols=27  Identities=22%  Similarity=0.309  Sum_probs=22.0

Q ss_pred             HHhcCCceEEeCCCCCchHHHHHHHHH
Q psy16285         30 AALTREFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        30 ~~~~~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+..+..+.+.||+|+||||++..++.
T Consensus       165 ~~l~geiv~l~G~sG~GKSTll~~l~g  191 (301)
T 1u0l_A          165 EYLKGKISTMAGLSGVGKSSLLNAINP  191 (301)
T ss_dssp             HHHSSSEEEEECSTTSSHHHHHHHHST
T ss_pred             HHhcCCeEEEECCCCCcHHHHHHHhcc
Confidence            334577889999999999999887754

>3cio_A ETK, tyrosine-protein kinase ETK; WZC, escherichia coli tyrosine kinase domain, signaling protein, transferase, inner membrane, membrane; 2.50A {Escherichia coli}

Probab=97.16  E-value=0.00069  Score=45.15  Aligned_cols=35  Identities=23%  Similarity=0.492  Sum_probs=28.2

Q ss_pred             CceEEeCC-CCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         35 EFAIIQGP-PGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        35 ~~~~v~Gp-~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      +.++|+++ +|.|||+++..++..+.+.       +++|+++-
T Consensus       105 kvI~vts~kgG~GKTtva~nLA~~lA~~-------G~rVLLID  140 (299)
T 3cio_A          105 NILMITGATPDSGKTFVSSTLAAVIAQS-------DQKVLFID  140 (299)
T ss_dssp             CEEEEEESSSSSCHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             eEEEEECCCCCCChHHHHHHHHHHHHhC-------CCcEEEEE
Confidence            45667776 7999999999999988765       77888874

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=97.14  E-value=0.00029  Score=43.52  Aligned_cols=23  Identities=22%  Similarity=0.359  Sum_probs=19.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.|++|+|||+++..++...
T Consensus        31 kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           31 KVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            57899999999999988887643

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=97.14  E-value=0.00069  Score=42.42  Aligned_cols=25  Identities=32%  Similarity=0.396  Sum_probs=21.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...+++.|++|+|||+++..++..+
T Consensus        30 ~~~i~i~G~~g~GKTTl~~~l~~~~   54 (221)
T 2wsm_A           30 TVAVNIMGAIGSGKTLLIERTIERI   54 (221)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3578999999999999999888775

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=97.13  E-value=0.00039  Score=45.07  Aligned_cols=24  Identities=42%  Similarity=0.470  Sum_probs=20.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      -.+-|.||||+||||.+..++..+
T Consensus         9 ~~~~~~G~pGsGKsT~a~~L~~~~   32 (230)
T 3gmt_A            9 MRLILLGAPGAGKGTQANFIKEKF   32 (230)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cceeeECCCCCCHHHHHHHHHHHh
Confidence            467899999999999988886644

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=97.12  E-value=0.0004  Score=44.49  Aligned_cols=25  Identities=24%  Similarity=0.306  Sum_probs=22.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+++.|++|+||||.+..+...+
T Consensus         5 g~~i~~eG~~g~GKst~~~~l~~~l   29 (216)
T 3tmk_A            5 GKLILIEGLDRTGKTTQCNILYKKL   29 (216)
T ss_dssp             CCEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            5678999999999999999988877

>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein COOC; Zn-bound dimer, nickel binding protein, ATPase; 1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A* 3kje_A 3kji_A*

Probab=97.11  E-value=0.00043  Score=43.98  Aligned_cols=33  Identities=27%  Similarity=0.327  Sum_probs=27.2

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      +.|.|..|+||||++..++..+.+.       +.+++++-
T Consensus         3 I~vs~kGGvGKTt~a~~LA~~la~~-------g~~VlliD   35 (254)
T 3kjh_A            3 LAVAGKGGVGKTTVAAGLIKIMASD-------YDKIYAVD   35 (254)
T ss_dssp             EEEECSSSHHHHHHHHHHHHHHTTT-------CSCEEEEE
T ss_pred             EEEecCCCCCHHHHHHHHHHHHHHC-------CCeEEEEe
Confidence            4458999999999999999988765       67887764

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=97.11  E-value=0.00018  Score=48.43  Aligned_cols=25  Identities=20%  Similarity=0.397  Sum_probs=20.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++.+.|.||+|+||||++..++..+
T Consensus        80 Ge~vaivG~sGsGKSTLl~ll~gl~  104 (306)
T 3nh6_A           80 GQTLALVGPSGAGKSTILRLLFRFY  104 (306)
T ss_dssp             TCEEEEESSSCHHHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCchHHHHHHHHHcCC
Confidence            6789999999999999987775443

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=97.10  E-value=0.00078  Score=43.79  Aligned_cols=38  Identities=26%  Similarity=0.375  Sum_probs=31.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      +...+++||.|+|||+.+..++......       +++++++.|.
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~~~r~~~~-------g~kvli~kp~   56 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRRVRRFQIA-------QYKCLVIKYA   56 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHTT-------TCCEEEEEET
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHC-------CCeEEEEeec
Confidence            4567889999999999988888877655       7888888874

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=97.10  E-value=0.00069  Score=49.69  Aligned_cols=26  Identities=27%  Similarity=0.394  Sum_probs=22.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+++.|.+|+||||++..+...+...
T Consensus        54 lIvLtGlsGSGKSTlAr~La~~L~~~   79 (630)
T 1x6v_B           54 TVWLTGLSGAGKTTVSMALEEYLVCH   79 (630)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            58899999999999999998887543

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=97.10  E-value=0.001  Score=42.10  Aligned_cols=24  Identities=33%  Similarity=0.610  Sum_probs=20.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.|+.|+||||.+..+...+
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~~L   26 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYHRL   26 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHH
Confidence            457889999999999988888877

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=97.10  E-value=0.00038  Score=47.50  Aligned_cols=33  Identities=24%  Similarity=0.183  Sum_probs=25.9

Q ss_pred             HHHHHHh---cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         26 EAYKAAL---TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        26 ~~i~~~~---~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++..+   +++.+.|.||+|+||||++..++...
T Consensus        60 ~ald~ll~i~~Gq~~gIiG~nGaGKTTLl~~I~g~~   95 (347)
T 2obl_A           60 RAIDGLLTCGIGQRIGIFAGSGVGKSTLLGMICNGA   95 (347)
T ss_dssp             HHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             EEEEeeeeecCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            4566554   47899999999999999977776654

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=97.09  E-value=0.0016  Score=45.78  Aligned_cols=25  Identities=24%  Similarity=0.498  Sum_probs=21.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .+++.|.||+||||++..++..+..
T Consensus        41 ~IvlvGlpGsGKSTia~~La~~l~~   65 (469)
T 1bif_A           41 LIVMVGLPARGKTYISKKLTRYLNF   65 (469)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhc
Confidence            6789999999999999999887653

>2woo_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; 3.01A {Schizosaccharomyces pombe}

Probab=97.09  E-value=0.00087  Score=45.19  Aligned_cols=36  Identities=19%  Similarity=0.363  Sum_probs=29.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ...+++.|..|.||||++..++..+.+.       +++++++.
T Consensus        19 ~~i~v~sgkGGvGKTTva~~LA~~lA~~-------G~rVllvD   54 (329)
T 2woo_A           19 LKWIFVGGKGGVGKTTTSCSLAIQMSKV-------RSSVLLIS   54 (329)
T ss_dssp             CCEEEEECSSSSSHHHHHHHHHHHHHTS-------SSCEEEEE
T ss_pred             CEEEEEeCCCCCcHHHHHHHHHHHHHHC-------CCeEEEEE
Confidence            3466788999999999999999888765       67787764

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=97.09  E-value=0.00043  Score=40.87  Aligned_cols=22  Identities=27%  Similarity=0.477  Sum_probs=18.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+++.|++|+|||+++..+...
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            3 KVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5789999999999998887643

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=97.08  E-value=0.00061  Score=47.62  Aligned_cols=22  Identities=18%  Similarity=0.223  Sum_probs=19.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+.|.||+|+||||++..++..
T Consensus        71 ~valvG~nGaGKSTLln~L~Gl   92 (413)
T 1tq4_A           71 NVAVTGETGSGKSSFINTLRGI   92 (413)
T ss_dssp             EEEEEECTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCcHHHHHHHHhCC
Confidence            7899999999999998887653

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=97.08  E-value=0.0008  Score=45.69  Aligned_cols=36  Identities=19%  Similarity=0.346  Sum_probs=30.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ..+++.|..|+||||++..++..+.+.       +++++++..
T Consensus        17 ~i~~~sgkGGvGKTt~a~~lA~~la~~-------g~~vllid~   52 (334)
T 3iqw_A           17 RWIFVGGKGGVGKTTTSCSLAIQLAKV-------RRSVLLLST   52 (334)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHTTS-------SSCEEEEEC
T ss_pred             EEEEEeCCCCccHHHHHHHHHHHHHhC-------CCcEEEEEC
Confidence            567889999999999999999888665       677877764

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=97.06  E-value=0.00037  Score=43.60  Aligned_cols=23  Identities=22%  Similarity=0.466  Sum_probs=19.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +.-+++.|++|+|||+++..++.
T Consensus        16 G~gvli~G~SGaGKStlal~L~~   38 (181)
T 3tqf_A           16 KMGVLITGEANIGKSELSLALID   38 (181)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH
Confidence            34679999999999999888876

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=97.06  E-value=0.0005  Score=47.07  Aligned_cols=27  Identities=22%  Similarity=0.458  Sum_probs=22.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .+..+|.||+|+|||+++-++...+..
T Consensus        23 ~g~~~i~G~NGaGKTTll~ai~~al~g   49 (365)
T 3qf7_A           23 SGITVVEGPNGAGKSSLFEAISFALFG   49 (365)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHS
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhcC
Confidence            347789999999999998888766653

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=97.06  E-value=0.00084  Score=42.18  Aligned_cols=26  Identities=19%  Similarity=0.318  Sum_probs=22.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ..++|.|.+|+|||+++..++.....
T Consensus        39 ~~i~ivG~~gvGKTtl~~~l~~~~~~   64 (226)
T 2hf9_A           39 VAFDFMGAIGSGKTLLIEKLIDNLKD   64 (226)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHTT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHhcc
Confidence            46789999999999999999887643

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=97.06  E-value=0.00028  Score=45.28  Aligned_cols=24  Identities=17%  Similarity=0.235  Sum_probs=20.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.|++|+||||++..+...+
T Consensus         3 ~~i~~~G~~g~GKtt~~~~l~~~l   26 (241)
T 2ocp_A            3 RRLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHC
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHc
Confidence            357899999999999998888776

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=97.05  E-value=0.0017  Score=45.46  Aligned_cols=40  Identities=23%  Similarity=0.304  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHh---cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         22 TIQFEAYKAAL---TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        22 ~~Q~~~i~~~~---~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +.-..+|+...   +++...|.||+|+|||+++..++..+..+
T Consensus       160 ~tGiraID~l~PigrGQR~lIfg~~g~GKT~Ll~~Ia~~i~~~  202 (427)
T 3l0o_A          160 IYSTRLIDLFAPIGKGQRGMIVAPPKAGKTTILKEIANGIAEN  202 (427)
T ss_dssp             CHHHHHHHHHSCCBTTCEEEEEECTTCCHHHHHHHHHHHHHHH
T ss_pred             hccchhhhhcccccCCceEEEecCCCCChhHHHHHHHHHHhhc
Confidence            34455666655   47899999999999999998888877653

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=97.04  E-value=0.001  Score=42.88  Aligned_cols=40  Identities=13%  Similarity=0.047  Sum_probs=30.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNH   80 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~   80 (97)
                      +...+++||-|+|||+.+...+..+...       +.+++++.|...
T Consensus        28 G~I~vitG~M~sGKTT~Llr~~~r~~~~-------g~kvli~kp~~D   67 (219)
T 3e2i_A           28 GWIECITGSMFSGKSEELIRRLRRGIYA-------KQKVVVFKPAID   67 (219)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHHT-------TCCEEEEEEC--
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHc-------CCceEEEEeccC
Confidence            4577999999999999777777666554       678999988543

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=97.04  E-value=0.0005  Score=40.59  Aligned_cols=22  Identities=27%  Similarity=0.593  Sum_probs=18.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+++.|++|+|||+++..+...
T Consensus         5 ~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5799999999999998777643

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=97.04  E-value=0.00044  Score=41.52  Aligned_cols=22  Identities=18%  Similarity=0.229  Sum_probs=18.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ..+++.|++|+|||+++..+..
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~   25 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTG   25 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            3578999999999999888764

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=97.03  E-value=0.0005  Score=40.80  Aligned_cols=22  Identities=23%  Similarity=0.391  Sum_probs=19.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+++.|++|+|||+++..+...
T Consensus         7 ~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            7 KMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            6789999999999998887653

>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATPase, exonuclease, endonucle binding, DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB: 3qkr_A*

Probab=97.03  E-value=0.0005  Score=43.34  Aligned_cols=27  Identities=26%  Similarity=0.411  Sum_probs=22.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .+..+|.||.|+|||+++-++...+..
T Consensus        23 ~~~~~I~G~NgsGKStil~ai~~~l~g   49 (203)
T 3qks_A           23 EGINLIIGQNGSGKSSLLDAILVGLYW   49 (203)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHhcC
Confidence            457899999999999998888766654

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=97.02  E-value=0.0015  Score=47.07  Aligned_cols=27  Identities=19%  Similarity=0.202  Sum_probs=22.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+++.|++|+||||++..+...+...
T Consensus       373 ~~I~l~G~~GsGKSTia~~La~~L~~~  399 (546)
T 2gks_A          373 FCVWLTGLPCAGKSTIAEILATMLQAR  399 (546)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             eEEEccCCCCCCHHHHHHHHHHHhhhc
Confidence            367889999999999999988877554

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=97.02  E-value=0.00058  Score=42.64  Aligned_cols=25  Identities=28%  Similarity=0.383  Sum_probs=20.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...+++.|++|+|||+++..+....
T Consensus        12 ~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           12 QPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3578999999999999988876543

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=96.99  E-value=0.00049  Score=40.52  Aligned_cols=22  Identities=18%  Similarity=0.545  Sum_probs=18.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+++.|++|+|||+++..+...
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5789999999999998877643

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=96.99  E-value=0.0011  Score=45.19  Aligned_cols=37  Identities=16%  Similarity=0.304  Sum_probs=30.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHh-chhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLK-NKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~-~~~~~~~~~~~ilv~~~   77 (97)
                      ..+++.|..|+||||++..++..+.. .      .+++++++..
T Consensus        19 ~i~~~~gkGGvGKTt~a~~lA~~la~~~------~g~~vllid~   56 (348)
T 3io3_A           19 KWIFVGGKGGVGKTTTSSSVAVQLALAQ------PNEQFLLIST   56 (348)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHHC------TTSCEEEEEC
T ss_pred             EEEEEeCCCCCcHHHHHHHHHHHHHHhc------CCCeEEEEEC
Confidence            57788999999999999999988872 3      2778877764

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=96.99  E-value=0.00053  Score=48.19  Aligned_cols=33  Identities=18%  Similarity=0.081  Sum_probs=25.3

Q ss_pred             HHHHHHh---cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         26 EAYKAAL---TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        26 ~~i~~~~---~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.++   +++.+.|.||+|+||||++..++...
T Consensus       146 ~vld~vl~i~~Gq~~~IvG~sGsGKSTLl~~Iag~~  181 (438)
T 2dpy_A          146 RAINALLTVGRGQRMGLFAGSGVGKSVLLGMMARYT  181 (438)
T ss_dssp             HHHHHHSCCBTTCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             eEEeeeEEecCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            3555544   46799999999999999977776654

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=96.99  E-value=0.00056  Score=41.78  Aligned_cols=23  Identities=30%  Similarity=0.434  Sum_probs=19.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      ..+++.|++|+|||+++..+...
T Consensus        49 ~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           49 PSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            37899999999999998887643

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=96.97  E-value=0.00061  Score=40.88  Aligned_cols=21  Identities=33%  Similarity=0.441  Sum_probs=18.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..+..
T Consensus         9 ~i~v~G~~~~GKSsli~~l~~   29 (177)
T 1wms_A            9 KVILLGDGGVGKSSLMNRYVT   29 (177)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            689999999999999888764

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=96.97  E-value=0.0006  Score=40.44  Aligned_cols=22  Identities=27%  Similarity=0.501  Sum_probs=18.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+++.|++|+|||+++..+...
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5789999999999998877643

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=96.97  E-value=0.00043  Score=42.31  Aligned_cols=21  Identities=29%  Similarity=0.491  Sum_probs=18.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|++|+|||+++..++.
T Consensus         4 kv~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            578999999999999888765

>2oze_A ORF delta'; para, walker type atpases, DNA segregation, PSM19035, plasmid, DNA binding protein; HET: AGS EPE; 1.83A {Streptococcus pyogenes}

Probab=96.96  E-value=0.003  Score=41.47  Aligned_cols=35  Identities=20%  Similarity=0.109  Sum_probs=27.0

Q ss_pred             CCceEEe---CCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEE
Q psy16285         34 REFAIIQ---GPPGTGKTYVALRIVEGFLKNKELARYMSGPILIV   75 (97)
Q Consensus        34 ~~~~~v~---Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~   75 (97)
                      ++.+.|.   +..|+||||++..++..+.+.       +.+++++
T Consensus        34 ~~~i~v~~~s~KGGvGKTT~a~nLA~~la~~-------G~rVlli   71 (298)
T 2oze_A           34 NEAIVILNNYFKGGVGKSKLSTMFAYLTDKL-------NLKVLMI   71 (298)
T ss_dssp             CSCEEEEECCSSSSSSHHHHHHHHHHHHHHT-------TCCEEEE
T ss_pred             CcEEEEEeccCCCCchHHHHHHHHHHHHHhC-------CCeEEEE
Confidence            4555555   488999999999999888655       6788775

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=96.96  E-value=0.00043  Score=50.00  Aligned_cols=26  Identities=19%  Similarity=0.307  Sum_probs=21.7

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..+....
T Consensus       368 ~G~~~~ivG~sGsGKSTll~~l~g~~  393 (582)
T 3b5x_A          368 QGKTVALVGRSGSGKSTIANLFTRFY  393 (582)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            36789999999999999988776544

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=96.95  E-value=0.00064  Score=40.15  Aligned_cols=21  Identities=29%  Similarity=0.488  Sum_probs=18.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..+..
T Consensus         6 ~i~v~G~~~~GKssl~~~l~~   26 (168)
T 1u8z_A            6 KVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            678999999999999877764

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=96.95  E-value=0.00065  Score=40.80  Aligned_cols=23  Identities=39%  Similarity=0.455  Sum_probs=19.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      -.++|.|++|+|||+++..+...
T Consensus         9 ~~i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A            9 LKVIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            36899999999999998877653

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=96.94  E-value=0.00068  Score=40.26  Aligned_cols=22  Identities=32%  Similarity=0.507  Sum_probs=19.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+++.|++|+|||+++..+...
T Consensus         8 ~i~v~G~~~~GKSsli~~l~~~   29 (170)
T 1z0j_A            8 KVCLLGDTGVGKSSIMWRFVED   29 (170)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            6899999999999998887654

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=96.94  E-value=0.0013  Score=42.50  Aligned_cols=32  Identities=25%  Similarity=0.423  Sum_probs=26.1

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEE
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIV   75 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~   75 (97)
                      +.|.|..|+||||++..++..+.+.       +.+++++
T Consensus         4 I~vs~KGGvGKTT~a~nLA~~la~~-------G~~Vlli   35 (269)
T 1cp2_A            4 VAIYGKGGIGKSTTTQNLTSGLHAM-------GKTIMVV   35 (269)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHTT-------TCCEEEE
T ss_pred             EEEecCCCCcHHHHHHHHHHHHHHC-------CCcEEEE
Confidence            4457899999999999999988765       6777775

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=96.94  E-value=0.0017  Score=46.57  Aligned_cols=28  Identities=14%  Similarity=0.292  Sum_probs=24.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.++|.|+||+|||+++..++..++..
T Consensus       167 ~pHlLIaG~TGSGKSt~L~~li~sLl~~  194 (512)
T 2ius_A          167 MPHLLVAGTTGSGASVGVNAMILSMLYK  194 (512)
T ss_dssp             SCSEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            4789999999999999999998776654

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=96.93  E-value=0.0014  Score=42.95  Aligned_cols=32  Identities=25%  Similarity=0.414  Sum_probs=26.2

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEE
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIV   75 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~   75 (97)
                      +.|.|..|+||||++..++..+.+.       +.+++++
T Consensus         5 Iavs~KGGvGKTT~a~nLA~~La~~-------G~rVlli   36 (289)
T 2afh_E            5 CAIYGKGGIGKSTTTQNLVAALAEM-------GKKVMIV   36 (289)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHT-------TCCEEEE
T ss_pred             EEEeCCCcCcHHHHHHHHHHHHHHC-------CCeEEEE
Confidence            4457899999999999999988765       6677765

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=96.92  E-value=0.00061  Score=40.49  Aligned_cols=21  Identities=33%  Similarity=0.610  Sum_probs=18.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|++|+|||+++..+..
T Consensus         5 ~i~v~G~~~~GKssli~~l~~   25 (170)
T 1g16_A            5 KILLIGDSGVGKSCLLVRFVE   25 (170)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECcCCCCHHHHHHHHHh
Confidence            578999999999999887763

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=96.92  E-value=0.00066  Score=40.59  Aligned_cols=21  Identities=33%  Similarity=0.507  Sum_probs=18.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..+..
T Consensus         6 ki~i~G~~~vGKSsl~~~l~~   26 (175)
T 2nzj_A            6 RVVLLGDPGVGKTSLASLFAG   26 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCccHHHHHHHHhc
Confidence            689999999999999887753

>1byi_A Dethiobiotin synthase; biotin synthesis, cyclo-ligase, ligase; 0.97A {Escherichia coli} SCOP: c.37.1.10 PDB: 1bs1_A* 1a82_A 1dad_A* 1dae_A* 1daf_A* 1dag_A* 1dah_A* 1dai_A* 1dak_A* 1dam_A* 1dbs_A 1dts_A

Probab=96.92  E-value=0.0018  Score=40.70  Aligned_cols=34  Identities=12%  Similarity=0.015  Sum_probs=26.4

Q ss_pred             eEEeC-CCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         37 AIIQG-PPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        37 ~~v~G-p~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +.|.+ -+|+|||+++..++..+.+.       +.+++++=|
T Consensus         4 I~v~s~kgGvGKTt~a~nLa~~la~~-------G~rVll~dp   38 (224)
T 1byi_A            4 YFVTGTDTEVGKTVASCALLQAAKAA-------GYRTAGYKP   38 (224)
T ss_dssp             EEEEESSTTSCHHHHHHHHHHHHHHT-------TCCEEEECS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-------CCCEEEEcc
Confidence            44444 58999999999999988766       678887643

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=96.92  E-value=0.00073  Score=40.20  Aligned_cols=22  Identities=32%  Similarity=0.424  Sum_probs=18.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++|.|++|+|||+++..+...
T Consensus         8 ~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            8 KVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            6899999999999998777643

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=96.92  E-value=0.00067  Score=40.29  Aligned_cols=21  Identities=33%  Similarity=0.542  Sum_probs=18.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..+..
T Consensus         5 ~i~v~G~~~~GKssli~~l~~   25 (172)
T 2erx_A            5 RVAVFGAGGVGKSSLVLRFVK   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            578999999999999877764

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=96.91  E-value=0.0041  Score=44.33  Aligned_cols=62  Identities=10%  Similarity=0.106  Sum_probs=41.4

Q ss_pred             HHHHHHh---cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe-CChHHHHHHHHHHHhh
Q psy16285         26 EAYKAAL---TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC-YTNHALDQFVEGVLKY   92 (97)
Q Consensus        26 ~~i~~~~---~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~-~~~~~~~~~~~~l~~~   92 (97)
                      .+|+...   +++...|.|++|+|||+++..++....+..     ....|++.+ .....+.++.+.+.+.
T Consensus       142 r~ID~l~pigkGQr~~Ifgg~G~GKT~L~~~i~~~~~~~~-----~~v~V~~~iGER~rEv~e~~~~~~~~  207 (482)
T 2ck3_D          142 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAH-----GGYSVFAGVGERTREGNDLYHEMIES  207 (482)
T ss_dssp             HHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHTTTTC-----SSEEEEEEESCCHHHHHHHHHHHHHH
T ss_pred             EEEecccccccCCeeeeecCCCCChHHHHHHHHHhhHhhC-----CCEEEEEECCCcchHHHHHHHHhhhc
Confidence            4555544   578999999999999999988888764431     122233222 3566677777777654

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=96.91  E-value=0.00066  Score=41.25  Aligned_cols=22  Identities=18%  Similarity=0.229  Sum_probs=19.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ..+++.|++|+|||+++..+..
T Consensus         8 ~~i~lvG~~gvGKStL~~~l~~   29 (188)
T 2wjg_A            8 YEIALIGNPNVGKSTIFNALTG   29 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            3689999999999999888764

>3qkt_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATP binding, DNA bindi MRE11, replication; HET: DNA ANP; 1.90A {Pyrococcus furiosus} PDB: 3qku_A* 1ii8_A 3qks_B* 3qkr_B* 1ii8_B

Probab=96.90  E-value=0.00075  Score=45.60  Aligned_cols=27  Identities=26%  Similarity=0.411  Sum_probs=22.3

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .+..+|.||+|+|||+++-++...+..
T Consensus        23 ~~~~~i~G~NGsGKS~lleAi~~~l~~   49 (339)
T 3qkt_A           23 EGINLIIGQNGSGKSSLLDAILVGLYW   49 (339)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHC
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhcC
Confidence            457799999999999999888766653

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=96.89  E-value=0.00085  Score=40.25  Aligned_cols=23  Identities=26%  Similarity=0.198  Sum_probs=19.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ...+++.|++|+|||+++..+..
T Consensus         8 ~~~i~v~G~~~~GKssl~~~l~~   30 (178)
T 2lkc_A            8 PPVVTIMGHVDHGKTTLLDAIRH   30 (178)
T ss_dssp             CCEEEEESCTTTTHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45789999999999999877754

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=96.89  E-value=0.00072  Score=40.24  Aligned_cols=20  Identities=25%  Similarity=0.341  Sum_probs=17.5

Q ss_pred             ceEEeCCCCCchHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      .+++.|++|+|||+++..+.
T Consensus         4 ki~ivG~~~~GKSsli~~l~   23 (169)
T 3q85_A            4 KVMLVGESGVGKSTLAGTFG   23 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            47899999999999988774

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=96.88  E-value=0.0008  Score=39.89  Aligned_cols=21  Identities=29%  Similarity=0.515  Sum_probs=18.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..+..
T Consensus         8 ~i~v~G~~~~GKssli~~l~~   28 (170)
T 1r2q_A            8 KLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            678999999999999887764

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=96.87  E-value=0.00082  Score=39.78  Aligned_cols=21  Identities=24%  Similarity=0.525  Sum_probs=18.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..+..
T Consensus         5 ki~v~G~~~~GKssli~~l~~   25 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            578999999999999887765

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=96.87  E-value=0.0015  Score=40.33  Aligned_cols=31  Identities=23%  Similarity=0.336  Sum_probs=24.8

Q ss_pred             EeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         39 IQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        39 v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ..+-.|+|||+++..++..+.+.       +.+++++-
T Consensus         7 ~s~kgG~GKTt~a~~la~~la~~-------g~~vlliD   37 (206)
T 4dzz_A            7 LNPKGGSGKTTAVINIATALSRS-------GYNIAVVD   37 (206)
T ss_dssp             CCSSTTSSHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             EeCCCCccHHHHHHHHHHHHHHC-------CCeEEEEE
Confidence            34677999999999999988765       66777765

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=96.87  E-value=0.0015  Score=47.31  Aligned_cols=26  Identities=15%  Similarity=0.176  Sum_probs=22.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+++.|++|+||||++..+...+...
T Consensus       398 ~I~l~GlsGSGKSTiA~~La~~L~~~  423 (573)
T 1m8p_A          398 TIFLTGYMNSGKDAIARALQVTLNQQ  423 (573)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHH
T ss_pred             EEEeecCCCCCHHHHHHHHHHHhccc
Confidence            57899999999999999998887653

>2woj_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; HET: ADP; 1.99A {Saccharomyces cerevisiae} PDB: 3h84_A 3zs8_A 3zs9_A* 3sja_A 3sjb_A 3sjc_A 3sjd_A* 3idq_A 3a36_A 3a37_A*

Probab=96.86  E-value=0.0015  Score=44.53  Aligned_cols=36  Identities=19%  Similarity=0.344  Sum_probs=29.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHH--hchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFL--KNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~--~~~~~~~~~~~~ilv~~~   77 (97)
                      ..+++.|-.|.|||+++..++..+-  +.       +++++++..
T Consensus        19 ~i~v~sgKGGvGKTTvaanLA~~lA~~~~-------G~rVLLvD~   56 (354)
T 2woj_A           19 KWIFVGGKGGVGKTTSSCSIAIQMALSQP-------NKQFLLIST   56 (354)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHHCT-------TSCEEEEEC
T ss_pred             EEEEEeCCCCCcHHHHHHHHHHHHHHhcC-------CCeEEEEEC
Confidence            4567789999999999999999887  44       677877764

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	97
d1uaaa1	306	c.37.1.19 (A:2-307) DEXX box DNA helicase {Escheri	2e-05
d1w36d1	359	c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha c	2e-05
d1pjra1	318	c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillu	2e-05
g1qhh.1	623	c.37.1.19 (A:,B:,C:,D:) DEXX box DNA helicase {Bac	5e-04
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	5e-04
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	0.002
d1yksa1	140	c.37.1.14 (A:185-324) YFV helicase domain {Yellow	0.002
d2i3ba1	189	c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57	0.004

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]} Length = 306

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

 Score = 39.3 bits (90), Expect = 2e-05
 Identities = 17/72 (23%), Positives = 29/72 (40%), Gaps = 5/72 (6%)

Query: 20 LNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN 79
          LN  Q +A +        ++    G+GKT V    +   ++      Y +  I  V +TN
Sbjct: 2  LNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGC---GYQARHIAAVTFTN 56

Query: 80 HALDQFVEGVLK 91
           A  +  E V +
Sbjct: 57 KAAREMKERVGQ 68

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]} Length = 359

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

 Score = 39.1 bits (90), Expect = 2e-05
 Identities = 19/73 (26%), Positives = 29/73 (39%), Gaps = 3/73 (4%)

Query: 15  QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILI 74
                    Q  A   ALTR  ++I G PGTGKT    +++   ++  +  R     I +
Sbjct: 144 FPVSDEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERC---RIRL 200

Query: 75  VCYTNHALDQFVE 87
              T  A  +  E
Sbjct: 201 AAPTGKAAARLTE 213

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]} Length = 318

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

 Score = 38.8 bits (89), Expect = 2e-05
 Identities = 21/74 (28%), Positives = 30/74 (40%), Gaps = 5/74 (6%)

Query: 19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT 78
           LN  Q EA +   T    +I    G+GKT V    +   +  K +A      IL + +T
Sbjct: 11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVA---PWNILAITFT 65

Query: 79 NHALDQFVEGVLKY 92
          N A  +  E V   
Sbjct: 66 NKAAREMRERVQSL 79

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 34.8 bits (78), Expect = 5e-04
 Identities = 14/58 (24%), Positives = 19/58 (32%), Gaps = 1/58 (1%)

Query: 23 IQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNH 80
           Q   Y         +I  P G GKT +A+ I E  L        M  P   +   + 
Sbjct: 13 YQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHA 69

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]} Length = 362

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

 Score = 33.5 bits (76), Expect = 0.002
 Identities = 11/65 (16%), Positives = 24/65 (36%), Gaps = 14/65 (21%)

Query: 19  GLNTIQFEAYKAALT----REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILI 74
            ++++ ++  K  +     + + + +GP  +GKT +A            L     G  L 
Sbjct: 135 KMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLA----------AALLELCGGKALN 184

Query: 75  VCYTN 79
           V    
Sbjct: 185 VNLPL 189

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 140

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score = 33.1 bits (74), Expect = 0.002
 Identities = 10/53 (18%), Positives = 16/53 (30%), Gaps = 6/53 (11%)

Query: 35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVE 87
             ++   PG GKT   L  +                 L++  T   L +  E
Sbjct: 8  MTTVLDFHPGAGKTRRFLPQILAE------CARRRLRTLVLAPTRVVLSEMKE 54

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]} Length = 189

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.3 bits (72), Expect = 0.004
 Identities = 8/26 (30%), Positives = 12/26 (46%)

Query: 38 IIQGPPGTGKTYVALRIVEGFLKNKE 63
           + GPPG GKT +  +  E    +  
Sbjct: 5  FLTGPPGVGKTTLIHKASEVLKSSGV 30

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	97
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	99.61
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.54
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	99.52
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	99.51
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.49
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.48
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.47
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.44
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	99.42
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.24
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.21
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.2
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.15
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.12
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.12
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.08
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.06
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.05
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.04
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.03
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.99
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	98.97
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	98.86
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	98.78
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	98.75
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.74
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	98.72
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.69
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.68
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	98.66
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.65
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.65
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	98.65
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.64
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.64
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	98.63
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.63
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.62
d1okkd2	207	GTPase domain of the signal recognition particle r	98.57
d1ls1a2	207	GTPase domain of the signal sequence recognition p	98.57
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	98.56
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.56
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	98.53
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	98.53
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	98.52
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.51
d1vmaa2	213	GTPase domain of the signal recognition particle r	98.51
d2qy9a2	211	GTPase domain of the signal recognition particle r	98.49
d1j8yf2	211	GTPase domain of the signal sequence recognition p	98.47
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	98.45
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	98.44
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.42
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.41
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	98.41
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.39
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	98.37
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	98.37
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.36
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	98.36
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	98.34
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	98.33
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	98.32
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	98.32
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.31
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	98.29
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	98.28
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	98.27
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	98.27
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	98.26
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	98.25
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	98.24
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.24
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	98.23
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	98.23
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.22
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	98.22
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	98.21
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	98.21
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	98.2
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	98.19
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	98.18
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	98.18
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	98.18
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	98.17
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	98.17
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	98.16
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	98.15
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	98.13
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	98.12
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	98.12
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	98.12
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	98.11
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	98.09
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	98.08
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.05
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	98.04
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.03
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	98.03
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	98.03
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.02
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	98.0
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	97.98
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.98
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	97.95
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	97.95
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	97.92
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	97.9
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	97.88
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.87
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	97.87
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	97.86
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	97.86
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	97.85
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	97.85
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	97.85
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	97.83
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.8
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	97.78
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.74
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	97.74
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	97.72
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.68
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	97.68
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	97.66
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	97.65
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	97.61
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	97.6
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	97.6
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	97.6
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	97.56
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	97.54
d2awna2	232	Maltose transport protein MalK, N-terminal domain	97.53
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	97.53
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	97.52
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	97.51
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.49
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	97.49
d1g2912	240	Maltose transport protein MalK, N-terminal domain	97.46
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	97.45
d1xpua3	289	Transcription termination factor Rho, ATPase domai	97.45
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	97.45
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	97.42
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	97.42
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	97.41
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	97.4
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	97.39
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	97.39
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	97.38
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	97.38
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	97.37
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	97.37
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	97.36
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	97.36
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	97.36
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	97.36
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	97.29
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	97.28
d1tuea_	205	Replication protein E1 helicase domain {Human papi	97.27
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	97.26
d1nrjb_	209	Signal recognition particle receptor beta-subunit	97.25
d2fh5b1	207	Signal recognition particle receptor beta-subunit	97.23
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	97.2
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	97.18
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	97.18
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	97.17
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	97.16
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	97.16
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	97.16
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	97.13
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	97.1
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	97.1
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	97.08
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	97.08
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	97.07
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	97.06
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	97.06
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	97.04
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	97.04
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	97.0
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	96.99
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	96.98
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	96.98
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.93
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	96.93
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	96.92
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	96.92
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	96.92
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	96.91
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	96.9
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	96.9
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	96.89
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	96.88
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	96.86
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	96.86
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	96.85
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	96.85
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	96.82
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	96.8
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	96.78
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	96.78
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	96.77
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	96.77
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	96.77
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	96.77
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	96.77
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	96.76
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	96.75
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	96.75
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	96.75
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	96.75
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	96.74
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	96.68
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	96.68
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	96.68
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	96.68
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	96.67
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	96.67
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	96.66
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	96.66
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	96.65
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	96.64
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	96.63
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	96.62
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	96.62
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	96.62
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	96.59
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	96.58
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	96.55
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	96.55
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	96.54
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	96.53
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	96.53
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	96.52
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	96.52
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	96.49
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	96.49
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	96.48
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	96.45
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	96.42
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	96.41
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	96.41
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	96.39
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	96.34
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	96.32
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	96.3
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	96.28
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	96.27
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	96.27
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	96.23
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	96.22
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	96.2
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	96.19
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	96.11
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	96.09
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	96.02
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	96.02
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	95.99
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	95.98
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	95.98
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	95.92
d1c9ka_	180	Adenosylcobinamide kinase/adenosylcobinamide phosp	95.89
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	95.87
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	95.78
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	95.67
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	95.65
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	95.64
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	95.59
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	95.55
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	95.53
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	95.47
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	95.43
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	95.41
d1d0xa2	712	Myosin S1, motor domain {Dictyostelium discoideum	95.4
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	95.35
d1lkxa_	684	Myosin S1, motor domain {Dictyostelium discoideum,	95.34
d1br2a2	710	Myosin S1, motor domain {Chicken (Gallus gallus),	95.29
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	95.25
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	95.25
d1g8fa3	122	ATP sulfurylase C-terminal domain {Baker's yeast (	95.22
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	95.2
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	95.18
d2mysa2	794	Myosin S1, motor domain {Chicken (Gallus gallus),	95.15
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	95.1
d2olra1	313	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	94.98
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	94.96
d1w7ja2	730	Myosin S1, motor domain {Chicken (Gallus gallus),	94.93
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	94.92
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	94.81
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	94.79
d1ii2a1	323	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	94.76
d1kk8a2	789	Myosin S1, motor domain {Bay scallop (Aequipecten	94.71
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	94.66
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	94.51
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	94.49
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	92.59
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	92.47
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	92.46
d1em8a_	147	DNA polymerase III chi subunit {Escherichia coli [	91.79
d1e8ca3	234	UDP-N-acetylmuramyl tripeptide synthetase MurE {Es	91.46
d1p3da3	215	UDP-N-acetylmuramate-alanine ligase MurC {Haemophi	91.32
d1d2ea3	196	Elongation factor Tu (EF-Tu), N-terminal (G) domai	91.21
d1jnya3	224	Elongation factor eEF-1alpha, N-terminal (G) domai	91.17
d2qn6a3	205	Initiation factor eIF2 gamma subunit, N-terminal (	91.06
d1zunb3	222	Sulfate adenylate transferase subunit cysN/C, EF-T	90.84
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	90.83
d2c07a1	251	beta-keto acyl carrier protein reductase {Malaria	90.81
d1jwyb_	306	Dynamin G domain {Dictyostelium discoideum [TaxId:	90.77
d2akab1	299	Dynamin G domain {Rat (Rattus norvegicus) [TaxId:	90.48
d1w6ua_	294	2,4-dienoyl-CoA reductase, mitochondrial (DECR) {H	90.43
d1kk1a3	195	Initiation factor eIF2 gamma subunit, N-terminal (	90.11
d1fmca_	255	7-alpha-hydroxysteroid dehydrogenase {Escherichia	90.1
d1gg4a4	214	UDP-murNac-tripeptide D-alanyl-D-alanine-adding en	89.98
d2rhca1	257	beta-keto acyl carrier protein reductase {Streptom	89.82
d1f60a3	239	Elongation factor eEF-1alpha, N-terminal (G) domai	89.68
d1ni3a1	296	YchF GTP-binding protein N-terminal domain {Fissio	89.66
d2ae2a_	259	Tropinone reductase {Jimsonweed (Datura stramonium	89.61
d1zema1	260	Xylitol dehydrogenase {Gluconobacter oxydans [TaxI	89.43
d2jfga3	204	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	89.27
d1ae1a_	258	Tropinone reductase {Jimsonweed (Datura stramonium	89.0
d1luaa1	191	Methylene-tetrahydromethanopterin dehydrogenase {M	88.7
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	88.7
d1wxqa1	319	GTP-binding protein PH0525 {Pyrococcus horikoshii	88.7
d1r0ka2	150	1-deoxy-D-xylulose-5-phosphate reductoisomerase {Z	88.61
d1j6ua3	207	UDP-N-acetylmuramate-alanine ligase MurC {Thermoto	88.6
d1xkqa_	272	Hypothetical protein R05D8.7 {Caenorhabditis elega	88.56
d1xg5a_	257	Putative dehydrogenase ARPG836 (MGC4172) {Human (H	87.98
d1eg7a_	549	Formyltetrahydrofolate synthetase {Moorella thermo	87.78
d1p77a1	171	Shikimate 5-dehydrogenase AroE {Haemophilus influe	87.34
d2gc6a2	296	Folylpolyglutamate synthetase {Lactobacillus casei	87.32
d1nyta1	170	Shikimate 5-dehydrogenase AroE {Escherichia coli [	87.12
d1xq1a_	259	Tropinone reductase {Thale cress (Arabidopsis thal	86.72
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	86.71
d1r5ba3	245	Eukaryotic peptide chain release factor ERF2, G do	86.51
d1xu9a_	269	11-beta-hydroxysteroid dehydrogenase 1 {Human (Hom	86.42
d1xhla_	274	Hypothetical protein F25D1.5 {Caenorhabditis elega	86.33
d1o5za2	296	Folylpolyglutamate synthetase {Thermotoga maritima	86.01
d1ulua_	256	Enoyl-ACP reductase {Thermus thermophilus [TaxId:	85.99
d1spxa_	264	Glucose dehydrogenase (5l265) {Nematode (Caenorhab	85.99
d1vl8a_	251	Gluconate 5-dehydrogenase {Thermotoga maritima [Ta	85.32
d1npya1	167	Shikimate 5-dehydrogenase-like protein HI0607 {Hae	85.22
d1geea_	261	Glucose dehydrogenase {Bacillus megaterium [TaxId:	85.05
d1yb1a_	244	17-beta-hydroxysteroid dehydrogenase type XI {Huma	84.73
d1gega_	255	meso-2,3-butanediol dehydrogenase {Klebsiella pneu	84.27
d2b2na1	308	Transcription-repair coupling factor, TRCF {Escher	83.68
d1g0oa_	272	1,3,8-trihydroxynaphtalene reductase (THNR, naphto	83.45
d1pr9a_	244	Carbonyl reductase {Human (Homo sapiens) [TaxId: 9	83.13
d1yxma1	297	Peroxisomal trans 2-enoyl CoA reductase {Human (Ho	82.93
d2bgka1	268	Rhizome secoisolariciresinol dehydrogenase {Mayapp	82.34
d1iy8a_	258	Levodione reductase {Corynebacterium aquaticum [Ta	81.85
d1q7ba_	243	beta-keto acyl carrier protein reductase {Escheric	81.79
d1nffa_	244	Putative oxidoreductase Rv2002 {Mycobacterium tube	81.69
d1zk4a1	251	R-specific alcohol dehydrogenase {Lactobacillus br	80.84
d1hxha_	253	3beta/17beta hydroxysteroid dehydrogenase {Comamon	80.72
d2gdza1	254	15-hydroxyprostaglandin dehydrogenase, PGDH {Human	80.56
d1bdba_	276	Cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase {Ps	80.47
d1q0qa2	151	1-deoxy-D-xylulose-5-phosphate reductoisomerase {E	80.43

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=99.61  E-value=9.8e-16  Score=99.90  Aligned_cols=70  Identities=23%  Similarity=0.216  Sum_probs=58.3

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .|+++|+++++.  ..++++|.||||||||+++...+..+++....   ++.+||++++|+.+++++.+++.+..
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~---~~~~ILvlt~tn~a~~~i~~~~~~~~   70 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGY---QARHIAAVTFTNKAAREMKERVGQTL   70 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCC---CGGGEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCC---ChhHEEEEeCcHHHHHHHHHHHHHhc
Confidence            478999999974  45678999999999999988888888765322   46789999999999999999997765

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.54  E-value=2.7e-14  Score=89.69  Aligned_cols=71  Identities=30%  Similarity=0.343  Sum_probs=61.8

Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         15 QEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ...+.|+++|+++++.+.++++.+|.+|+|+|||.++..++..+          ..++||+||+..+++|+.+.+.+++.
T Consensus        66 ~~~~~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~----------~~~~Liv~p~~~L~~q~~~~~~~~~~  135 (206)
T d2fz4a1          66 DAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL----------STPTLIVVPTLALAEQWKERLGIFGE  135 (206)
T ss_dssp             CCCCCCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS----------CSCEEEEESSHHHHHHHHHHHGGGCG
T ss_pred             CCCCCcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHHHHh----------cCceeEEEcccchHHHHHHHHHhhcc
Confidence            45678999999999999988889999999999999877665443          56899999999999999999999875


Q ss_pred             C
Q psy16285         95 N   95 (97)
Q Consensus        95 ~   95 (97)
                      +
T Consensus       136 ~  136 (206)
T d2fz4a1         136 E  136 (206)
T ss_dssp             G
T ss_pred             c
Confidence            3

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=99.52  E-value=2.4e-14  Score=94.02  Aligned_cols=70  Identities=29%  Similarity=0.305  Sum_probs=58.4

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .|+++|+++++.  ..+.++|.||||||||+++...+..++.....   ++.+|+++++|+.+++++..++.+..
T Consensus        11 ~L~~eQ~~~v~~--~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~---~p~~il~lt~t~~aa~~~~~~~~~~~   80 (318)
T d1pjra1          11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHV---APWNILAITFTNKAAREMRERVQSLL   80 (318)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCC---CGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHhC--CCCCEEEEecCCccHHHHHHHHHHHHHHcCCC---CHHHeEeEeccHHHHHHHHHHHHhhc
Confidence            489999999984  34579999999999999998888877765322   45789999999999999999998754

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=99.51  E-value=3.2e-14  Score=96.12  Aligned_cols=71  Identities=27%  Similarity=0.293  Sum_probs=60.3

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      .+.++|+.|+..+..++..+|+||||||||+++..++..+.+....   ++.+|++++||+.+++++.+.+...
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~---~~~~I~l~ApTgkAA~~L~e~~~~~  218 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADG---ERCRIRLAAPTGKAAARLTESLGKA  218 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSS---CCCCEEEEBSSHHHHHHHHHHHTHH
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHHhc---cCCeEEEecCcHHHHHHHHHHHHHH
Confidence            4577899999999999999999999999999998888877664221   4679999999999999999887653

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.49  E-value=7.5e-14  Score=88.92  Aligned_cols=69  Identities=23%  Similarity=0.175  Sum_probs=59.3

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+.+.|++++..+..++++++.+|||+|||.++...+......       +.++++++|++.++.|+.++++++..
T Consensus        43 ~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~-------~~rvliv~Pt~~La~Q~~~~l~~~~~  111 (237)
T d1gkub1          43 EPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK-------GKRCYVIFPTSLLVIQAAETIRKYAE  111 (237)
T ss_dssp             SCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT-------SCCEEEEESCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHh-------cCeEEEEeccHHHHHHHHHHHHHHHH
Confidence            5689999999999999999999999999998765555444443       78999999999999999999998764

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.48  E-value=2.2e-13  Score=84.33  Aligned_cols=71  Identities=24%  Similarity=0.247  Sum_probs=59.7

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+.++++|.++++.+.+ ++.+|.+|+|+|||.++..++.....+      .+.++++++|+..++.|+.+.+.+++.
T Consensus         7 ~~~pr~~Q~~~~~~~~~-~n~lv~~pTGsGKT~i~~~~~~~~~~~------~~~~il~i~P~~~L~~q~~~~~~~~~~   77 (200)
T d1wp9a1           7 LIQPRIYQEVIYAKCKE-TNCLIVLPTGLGKTLIAMMIAEYRLTK------YGGKVLMLAPTKPLVLQHAESFRRLFN   77 (200)
T ss_dssp             HHCCCHHHHHHHHHGGG-SCEEEECCTTSCHHHHHHHHHHHHHHH------SCSCEEEECSSHHHHHHHHHHHHHHBC
T ss_pred             CCCCCHHHHHHHHHHhc-CCeEEEeCCCCcHHHHHHHHHHHHHHh------cCCcEEEEcCchHHHHHHHHHHHHhhc
Confidence            45679999999998764 468899999999999877776666555      478999999999999999999999864

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=99.47  E-value=9.9e-14  Score=90.94  Aligned_cols=73  Identities=21%  Similarity=0.315  Sum_probs=65.7

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ..+.++++|++++..+.++++.++..|+|+|||.++..++..+...      ...++|+++|+..+++|+.+++.+++.
T Consensus       110 ~~~~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~~~~~~------~~~k~Liivp~~~Lv~Q~~~~f~~~~~  182 (282)
T d1rifa_         110 KRIEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN------YEGKILIIVPTTALTTQMADDFVDYRL  182 (282)
T ss_dssp             EECCCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHH------CSSEEEEECSSHHHHHHHHHHHHHHTS
T ss_pred             CccccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHHHhhhc------ccceEEEEEcCchhHHHHHHHHHHhhc
Confidence            3578999999999999999999999999999999988888777666      467899999999999999999998864

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.44  E-value=8.2e-14  Score=86.85  Aligned_cols=69  Identities=20%  Similarity=0.145  Sum_probs=58.3

Q ss_pred             CCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         19 GLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+.+.|.+++..+.+++++++.+|+|+|||+++...+......       ..++++++|++.++.+..++++++..
T Consensus        25 ~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~-------~~~vl~l~P~~~L~~q~~~~~~~~~~   93 (202)
T d2p6ra3          25 ELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK-------GGKSLYVVPLRALAGEKYESFKKWEK   93 (202)
T ss_dssp             CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHHTTTTT
T ss_pred             CCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhc-------cCcceeecccHHHHHHHHHHHHHHhh
Confidence            5778899999999999999999999999999865444433333       67899999999999999999998764

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.24  E-value=4.7e-11  Score=77.53  Aligned_cols=73  Identities=18%  Similarity=0.069  Sum_probs=64.6

Q ss_pred             ccCCCCCHHHHHHHHHHhc----C--CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALT----R--EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~----~--~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      .-.+.+++.|++++..+..    +  -..+++|.+|||||-++...+...+..       +.++++++||..++.|..+.
T Consensus        79 ~LPFeLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~-------g~q~~~m~Pt~~La~Qh~~~  151 (264)
T d1gm5a3          79 SLPFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA-------GFQTAFMVPTSILAIQHYRR  151 (264)
T ss_dssp             HSSSCCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH-------TSCEEEECSCHHHHHHHHHH
T ss_pred             hccccCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc-------ccceeEEeehHhhhHHHHHH
Confidence            4567899999999998863    2  367999999999999999998888887       88999999999999999999


Q ss_pred             HHhhcc
Q psy16285         89 VLKYTQ   94 (97)
Q Consensus        89 l~~~~~   94 (97)
                      +.+++.
T Consensus       152 ~~~~f~  157 (264)
T d1gm5a3         152 TVESFS  157 (264)
T ss_dssp             HHHHHT
T ss_pred             HHHhhh
Confidence            999885

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=99.21  E-value=7.5e-11  Score=75.31  Aligned_cols=73  Identities=21%  Similarity=0.138  Sum_probs=63.7

Q ss_pred             ccCCCCCHHHHHHHHHHhc---C---CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALT---R---EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~---~---~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      .-.+.+++.|..++..+..   .   ...+|+|.+|+|||-++...+...+.+       ++++++++|+..++.|..++
T Consensus        51 ~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~-------g~qv~~l~Pt~~La~Q~~~~  123 (233)
T d2eyqa3          51 SFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN-------HKQVAVLVPTTLLAQQHYDN  123 (233)
T ss_dssp             TCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT-------TCEEEEECSSHHHHHHHHHH
T ss_pred             ccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHc-------CCceEEEccHHHhHHHHHHH
Confidence            4568899999999988753   2   267999999999999999999888887       89999999999999999999


Q ss_pred             HHhhcc
Q psy16285         89 VLKYTQ   94 (97)
Q Consensus        89 l~~~~~   94 (97)
                      +++++.
T Consensus       124 ~~~~~~  129 (233)
T d2eyqa3         124 FRDRFA  129 (233)
T ss_dssp             HHHHST
T ss_pred             HHHHHh
Confidence            998754

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.20  E-value=1.9e-11  Score=75.99  Aligned_cols=68  Identities=16%  Similarity=0.131  Sum_probs=56.8

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         18 LGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      ..++++|.+++..+.+++++++..|||+|||.+.....   +.       ...++++++|+..++.+..+.++.++..
T Consensus        24 ~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~---~~-------~~~~~~~v~P~~~L~~q~~~~l~~~~~~   91 (206)
T d1oywa2          24 QQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPA---LL-------LNGLTVVVSPLISLMKDQVDQLQANGVA   91 (206)
T ss_dssp             SSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHH---HH-------SSSEEEEECSCHHHHHHHHHHHHHTTCC
T ss_pred             CCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhh---hh-------ccCceEEeccchhhhhhHHHHHHhhccc
Confidence            36788999999999999999999999999997653222   22       2678999999999999999999888643

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.15  E-value=2.9e-10  Score=71.06  Aligned_cols=75  Identities=19%  Similarity=0.146  Sum_probs=58.9

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +...+++.|.+++..+.+++.+++.+|+|||||.....-+........    ...+.++++|+++++.|+.+.+..+..
T Consensus        20 g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~----~~~~~lil~PtreL~~qi~~~~~~~~~   94 (207)
T d1t6na_          20 GFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT----GQVSVLVMCHTRELAFQISKEYERFSK   94 (207)
T ss_dssp             TCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCT----TCCCEEEECSCHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccC----CCceEEEEeccchhhHHHHHHHHHHHh
Confidence            445689999999999999999999999999999754333322222211    356899999999999999999888764

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.12  E-value=3e-10  Score=70.99  Aligned_cols=74  Identities=16%  Similarity=0.070  Sum_probs=59.6

Q ss_pred             cCCCCCHHHHHHHHHHhcCC-ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTRE-FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~-~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +...+++.|.+++..+.+++ ++++.+|+|+|||......+.......     .+.++++++|+.+++.++.+.++++..
T Consensus        23 g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~-----~~~~~lil~pt~~l~~q~~~~~~~~~~   97 (208)
T d1hv8a1          23 GFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-----NGIEAIILTPTRELAIQVADEIESLKG   97 (208)
T ss_dssp             TCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-----SSCCEEEECSCHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccc-----cCcceEEEeeccccchhhhhhhhhhcc
Confidence            34467899999999988775 899999999999987655554443332     467899999999999999999988764

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.12  E-value=3.7e-10  Score=71.18  Aligned_cols=75  Identities=19%  Similarity=0.082  Sum_probs=59.4

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +...+++.|..++..+..++.+++.+|+|||||.....-+...+...    ....+.++++||.+++.|+.+.+.++..
T Consensus        31 g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~----~~~~~alil~Pt~eL~~Q~~~~~~~~~~  105 (218)
T d2g9na1          31 GFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD----LKATQALVLAPTRELAQQIQKVVMALGD  105 (218)
T ss_dssp             TCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTT----CCSCCEEEECSSHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheeccc----ccCccEEEEcccchhhhhHHHHHhhhcc
Confidence            34568999999999999999999999999999986433333322221    1467899999999999999999988764

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.08  E-value=6.4e-10  Score=70.33  Aligned_cols=74  Identities=23%  Similarity=0.146  Sum_probs=58.9

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHH-HHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALR-IVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~-~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +...+++.|..++..+.+++.+++.+|+|||||..... ++..+....     ...+.++++||++++.|+.+.+.++..
T Consensus        36 g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~-----~~~~~lil~PtreLa~Qi~~~~~~l~~  110 (222)
T d2j0sa1          36 GFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV-----RETQALILAPTRELAVQIQKGLLALGD  110 (222)
T ss_dssp             TCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTS-----CSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccc-----cCceeEEecchHHHHHHHHHHHHHHhC
Confidence            45678999999999999999999999999999975332 333332221     356799999999999999999988864

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.06  E-value=1.1e-09  Score=68.74  Aligned_cols=75  Identities=17%  Similarity=0.036  Sum_probs=59.5

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +...+++.|.+++..+..++.+++.+|+|||||.....-+-..+...    ....++++++|+.+++.+..+.+..+..
T Consensus        29 g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~----~~~~~~lil~pt~el~~q~~~~~~~~~~  103 (212)
T d1qdea_          29 GFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS----VKAPQALMLAPTRELALQIQKVVMALAF  103 (212)
T ss_dssp             TCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT----CCSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhcc----CCCcceEEEcccHHHhhhhhhhhccccc
Confidence            45678999999999999999999999999999986433332222221    1467899999999999999999887754

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.05  E-value=1.2e-09  Score=68.20  Aligned_cols=74  Identities=18%  Similarity=0.057  Sum_probs=57.9

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHH-HHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRI-VEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~-~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +...+++.|++++..+.+++.+++.+|+|||||.....- +..+...     ....++++++|+.+++.|+.+.+..+..
T Consensus        22 g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~-----~~~~~~lil~pt~el~~q~~~~~~~~~~   96 (206)
T d1veca_          22 GWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK-----KDNIQAMVIVPTRELALQVSQICIQVSK   96 (206)
T ss_dssp             TCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT-----SCSCCEEEECSCHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhccccc-----ccCcceEEEeecchhhHHHHHHHHHHhh
Confidence            345789999999999999999999999999999653322 2222222     1467899999999999999998877653

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.04  E-value=1.6e-10  Score=67.43  Aligned_cols=51  Identities=18%  Similarity=0.112  Sum_probs=41.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      .+..+|.+|+|+|||+++...+    ..      .+.++++++|+..+++|+.+++.++..
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~----~~------~~~~vli~~P~~~l~~q~~~~~~~~~~   58 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAY----AA------QGYKVLVLNPSVAATLGFGAYMSKAHG   58 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHH----HT------TTCCEEEEESCHHHHHHHHHHHHHHHS
T ss_pred             CCEEEEEeCCCCCHHHHHHHHH----HH------cCCcEEEEcChHHHHHHHHHHHHHHhh
Confidence            4578999999999998754332    22      378999999999999999999988753

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=99.03  E-value=3.4e-09  Score=67.40  Aligned_cols=80  Identities=20%  Similarity=0.164  Sum_probs=61.2

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHH-HHHHHHHHHhchh----hhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYV-ALRIVEGFLKNKE----LARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~-~~~~~~~~~~~~~----~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      +...+++.|..++..+.++.++++++|+|||||.. +.-++..+.....    .......++++++|+++++.|+.+.+.
T Consensus        40 g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~~~alil~pt~el~~q~~~~~~  119 (238)
T d1wrba1          40 SYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQ  119 (238)
T ss_dssp             TCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCCCceEEEeccchhhhcchheeee
Confidence            55668999999999999999999999999999984 3444555543211    111235689999999999999999888


Q ss_pred             hhccC
Q psy16285         91 KYTQN   95 (97)
Q Consensus        91 ~~~~~   95 (97)
                      .+..+
T Consensus       120 ~~~~~  124 (238)
T d1wrba1         120 KFSLN  124 (238)
T ss_dssp             HHHTT
T ss_pred             ecccC
Confidence            77643

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=98.99  E-value=2.7e-10  Score=65.77  Aligned_cols=55  Identities=18%  Similarity=0.125  Sum_probs=42.9

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ++.+.+|.+|||+|||.++...+......      .+.++++++|+...++|+.+.+....
T Consensus         6 ~~~~~il~~~tGsGKT~~~~~~~~~~~~~------~~~~vli~~p~~~l~~q~~~~~~~~~   60 (140)
T d1yksa1           6 KGMTTVLDFHPGAGKTRRFLPQILAECAR------RRLRTLVLAPTRVVLSEMKEAFHGLD   60 (140)
T ss_dssp             TTCEEEECCCTTSSTTTTHHHHHHHHHHH------TTCCEEEEESSHHHHHHHHHHTTTSC
T ss_pred             cCCcEEEEcCCCCChhHHHHHHHHHHhhh------cCceeeeeecchhHHHHHHHHhhhhh
Confidence            46789999999999998775444333333      37899999999999999988776554

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=98.97  E-value=4.2e-10  Score=72.74  Aligned_cols=55  Identities=24%  Similarity=0.255  Sum_probs=44.8

Q ss_pred             cCCceEEeCCCCCchHH-HHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         33 TREFAIIQGPPGTGKTY-VALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~-~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +++..+|.+|||+|||+ .+..++......       +.++++++|+.+++.|+.++++++..
T Consensus         8 ~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~-------~~~~lvi~Ptr~La~q~~~~l~~~~~   63 (305)
T d2bmfa2           8 KKRLTIMDLHPGAGKTKRYLPAIVREAIKR-------GLRTLILAPTRVVAAEMEEALRGLPI   63 (305)
T ss_dssp             TTCEEEECCCTTSSTTTTHHHHHHHHHHHH-------TCCEEEEESSHHHHHHHHHHTTTSCC
T ss_pred             cCCcEEEEECCCCCHHHHHHHHHHHHHHhc-------CCEEEEEccHHHHHHHHHHHHhcCCc
Confidence            46788999999999996 344566655554       67899999999999999999887653

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=98.86  E-value=2.4e-09  Score=72.51  Aligned_cols=60  Identities=18%  Similarity=0.227  Sum_probs=46.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhh-----hhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKEL-----ARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~-----~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ++..+|.+++|||||+++...+..++.....     .+-.+.+||++++|+.|+.+|.+|+.+..
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~~L   80 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNI   80 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHHHH
Confidence            5789999999999999888877777643211     01134679999999999999999986643

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.78  E-value=4.8e-09  Score=62.57  Aligned_cols=27  Identities=30%  Similarity=0.546  Sum_probs=24.7

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++++|+|||||||||++..++..+...
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~~   28 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKSS   28 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHC
Confidence            578999999999999999999998776

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.75  E-value=5.8e-08  Score=60.10  Aligned_cols=75  Identities=24%  Similarity=0.053  Sum_probs=57.5

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +...+++.|.+++..+.+++.+++.+|+|||||......+.......    ....+.++++++...+.+.......+..
T Consensus        20 g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~   94 (206)
T d1s2ma1          20 GFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK----LNKIQALIMVPTRELALQTSQVVRTLGK   94 (206)
T ss_dssp             TCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT----SCSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccc----cccccceeeccchhhhhhhhhhhhhccc
Confidence            45568999999999999999999999999999965433222222221    1467889999999999998888877654

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.74  E-value=1.2e-08  Score=64.31  Aligned_cols=46  Identities=26%  Similarity=0.307  Sum_probs=35.5

Q ss_pred             cCCCCCHHHHHHHHHHhc---------CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         16 EELGLNTIQFEAYKAALT---------REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~---------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ..+.-++.|.+.+..++.         .+.++|.||||||||+++..++..+...
T Consensus        16 ~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~   70 (276)
T d1fnna2          16 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDK   70 (276)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTS
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcc
Confidence            345667788777766653         1578999999999999999998888554

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=98.72  E-value=4.5e-08  Score=60.44  Aligned_cols=74  Identities=26%  Similarity=0.148  Sum_probs=54.4

Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         16 EELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +...+++.|++++..+.+++.+++++|+|||||.....-+........    .....++++++.....+....+....
T Consensus        20 g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (209)
T d1q0ua_          20 RFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPER----AEVQAVITAPTRELATQIYHETLKIT   93 (209)
T ss_dssp             TCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTS----CSCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeecccccccc----ccccccccccccchhHHHHHHHHhhh
Confidence            344689999999999999999999999999999754333333322211    35678888888888888777665543

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.69  E-value=1.9e-08  Score=63.63  Aligned_cols=48  Identities=23%  Similarity=0.113  Sum_probs=34.4

Q ss_pred             ccCCCCCHHHHHHHHHHh-----cC--C-----ceEEeCCCCCchHHHHHHHHHHHHhch
Q psy16285         15 QEELGLNTIQFEAYKAAL-----TR--E-----FAIIQGPPGTGKTYVALRIVEGFLKNK   62 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~-----~~--~-----~~~v~Gp~GtGKT~~~~~~~~~~~~~~   62 (97)
                      +..+.-++.|.+.+..+.     ++  +     .+++.||||||||+++..++..+.+..
T Consensus        15 P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~   74 (287)
T d1w5sa2          15 PPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAA   74 (287)
T ss_dssp             CSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhc
Confidence            355666777877776543     11  1     245679999999999999999886653

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=98.68  E-value=2.7e-08  Score=62.16  Aligned_cols=57  Identities=19%  Similarity=0.334  Sum_probs=40.6

Q ss_pred             cccccccCCcccccCCCCCHHHHHHHHHHhcC---CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285          3 SILDAYDLSANVQEELGLNTIQFEAYKAALTR---EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus         3 ~~~~~~~~~~~~~~~~~l~~~Q~~~i~~~~~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +|.|.|.+.  .-.++..++...+.+..+.++   +.+++.||||+|||+++..++..+...
T Consensus        13 ~w~~ky~P~--~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak~l~~~   72 (231)
T d1iqpa2          13 PWVEKYRPQ--RLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGE   72 (231)
T ss_dssp             CHHHHTCCC--STTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGG
T ss_pred             hHHHHhCCC--CHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHHhc
Confidence            455555442  234455566777777777642   578999999999999999999887543

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.66  E-value=1.1e-07  Score=59.35  Aligned_cols=49  Identities=27%  Similarity=0.280  Sum_probs=35.3

Q ss_pred             CHHHHHHHHHHhcC-----CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         21 NTIQFEAYKAALTR-----EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        21 ~~~Q~~~i~~~~~~-----~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      +..-..++..+.+.     ..++|.||+||||||++.+++..+.+.       +.+++++.
T Consensus        18 N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~-------~~~~~~~~   71 (213)
T d1l8qa2          18 NRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKR-------GYRVIYSS   71 (213)
T ss_dssp             THHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             HHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHHhccC-------ccceEEec
Confidence            44444455554432     248999999999999999999998776       55666665

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.65  E-value=1.9e-08  Score=63.40  Aligned_cols=53  Identities=25%  Similarity=0.254  Sum_probs=37.5

Q ss_pred             ccccccCCcccccCCCCCHHHHHHHHHHhc--------------------CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285          4 ILDAYDLSANVQEELGLNTIQFEAYKAALT--------------------REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus         4 ~~~~~~~~~~~~~~~~l~~~Q~~~i~~~~~--------------------~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      |.|.|.+.  ....+..++...+.+..+..                    .+.+++.||||||||+++..++..+
T Consensus         4 W~eky~P~--~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~   76 (253)
T d1sxja2           4 WTVKYAPT--NLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL   76 (253)
T ss_dssp             HHHHTCCS--SGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             cccCcCCC--CHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            44555432  34556667777777766542                    1468999999999999999998765

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.65  E-value=2.9e-08  Score=61.79  Aligned_cols=56  Identities=18%  Similarity=0.300  Sum_probs=41.8

Q ss_pred             cccccccCCcccccCCCCCHHHHHHHHHHhcC---CceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285          3 SILDAYDLSANVQEELGLNTIQFEAYKAALTR---EFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus         3 ~~~~~~~~~~~~~~~~~l~~~Q~~~i~~~~~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ||.|.|.+.  .-.++..++...+.+..+...   +++++.||||+|||+++..++..+..
T Consensus         3 pw~ekyrP~--~~~divg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~l~~   61 (227)
T d1sxjc2           3 PWVEKYRPE--TLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYG   61 (227)
T ss_dssp             CHHHHTCCS--SGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHT
T ss_pred             chhhhhCCC--CHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHHhhc
Confidence            566777543  334456677788888887753   36899999999999999999988753

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=98.65  E-value=1.1e-07  Score=64.71  Aligned_cols=73  Identities=15%  Similarity=0.247  Sum_probs=58.6

Q ss_pred             ccccCCCCCHHHHHHHHHHhc----C-CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHH
Q psy16285         13 NVQEELGLNTIQFEAYKAALT----R-EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVE   87 (97)
Q Consensus        13 ~~~~~~~l~~~Q~~~i~~~~~----~-~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~   87 (97)
                      .....+.....|-++|..+.+    + +..+|.|-+|||||+++..++...          ++++||++|+...+.++.+
T Consensus         5 ~~~~~~~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA~l~~~~----------~rp~LVVt~n~~~A~qL~~   74 (413)
T d1t5la1           5 QLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQV----------NKPTLVIAHNKTLAGQLYS   74 (413)
T ss_dssp             CCCCSSCCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHHHHHHHH----------TCCEEEECSSHHHHHHHHH
T ss_pred             EEecCCCCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHHHHHHHh----------CCCEEEEeCCHHHHHHHHH
Confidence            344556667778777776654    3 467899999999999987777654          6789999999999999999


Q ss_pred             HHHhhccC
Q psy16285         88 GVLKYTQN   95 (97)
Q Consensus        88 ~l~~~~~~   95 (97)
                      .|+.|..+
T Consensus        75 dL~~~l~~   82 (413)
T d1t5la1          75 ELKEFFPH   82 (413)
T ss_dssp             HHHHHCTT
T ss_pred             HHHHHcCC
Confidence            99998753

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.64  E-value=3.1e-08  Score=61.72  Aligned_cols=57  Identities=21%  Similarity=0.289  Sum_probs=39.7

Q ss_pred             cccccccCCcccccCCCCCHHHHHHHHHHhcC---CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285          3 SILDAYDLSANVQEELGLNTIQFEAYKAALTR---EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus         3 ~~~~~~~~~~~~~~~~~l~~~Q~~~i~~~~~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ||.|.|.+.  ...++...+...+.+..+...   +++++.||||+|||+++..++..+...
T Consensus         4 pw~eKyrP~--~~~d~ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~   63 (224)
T d1sxjb2           4 PWVEKYRPQ--VLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGR   63 (224)
T ss_dssp             CHHHHTCCS--SGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGG
T ss_pred             chHhHhCCC--CHHHhcCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHHHhcc
Confidence            455555432  223344555667777777643   478999999999999999999887654

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.64  E-value=2.4e-07  Score=57.96  Aligned_cols=73  Identities=18%  Similarity=0.236  Sum_probs=55.6

Q ss_pred             CCCCCHHHHHHHHHHhc---C-CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         17 ELGLNTIQFEAYKAALT---R-EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~---~-~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      .-.|.++|.+++..+..   . ...++.=++|+|||..+.+++..+....     ...++||+||... ..+|.+.+.++
T Consensus        10 ~~~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~~~~~~~~-----~~~~~LIv~p~~l-~~~W~~e~~~~   83 (230)
T d1z63a1          10 KANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKEN-----ELTPSLVICPLSV-LKNWEEELSKF   83 (230)
T ss_dssp             SSCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTT-----CCSSEEEEECSTT-HHHHHHHHHHH
T ss_pred             hcchhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhhhhhhhcc-----cccccceecchhh-hhHHHHHHHhh
Confidence            34689999999986542   2 3455556899999999988888877663     3578999998554 78899998887


Q ss_pred             ccC
Q psy16285         93 TQN   95 (97)
Q Consensus        93 ~~~   95 (97)
                      ..+
T Consensus        84 ~~~   86 (230)
T d1z63a1          84 APH   86 (230)
T ss_dssp             CTT
T ss_pred             ccc
Confidence            643

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=98.63  E-value=2.6e-08  Score=58.91  Aligned_cols=36  Identities=14%  Similarity=0.114  Sum_probs=30.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +.+.|+|++||||||++..++..+..+       +.++.++-+
T Consensus         3 Pvi~itG~~GSGKTTL~~~L~~~l~~~-------g~~v~v~~~   38 (170)
T d1np6a_           3 PLLAFAAWSGTGKTTLLKKLIPALCAR-------GIRPGLIKH   38 (170)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHT-------TCCEEEEEE
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHC-------CCeEEEecc
Confidence            467899999999999999999998776       666666654

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=98.63  E-value=8.7e-08  Score=59.96  Aligned_cols=25  Identities=36%  Similarity=0.659  Sum_probs=22.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +++++.||||||||+++..++..+.
T Consensus        36 ~~~L~~GPpGtGKT~lA~~la~~~~   60 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLAHIIASELQ   60 (238)
T ss_dssp             CCEEEESSTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCcHHHHHHHHHhccC
Confidence            5799999999999999999988773

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.62  E-value=2.2e-08  Score=62.51  Aligned_cols=57  Identities=23%  Similarity=0.373  Sum_probs=37.7

Q ss_pred             cccccccCCcccccCCCCCHHHHHHHHHHhcC---CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285          3 SILDAYDLSANVQEELGLNTIQFEAYKAALTR---EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus         3 ~~~~~~~~~~~~~~~~~l~~~Q~~~i~~~~~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ||.|.|.+.  .-.++..++...+.+..+..+   +++++.||||+|||+++..++..+...
T Consensus         1 ~w~~ky~P~--~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~   60 (237)
T d1sxjd2           1 PWVEKYRPK--NLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGP   60 (237)
T ss_dssp             CHHHHTCCS--STTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHH
T ss_pred             CcchhhCCC--CHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHHcCC
Confidence            345555432  112233344456667766643   468999999999999999999887543

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=98.57  E-value=1.1e-07  Score=59.40  Aligned_cols=47  Identities=15%  Similarity=0.193  Sum_probs=35.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC---ChHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY---TNHALDQFVE   87 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~---~~~~~~~~~~   87 (97)
                      +..+++.||+|+||||++..++.++...       ++++.+++-   ...+.+|+..
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~~~~~-------g~kV~lit~Dt~R~gA~eQL~~   55 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRYYQNL-------GKKVMFCAGDTFRAAGGTQLSE   55 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHTT-------TCCEEEECCCCSSTTHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHC-------CCcEEEEEeccccccchhhHhh
Confidence            3567889999999999999998877544       667777774   3456666544

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=98.57  E-value=1.3e-07  Score=59.00  Aligned_cols=47  Identities=21%  Similarity=0.199  Sum_probs=34.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC---ChHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY---TNHALDQFVEG   88 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~---~~~~~~~~~~~   88 (97)
                      ..+++.||+|+||||++..++.++..+       +.++.+++.   ...+.+|+..-
T Consensus        11 ~vi~lvGp~GvGKTTTiaKLA~~~~~~-------g~kV~lit~Dt~R~gA~eQL~~~   60 (207)
T d1ls1a2          11 NLWFLVGLQGSGKTTTAAKLALYYKGK-------GRRPLLVAADTQRPAAREQLRLL   60 (207)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHHHHHT-------TCCEEEEECCSSCHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHC-------CCcEEEEecccccchHHHHHHHH
Confidence            356779999999999999999888655       667777764   44555555443

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=98.56  E-value=3.1e-07  Score=59.58  Aligned_cols=76  Identities=18%  Similarity=0.169  Sum_probs=56.7

Q ss_pred             CCCCHHHHHHHHHHhc--------CC-ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHH
Q psy16285         18 LGLNTIQFEAYKAALT--------RE-FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEG   88 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~~--------~~-~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~   88 (97)
                      -.|++.|.+++..+.+        .. ..++.=..|+|||..+.+++..+........+...++||+||.. .+.+|.+.
T Consensus        54 ~~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~s-l~~qW~~E  132 (298)
T d1z3ix2          54 KVLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSS-LVRNWYNE  132 (298)
T ss_dssp             TTCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECHH-HHHHHHHH
T ss_pred             ccccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccch-hhHHHHHH
Confidence            3689999999987542        22 34555578999999988888888776433222345799999986 68999999


Q ss_pred             HHhhcc
Q psy16285         89 VLKYTQ   94 (97)
Q Consensus        89 l~~~~~   94 (97)
                      +.++..
T Consensus       133 i~k~~~  138 (298)
T d1z3ix2         133 VGKWLG  138 (298)
T ss_dssp             HHHHHG
T ss_pred             HHhhcC
Confidence            998764

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.56  E-value=5.1e-08  Score=61.26  Aligned_cols=54  Identities=22%  Similarity=0.309  Sum_probs=38.2

Q ss_pred             ccccccCCcccccCCCCCHHHHHHHHHHhc----CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285          4 ILDAYDLSANVQEELGLNTIQFEAYKAALT----REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus         4 ~~~~~~~~~~~~~~~~l~~~Q~~~i~~~~~----~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      |.|.|.+.  .-.++...+...+.+..+..    .+.+++.||||+|||+++..++..+.
T Consensus         1 W~eky~P~--~~~diig~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l~   58 (252)
T d1sxje2           1 WVDKYRPK--SLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIF   58 (252)
T ss_dssp             CTTTTCCC--SGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHS
T ss_pred             CCcccCCC--CHHHccCcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhhc
Confidence            44555432  22345556777777776653    24689999999999999999998874

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=98.53  E-value=3.2e-08  Score=58.62  Aligned_cols=24  Identities=25%  Similarity=0.450  Sum_probs=21.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++++|.|||||||||++..++..+
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~l   28 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASKS   28 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            578999999999999999887765

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=98.53  E-value=2.8e-08  Score=58.01  Aligned_cols=25  Identities=20%  Similarity=0.513  Sum_probs=22.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++++.||||+||||++..++..+
T Consensus         2 ~k~I~l~G~~GsGKSTvak~La~~L   26 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQLAQQL   26 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHh
Confidence            3578999999999999999998876

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=98.52  E-value=8.2e-08  Score=60.03  Aligned_cols=52  Identities=23%  Similarity=0.411  Sum_probs=39.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +..++|.||||+|||+++..++..+..+       +.++++++.. .....+.+.+.+++
T Consensus        26 gsl~li~G~pGsGKT~l~~qia~~~~~~-------~~~~~~is~e-~~~~~~~~~~~~~~   77 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRFVENACAN-------KERAILFAYE-ESRAQLLRNAYSWG   77 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHHTT-------TCCEEEEESS-SCHHHHHHHHHTTS
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHh-------ccccceeecc-CCHHHHHHHHHHcC
Confidence            4578999999999999999999998776       6677777743 33555666666554

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=98.51  E-value=7.8e-08  Score=60.28  Aligned_cols=25  Identities=40%  Similarity=0.593  Sum_probs=22.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +++++.||||||||+++..++..+.
T Consensus        36 ~~~Ll~GPpG~GKTtla~~la~~~~   60 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAHVIAHELG   60 (239)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhC
Confidence            5799999999999999999987763

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=98.51  E-value=2.4e-07  Score=58.04  Aligned_cols=45  Identities=20%  Similarity=0.358  Sum_probs=33.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC---ChHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY---TNHALDQFVE   87 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~---~~~~~~~~~~   87 (97)
                      .+++.||+|+||||++..++.++..+       +++|.+++-   ...+.+|+..
T Consensus        13 vi~lvGptGvGKTTTiAKLAa~~~~~-------~~kV~lit~Dt~R~gA~eQL~~   60 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLAKMFVDE-------GKSVVLAAADTFRAAAIEQLKI   60 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHT-------TCCEEEEEECTTCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-------CCceEEEeecccccchhHHHHH
Confidence            56789999999999999999888655       567777763   4455555544

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=98.49  E-value=2.6e-07  Score=57.85  Aligned_cols=45  Identities=18%  Similarity=0.313  Sum_probs=33.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC---ChHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY---TNHALDQFVE   87 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~---~~~~~~~~~~   87 (97)
                      .+++.||+|+||||++..++.++.++       +.+|.+++.   ...+.+|+..
T Consensus        11 vi~lvGptGvGKTTTiAKLA~~~~~~-------g~kV~lit~Dt~R~gA~eQL~~   58 (211)
T d2qy9a2          11 VILMVGVNGVGKTTTIGKLARQFEQQ-------GKSVMLAAGDTFRAAAVEQLQV   58 (211)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTT-------TCCEEEECCCTTCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-------CCcEEEEecccccccchhhhhh
Confidence            46779999999999999998877544       677887775   3445555543

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=98.47  E-value=2.9e-07  Score=57.55  Aligned_cols=45  Identities=24%  Similarity=0.264  Sum_probs=29.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC---ChHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY---TNHALDQFVE   87 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~---~~~~~~~~~~   87 (97)
                      .+++.||+|+||||++..++.++..+       +.+|.+++-   ...+.+|+..
T Consensus        14 vi~lvGptGvGKTTTiAKLA~~~~~~-------g~kV~lit~Dt~R~ga~eQL~~   61 (211)
T d1j8yf2          14 VIMLVGVQGTGKATTAGKLAYFYKKK-------GFKVGLVGADVYRPAALEQLQQ   61 (211)
T ss_dssp             EEEEECSCCC----HHHHHHHHHHHT-------TCCEEEEECCCSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-------CCceEEEEeeccccchhHHHHH
Confidence            46779999999999999999877544       667777775   4455555443

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=98.45  E-value=2e-07  Score=59.34  Aligned_cols=23  Identities=39%  Similarity=0.673  Sum_probs=20.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.||||||||+++.+++..+
T Consensus        42 ~vLL~GppGtGKT~la~alA~~~   64 (246)
T d1d2na_          42 SVLLEGPPHSGKTALAAKIAEES   64 (246)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECcCCCCHHHHHHHHhhcc
Confidence            58999999999999999998775

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=98.44  E-value=2.1e-07  Score=55.33  Aligned_cols=36  Identities=19%  Similarity=0.350  Sum_probs=28.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      ++.++|.|+||+||||++..+...+-..       +.++.+++
T Consensus         1 ~kiI~i~G~~GsGKsT~~~~L~~~l~~~-------~~~~~~~~   36 (190)
T d1khta_           1 NKVVVVTGVPGVGSTTSSQLAMDNLRKE-------GVNYKMVS   36 (190)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHTT-------TCCCEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHc-------CCCeEEEe
Confidence            3568999999999999999998887554       44555554

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=98.42  E-value=3.4e-07  Score=58.67  Aligned_cols=24  Identities=42%  Similarity=0.623  Sum_probs=21.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++..++..+
T Consensus        46 ~~iLL~GppGtGKT~la~~iA~~~   69 (256)
T d1lv7a_          46 KGVLMVGPPGTGKTLLAKAIAGEA   69 (256)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEeeCCCCCCccHHHHHHHHHc
Confidence            458999999999999999998877

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=98.41  E-value=6e-08  Score=61.29  Aligned_cols=23  Identities=35%  Similarity=0.518  Sum_probs=20.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.||||||||+++..++..+
T Consensus        34 ~ilL~GpPGtGKT~la~~la~~~   56 (273)
T d1gvnb_          34 AFLLGGQPGSGKTSLRSAIFEET   56 (273)
T ss_dssp             EEEEECCTTSCTHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999888776

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=98.41  E-value=4.8e-08  Score=58.09  Aligned_cols=24  Identities=21%  Similarity=0.355  Sum_probs=21.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++++|.|||||||||++..++..+
T Consensus         8 K~I~i~G~~GsGKTTla~~La~~~   31 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVNKLAAVF   31 (192)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            578999999999999999988765

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=98.39  E-value=2e-07  Score=59.46  Aligned_cols=23  Identities=35%  Similarity=0.554  Sum_probs=20.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.||||||||+++.+++..+
T Consensus        44 giLl~GppGtGKT~la~aia~~~   66 (247)
T d1ixza_          44 GVLLVGPPGVGKTHLARAVAGEA   66 (247)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT
T ss_pred             eEEEecCCCCChhHHHHHHHHHc
Confidence            58999999999999999998765

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=98.37  E-value=5.3e-07  Score=61.00  Aligned_cols=47  Identities=15%  Similarity=0.408  Sum_probs=39.8

Q ss_pred             ccCCCCCHHHHHHHHHHhc--CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         15 QEELGLNTIQFEAYKAALT--REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~--~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ...+.+.+.|.+.++.+..  ++.++|.||+|+||||++..++..+...
T Consensus       137 l~~LG~~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl~~~l~~~~~~  185 (401)
T d1p9ra_         137 LHSLGMTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLYAGLQELNSS  185 (401)
T ss_dssp             GGGSCCCHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHHHHHHHHCCT
T ss_pred             hhhhcccHHHHHHHHHHHhhhhceEEEEcCCCCCccHHHHHHhhhhcCC
Confidence            4567789999999998774  4688999999999999999999987544

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=98.37  E-value=1.4e-07  Score=61.81  Aligned_cols=26  Identities=31%  Similarity=0.420  Sum_probs=22.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      .+.+++.||||||||.++.+++..+.
T Consensus        49 ~~~iLl~GPpG~GKT~lAkalA~~~~   74 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIARRLAKLAN   74 (309)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CceEEEECCCCCCHHHHHHHHhhccc
Confidence            46789999999999999999988763

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.36  E-value=1.4e-07  Score=56.25  Aligned_cols=25  Identities=48%  Similarity=0.639  Sum_probs=21.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .++|+||||+||||++..++..+-.
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l~~   26 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGG
T ss_pred             EEEEECCCCcHHHHHHHHHHhcCCC
Confidence            4789999999999999998887744

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=98.36  E-value=9.9e-08  Score=56.21  Aligned_cols=24  Identities=33%  Similarity=0.646  Sum_probs=20.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.++|.|||||||||++..++..+
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~   26 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQL   26 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            357899999999999998887664

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=98.34  E-value=1.4e-07  Score=55.78  Aligned_cols=25  Identities=24%  Similarity=0.478  Sum_probs=21.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..++|.|||||||||++..++..+
T Consensus         6 ~~iivl~G~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3467889999999999999998776

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=98.33  E-value=1.6e-07  Score=54.68  Aligned_cols=22  Identities=27%  Similarity=0.492  Sum_probs=18.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ..+++.||||+||||++..++.
T Consensus         3 klIii~G~pGsGKTTla~~L~~   24 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIA   24 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            3578899999999999887754

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=98.32  E-value=1.5e-07  Score=55.71  Aligned_cols=25  Identities=16%  Similarity=0.284  Sum_probs=21.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+.++|.||||+||||++..++..+
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l   27 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHc
Confidence            4678889999999999999988875

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=98.32  E-value=1.8e-07  Score=55.34  Aligned_cols=28  Identities=14%  Similarity=0.106  Sum_probs=23.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +-.++++|+||+||||++..++..+...
T Consensus         6 g~~I~l~G~~GsGKTTia~~La~~L~~~   33 (183)
T d1m8pa3           6 GFTIFLTGYMNSGKDAIARALQVTLNQQ   33 (183)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhc
Confidence            3456799999999999999999888654

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.31  E-value=4e-07  Score=58.14  Aligned_cols=33  Identities=27%  Similarity=0.460  Sum_probs=26.1

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      ..+++.||||||||+++.+++..+          +..++.+.+
T Consensus        39 ~giLL~GppGtGKT~l~~ala~~~----------~~~~~~i~~   71 (258)
T d1e32a2          39 RGILLYGPPGTGKTLIARAVANET----------GAFFFLING   71 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHT----------TCEEEEECH
T ss_pred             ceeEEecCCCCCchHHHHHHHHHh----------CCeEEEEEc
Confidence            468999999999999998888765          445666654

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=98.29  E-value=1.7e-07  Score=55.51  Aligned_cols=24  Identities=42%  Similarity=0.540  Sum_probs=20.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      -+++|.||||+||||++..+...+
T Consensus         6 ~~I~i~G~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_           6 INILITGTPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHh
Confidence            468999999999999998887765

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=98.28  E-value=2.6e-07  Score=55.34  Aligned_cols=23  Identities=35%  Similarity=0.585  Sum_probs=19.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++|.|||||||||++..++..+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999998887665

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.27  E-value=1.4e-06  Score=52.91  Aligned_cols=34  Identities=21%  Similarity=0.315  Sum_probs=26.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      .+++.|.||+||||++..++..+-..       ..++.++.
T Consensus         4 li~l~GlpgsGKSTla~~L~~~l~~~-------~~~~~~~~   37 (213)
T d1bifa1           4 LIVMVGLPARGKTYISKKLTRYLNFI-------GVPTREFN   37 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhc-------CCCCeEEc
Confidence            36789999999999999999877544       45565555

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.27  E-value=3.4e-07  Score=54.48  Aligned_cols=24  Identities=29%  Similarity=0.627  Sum_probs=21.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++++.|+||+||||++..++..+
T Consensus         2 p~IvliG~~G~GKSTig~~La~~l   25 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIGRRLAKAL   25 (165)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Confidence            568888999999999999998776

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.26  E-value=3.4e-07  Score=55.11  Aligned_cols=23  Identities=35%  Similarity=0.717  Sum_probs=20.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++|.|||||||||++..++..+
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999999887765

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=98.25  E-value=3.9e-07  Score=54.19  Aligned_cols=23  Identities=22%  Similarity=0.346  Sum_probs=20.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++++.|+||+||||++..++..+
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~l   24 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKDL   24 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Confidence            57889999999999999998877

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=98.24  E-value=1.1e-06  Score=52.08  Aligned_cols=37  Identities=16%  Similarity=0.073  Sum_probs=30.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCCh
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN   79 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~   79 (97)
                      .+-|.|++||||||++..++..+-.+       +.++.++-+..
T Consensus         3 ii~I~G~~gSGKTTli~~l~~~L~~~-------g~~v~vik~d~   39 (165)
T d1xjca_           3 VWQVVGYKHSGKTTLMEKWVAAAVRE-------GWRVGTVKHHG   39 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHT-------TCCEEEEECCC
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhC-------CCeEEEEEecc
Confidence            35699999999999999999999776       67777776543

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.24  E-value=6.3e-07  Score=57.48  Aligned_cols=24  Identities=38%  Similarity=0.602  Sum_probs=21.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..+++.||||||||+++.+++..+
T Consensus        42 ~giLL~Gp~GtGKT~l~~ala~~~   65 (265)
T d1r7ra3          42 KGVLFYGPPGCGKTLLAKAIANEC   65 (265)
T ss_dssp             CEEEEBCCTTSSHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCcchhHHHHHHHHh
Confidence            468999999999999999998876

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=98.23  E-value=5.2e-07  Score=53.88  Aligned_cols=24  Identities=25%  Similarity=0.374  Sum_probs=20.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.+++.|+||+||||++..++..+
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~L   26 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARAL   26 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHh
Confidence            457889999999999999998765

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=98.23  E-value=1.8e-06  Score=54.92  Aligned_cols=40  Identities=13%  Similarity=0.148  Sum_probs=33.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      .+..++|.|+||+|||+++..++..+...      .+.++++++..
T Consensus        34 ~G~l~vi~G~~G~GKT~~~~~la~~~a~~------~g~~v~~~s~E   73 (277)
T d1cr2a_          34 GGEVIMVTSGSGMGKSTFVRQQALQWGTA------MGKKVGLAMLE   73 (277)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHHHHT------SCCCEEEEESS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHhhhhh------cccceeEeeec
Confidence            45789999999999999999998876544      37889998853

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.22  E-value=4.6e-06  Score=51.43  Aligned_cols=58  Identities=14%  Similarity=0.212  Sum_probs=39.9

Q ss_pred             CCHHHHHHHHHHhc---CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         20 LNTIQFEAYKAALT---REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        20 l~~~Q~~~i~~~~~---~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      -++...+.+..++.   ..+.++.||||+|||.++..++..+....-.....+.+++-+..
T Consensus        26 gRd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~   86 (195)
T d1jbka_          26 GRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDM   86 (195)
T ss_dssp             SCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECH
T ss_pred             CcHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeH
Confidence            35656655655553   35899999999999999999999988753212223456665554

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=98.22  E-value=5.2e-06  Score=56.28  Aligned_cols=67  Identities=21%  Similarity=0.289  Sum_probs=52.4

Q ss_pred             CCCHHHHHHHHHHh----cCC-ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         19 GLNTIQFEAYKAAL----TRE-FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        19 ~l~~~Q~~~i~~~~----~~~-~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +....|-++|..+.    ++. ...|.|.+||+|++++.++....          ++++||+|++...+.++.+.|+.+.
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A~l~~~~----------~rp~LvVt~~~~~A~~l~~dL~~~l   77 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVIEAL----------GRPALVLAPNKILAAQLAAEFRELF   77 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHH----------TCCEEEEESSHHHHHHHHHHHHHHC
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHHHHHHHh----------CCCEEEEeCCHHHHHHHHHHHHHhc
Confidence            44456766666544    333 46899999999999987776654          6789999999999999999999986


Q ss_pred             cC
Q psy16285         94 QN   95 (97)
Q Consensus        94 ~~   95 (97)
                      .+
T Consensus        78 ~~   79 (408)
T d1c4oa1          78 PE   79 (408)
T ss_dssp             TT
T ss_pred             Cc
Confidence            43

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=98.21  E-value=4.2e-07  Score=55.09  Aligned_cols=24  Identities=25%  Similarity=0.338  Sum_probs=20.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      -.++|.|||||||||++..++..+
T Consensus         4 m~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            368899999999999998886655

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=98.21  E-value=5.9e-07  Score=54.39  Aligned_cols=25  Identities=36%  Similarity=0.656  Sum_probs=20.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +-++++.|||||||||++..++..+
T Consensus         3 ~~riil~G~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHHh
Confidence            3467889999999999998887654

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=98.20  E-value=1.2e-06  Score=53.80  Aligned_cols=52  Identities=15%  Similarity=0.380  Sum_probs=35.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +..++|.|+||+|||+++..++......      .+..+++++... ....+...+.++
T Consensus        26 G~~~~I~G~~G~GKT~la~~~~~~~~~~------~~~~~~~~s~e~-~~~~~~~~~~~~   77 (242)
T d1tf7a1          26 GRSTLVSGTSGTGKTLFSIQFLYNGIIE------FDEPGVFVTFEE-TPQDIIKNARSF   77 (242)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHH------HCCCEEEEESSS-CHHHHHHHHGGG
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHh------cCCCcccccccC-CHHHHHHHHHHc
Confidence            4688999999999999998887765555      256788777432 233444444433

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=98.19  E-value=3.2e-07  Score=54.31  Aligned_cols=24  Identities=25%  Similarity=0.523  Sum_probs=19.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +..++|.|||||||||++..+...
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~   27 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANL   27 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            456789999999999998777543

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=98.18  E-value=1.4e-06  Score=51.94  Aligned_cols=35  Identities=29%  Similarity=0.412  Sum_probs=27.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      .++|.|+||+||||++..+...+-..       +.++.++.+
T Consensus         3 iivi~G~~GsGKTT~~~~La~~L~~~-------~~~~~~~~~   37 (194)
T d1nksa_           3 IGIVTGIPGVGKSTVLAKVKEILDNQ-------GINNKIINY   37 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTT-------TCCEEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc-------CCCEEEEEC
Confidence            35789999999999999998887554       556666553

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=98.18  E-value=6.3e-07  Score=54.52  Aligned_cols=26  Identities=27%  Similarity=0.465  Sum_probs=21.6

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+...++|.|||||||||++..++..
T Consensus         6 ~~~~iI~l~G~pGSGKsT~a~~La~~   31 (194)
T d3adka_           6 KKSKIIFVVGGPGSGKGTQCEKIVQK   31 (194)
T ss_dssp             HTSCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            34577889999999999998888654

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=98.18  E-value=6e-07  Score=54.07  Aligned_cols=23  Identities=43%  Similarity=0.631  Sum_probs=19.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++|.|||||||||++..++..+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            46899999999999998887665

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=98.17  E-value=5.6e-07  Score=54.60  Aligned_cols=23  Identities=35%  Similarity=0.627  Sum_probs=19.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||+||||++..++..+
T Consensus         8 iI~i~G~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            57889999999999988887654

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=98.17  E-value=7.2e-07  Score=55.61  Aligned_cols=28  Identities=21%  Similarity=0.204  Sum_probs=24.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..++|.||||+|||+++..++.....+
T Consensus        36 G~~~li~G~pGsGKT~~~lq~~~~~~~~   63 (254)
T d1pzna2          36 QAITEVFGEFGSGKTQLAHTLAVMVQLP   63 (254)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSC
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHhhch
Confidence            3478999999999999999998887654

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.16  E-value=2.8e-07  Score=55.47  Aligned_cols=26  Identities=27%  Similarity=0.394  Sum_probs=21.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .++++|+||+||||++..+...+...
T Consensus        21 vI~L~G~pGSGKTTiAk~La~~l~~~   46 (195)
T d1x6va3          21 TVWLTGLSGAGKTTVSMALEEYLVCH   46 (195)
T ss_dssp             EEEEESSCHHHHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            55688999999999999998887543

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.15  E-value=7.9e-07  Score=53.83  Aligned_cols=23  Identities=39%  Similarity=0.679  Sum_probs=20.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||+||||.+..++..+
T Consensus         3 iI~i~GppGSGKsT~a~~La~~~   25 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999998887654

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.13  E-value=9e-07  Score=53.26  Aligned_cols=23  Identities=39%  Similarity=0.663  Sum_probs=19.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||||+||||++..++..+
T Consensus         4 rIvl~G~pGSGKtT~a~~La~~~   26 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57889999999999998887654

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.12  E-value=5.5e-07  Score=54.77  Aligned_cols=24  Identities=25%  Similarity=0.558  Sum_probs=20.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.++|.||||+||||++..++..+
T Consensus         9 ~iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_           9 SVIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            468899999999999998886643

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=98.12  E-value=8.3e-07  Score=53.22  Aligned_cols=23  Identities=35%  Similarity=0.423  Sum_probs=19.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++++.||||+||||++..++..+
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            46889999999999988886554

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=98.12  E-value=3.7e-06  Score=50.32  Aligned_cols=25  Identities=24%  Similarity=0.290  Sum_probs=21.0

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +-|.||+|+||||++..+...+-..
T Consensus        25 IgI~G~~GSGKSTla~~L~~~l~~~   49 (198)
T d1rz3a_          25 LGIDGLSRSGKTTLANQLSQTLREQ   49 (198)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhccc
Confidence            3489999999999999998777554

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=98.11  E-value=7e-07  Score=54.49  Aligned_cols=23  Identities=48%  Similarity=0.706  Sum_probs=19.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++|.||||+||||++..++..+
T Consensus         8 rIiliG~PGSGKtT~a~~La~~~   30 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRITKHF   30 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHB
T ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Confidence            67899999999999988887643

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=98.09  E-value=1.2e-06  Score=53.56  Aligned_cols=24  Identities=29%  Similarity=0.556  Sum_probs=21.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.++|.|||||||+|.+..++..+
T Consensus         4 piI~I~GppGSGKgT~ak~La~~~   27 (225)
T d1ckea_           4 PVITIDGPSGAGKGTLCKAMAEAL   27 (225)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            467788999999999999998776

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=98.08  E-value=9.7e-07  Score=59.09  Aligned_cols=25  Identities=28%  Similarity=0.519  Sum_probs=22.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++.+++.||||||||+++..++..+
T Consensus       154 ~~~~~~~g~~~~gk~~~~~~~~~~~  178 (362)
T d1svma_         154 KRYWLFKGPIDSGKTTLAAALLELC  178 (362)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cCeEEEECCCCCCHHHHHHHHHHHc
Confidence            3578999999999999999998887

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.05  E-value=5.5e-06  Score=51.69  Aligned_cols=44  Identities=14%  Similarity=0.153  Sum_probs=32.8

Q ss_pred             cccCCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         14 VQEELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        14 ~~~~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ....+.=++...+.+... .++.++|.||+|+|||+++..++..+
T Consensus        10 ~~~~f~GR~~el~~l~~~-~~~~i~i~G~~G~GKTsLl~~~~~~~   53 (283)
T d2fnaa2          10 NRKDFFDREKEIEKLKGL-RAPITLVLGLRRTGKSSIIKIGINEL   53 (283)
T ss_dssp             SGGGSCCCHHHHHHHHHT-CSSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             ChhhCCChHHHHHHHHhc-cCCEEEEEcCCCCcHHHHHHHHHHHC
Confidence            356666677776666553 45678899999999999988876654

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=98.04  E-value=4.5e-06  Score=52.77  Aligned_cols=60  Identities=15%  Similarity=0.296  Sum_probs=39.3

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhh---cCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELAR---YMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~---~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      .+...+|.|+||+|||+++..++..+........   ..+.++++++... ...++..++....
T Consensus        28 pg~~~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~E~-~~~~~~~Rl~~~~   90 (274)
T d1nlfa_          28 AGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAED-PPTAIHHRLHALG   90 (274)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESSS-CHHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEeccc-hHHHHHHHHHHHh
Confidence            4568899999999999999999887654321110   1345788877533 3445656655443

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.03  E-value=8.4e-06  Score=51.03  Aligned_cols=46  Identities=20%  Similarity=0.239  Sum_probs=33.7

Q ss_pred             cCCCCCHHHHHHHHHHhcC---C-ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         16 EELGLNTIQFEAYKAALTR---E-FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        16 ~~~~l~~~Q~~~i~~~~~~---~-~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .++...+.-.+.+..+...   + .+++.||||+|||+++..++..+...
T Consensus        12 ~dlig~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~   61 (239)
T d1njfa_          12 ADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCE   61 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHHHCT
T ss_pred             HHccChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCc
Confidence            4455566666667665543   2 37899999999999999998887654

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=98.03  E-value=1.4e-06  Score=59.64  Aligned_cols=25  Identities=32%  Similarity=0.477  Sum_probs=22.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ..++++.||||||||.++..++..+
T Consensus        49 ksNILliGPTGvGKTlLAr~LAk~l   73 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIARRLAKLA   73 (443)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             cccEEEECCCCCCHHHHHHHHHHHh
Confidence            3589999999999999999998765

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.03  E-value=3.1e-06  Score=50.78  Aligned_cols=29  Identities=17%  Similarity=0.075  Sum_probs=24.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhch
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNK   62 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~   62 (97)
                      +..++|.||||+|||+++..++.......
T Consensus        23 G~v~~i~G~~GsGKT~l~l~la~~~~~~~   51 (242)
T d1n0wa_          23 GSITEMFGEFRTGKTQICHTLAVTCQLPI   51 (242)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTSCG
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHHHHHhh
Confidence            45889999999999999999988776553

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.02  E-value=3.3e-06  Score=52.12  Aligned_cols=24  Identities=25%  Similarity=0.380  Sum_probs=21.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      .+++.||||+|||+++..++..++
T Consensus        26 ~lLl~Gp~G~GKtt~a~~~a~~l~   49 (207)
T d1a5ta2          26 ALLIQALPGMGDDALIYALSRYLL   49 (207)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCcHHHHHHHHHHhcc
Confidence            489999999999999999998875

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=98.00  E-value=1.7e-06  Score=57.09  Aligned_cols=26  Identities=23%  Similarity=0.296  Sum_probs=22.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +++++.||||||||.++.+++..+..
T Consensus       124 g~~l~~G~pG~GKT~la~ala~~~~~  149 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGEALGG  149 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHHHHHT
T ss_pred             ceEEEECCCCccHHHHHHHHHHHhcC
Confidence            45666899999999999999988753

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.98  E-value=6.4e-07  Score=55.37  Aligned_cols=26  Identities=15%  Similarity=0.123  Sum_probs=21.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +..++|.||||||||+++..++....
T Consensus        34 G~~~li~G~pGsGKT~l~lq~~~~~~   59 (251)
T d1szpa2          34 GSITELFGEFRTGKSQLCHTLAVTCQ   59 (251)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHTTTTT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHhh
Confidence            45889999999999999988876554

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.98  E-value=1.3e-05  Score=51.56  Aligned_cols=58  Identities=16%  Similarity=0.138  Sum_probs=39.2

Q ss_pred             CCHHHHHHHHHHhc---CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         20 LNTIQFEAYKAALT---REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        20 l~~~Q~~~i~~~~~---~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      -++...+.+..++.   ..+.++.||||+|||.++..++..+....-.......+++.+..
T Consensus        22 gRd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~   82 (268)
T d1r6bx2          22 GREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDI   82 (268)
T ss_dssp             SCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCC
T ss_pred             ChHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeee
Confidence            45555556655553   35899999999999999999999888753222223445555444

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=97.95  E-value=3.7e-06  Score=55.37  Aligned_cols=37  Identities=27%  Similarity=0.295  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHh-cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         22 TIQFEAYKAAL-TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        22 ~~Q~~~i~~~~-~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.+...+..+. .+.+++|.||+|+||||++.+++..+
T Consensus       153 ~~~~~~l~~~v~~~~nili~G~tgSGKTT~l~al~~~i  190 (323)
T d1g6oa_         153 EQAISAIKDGIAIGKNVIVCGGTGSGKTTYIKSIMEFI  190 (323)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEESTTSSHHHHHHHHGGGS
T ss_pred             HHHHHHHHHHHHhCCCEEEEeeccccchHHHHHHhhhc
Confidence            44556666655 46789999999999999988877654

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=97.95  E-value=3.1e-06  Score=52.01  Aligned_cols=23  Identities=39%  Similarity=0.583  Sum_probs=19.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+.|-||||+||||++..++..+
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~l   27 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDF   27 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            34577999999999999997765

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=97.92  E-value=6.6e-06  Score=54.16  Aligned_cols=34  Identities=18%  Similarity=0.202  Sum_probs=27.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      .+-|+||||+||||++..++..+...       +.++-|++
T Consensus        53 ~igitG~pGaGKSTli~~l~~~~~~~-------g~~vaVia   86 (323)
T d2qm8a1          53 RVGITGVPGVGKSTTIDALGSLLTAA-------GHKVAVLA   86 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             EEeeeCCCCCCHHHHHHHHHHHHhhc-------CCceeeee
Confidence            56789999999999999999887665       55666665

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=97.90  E-value=6.4e-06  Score=50.95  Aligned_cols=28  Identities=14%  Similarity=0.307  Sum_probs=24.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..+.++|.||+||||++..+...+...
T Consensus        24 g~vIwltGlsGsGKTTia~~L~~~l~~~   51 (208)
T d1m7ga_          24 GLTIWLTGLSASGKSTLAVELEHQLVRD   51 (208)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            3478899999999999999999888665

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=97.88  E-value=7.1e-06  Score=52.61  Aligned_cols=35  Identities=26%  Similarity=0.444  Sum_probs=28.4

Q ss_pred             HHHHHhc-C-----CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         27 AYKAALT-R-----EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        27 ~i~~~~~-~-----~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .++.++. +     ..+.+.||||+|||+++..++..+.++
T Consensus        41 ~lD~~Lg~GGi~~g~itei~G~~gsGKTtl~l~~~~~~q~~   81 (263)
T d1u94a1          41 SLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE   81 (263)
T ss_dssp             HHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             HHHHHhcCCCccCceEEEEecCCCcHHHHHHHHHHHHHHcC
Confidence            5666663 3     478999999999999999998888765

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.87  E-value=4.3e-06  Score=50.22  Aligned_cols=21  Identities=29%  Similarity=0.466  Sum_probs=18.1

Q ss_pred             CceEEeCCCCCchHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      ..+++.|+||+||||++..++
T Consensus        15 ~liil~G~pGsGKST~a~~l~   35 (172)
T d1yj5a2          15 EVVVAVGFPGAGKSTFIQEHL   35 (172)
T ss_dssp             CEEEEECCTTSSHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            478999999999999987763

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=97.87  E-value=2.9e-06  Score=55.56  Aligned_cols=26  Identities=19%  Similarity=0.198  Sum_probs=22.1

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+.++++.||||||||+++..+...+
T Consensus        27 ~~h~vLl~G~pG~GKT~lar~~~~iL   52 (333)
T d1g8pa_          27 GIGGVLVFGDRGTGKSTAVRALAALL   52 (333)
T ss_dssp             GGCCEEEECCGGGCTTHHHHHHHHHS
T ss_pred             CCCeEEEECCCCccHHHHHHHHHHhC
Confidence            34679999999999999999887654

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=97.86  E-value=1.2e-05  Score=53.87  Aligned_cols=41  Identities=22%  Similarity=0.298  Sum_probs=34.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHAL   82 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~   82 (97)
                      +.++|.|+||+|||+++..++..++..       +..++|+-|.++..
T Consensus        51 ~H~~I~G~tGsGKT~~l~~li~~~~~~-------g~~~iiiD~kge~~   91 (433)
T d1e9ra_          51 RHLLVNGATGTGKSVLLRELAYTGLLR-------GDRMVIVDPNGDML   91 (433)
T ss_dssp             GCEEEEECTTSSHHHHHHHHHHHHHHT-------TCEEEEEEETTHHH
T ss_pred             ceEEEEeCCCCcHHHHHHHHHHHHHhC-------CCCEEEEeCChhHH
Confidence            468999999999999988888888776       67788888887643

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.86  E-value=6.1e-06  Score=49.56  Aligned_cols=25  Identities=24%  Similarity=0.450  Sum_probs=20.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..++|.||+|+||||++..+....
T Consensus         2 G~iivl~GpsG~GK~tl~~~L~~~~   26 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVVRCLRERI   26 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhhC
Confidence            4568899999999999977776553

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.85  E-value=6.8e-06  Score=49.93  Aligned_cols=23  Identities=22%  Similarity=0.559  Sum_probs=20.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||+|+|||+++..++...
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~   24 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEH   24 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHhC
Confidence            47899999999999988887765

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=97.85  E-value=7e-06  Score=54.83  Aligned_cols=24  Identities=29%  Similarity=0.578  Sum_probs=21.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++++.||||+|||.++..++..+
T Consensus        69 ~niLfiGPTGvGKTElAk~LA~~~   92 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMAQTLAKHL   92 (364)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             cceeeeCCCCccHHHHHHHHHhhc
Confidence            579999999999999999887654

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=97.85  E-value=1.1e-05  Score=53.19  Aligned_cols=34  Identities=15%  Similarity=0.240  Sum_probs=27.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      .+-|+||||+|||+++..++..+...       +.++-+++
T Consensus        56 ~IgitG~pGaGKSTLi~~l~~~~~~~-------g~~vavla   89 (327)
T d2p67a1          56 RLGVTGTPGAGKSTFLEAFGMLLIRE-------GLKVAVIA   89 (327)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             EEEeeCCCCCCHHHHHHHHHHHHHhc-------CCceeeec
Confidence            57889999999999999999888776       55665555

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.83  E-value=7.6e-06  Score=49.47  Aligned_cols=24  Identities=29%  Similarity=0.620  Sum_probs=20.5

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.++|.||+|+|||+++..++...
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~   25 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhC
Confidence            458999999999999988887664

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.80  E-value=4.1e-05  Score=46.93  Aligned_cols=60  Identities=18%  Similarity=0.153  Sum_probs=40.6

Q ss_pred             HHHHHHHHhcC---CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChH--HHHHHHH
Q psy16285         24 QFEAYKAALTR---EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNH--ALDQFVE   87 (97)
Q Consensus        24 Q~~~i~~~~~~---~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~--~~~~~~~   87 (97)
                      |.+.+..+.++   ..+++.||||+|||+++..+...+.....    .-..++.+.|...  .++++.+
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~----~h~D~~~i~~~~~~I~Id~IR~   66 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPP----KASDVLEIDPEGENIGIDDIRT   66 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCC----CTTTEEEECCSSSCBCHHHHHH
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhcccc----CCCCEEEEeCCcCCCCHHHHHH
Confidence            66777776653   47899999999999999999987654411    1234777776432  2455544

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=97.78  E-value=1.5e-05  Score=48.28  Aligned_cols=34  Identities=12%  Similarity=0.061  Sum_probs=29.0

Q ss_pred             CceEEeCC-CCCchHHHHHHHHHHHHhchhhhhcCCCCEEEE
Q psy16285         35 EFAIIQGP-PGTGKTYVALRIVEGFLKNKELARYMSGPILIV   75 (97)
Q Consensus        35 ~~~~v~Gp-~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~   75 (97)
                      ++++|+|- +|.|||+++..++..+.+.       +.+++++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~-------G~rVl~i   36 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAA-------GYRTAGY   36 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHT-------TCCEEEE
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHC-------CCeEEEE
Confidence            45788887 6999999999999999887       7788886

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.74  E-value=5.6e-05  Score=50.78  Aligned_cols=60  Identities=15%  Similarity=0.191  Sum_probs=38.9

Q ss_pred             CCHHHHHHHHHHhc---CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCCh
Q psy16285         20 LNTIQFEAYKAALT---REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN   79 (97)
Q Consensus        20 l~~~Q~~~i~~~~~---~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~   79 (97)
                      -++...+.+..++.   ..+.++.|+||.|||.++..++..+....-.....+.+++-+....
T Consensus        26 gr~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~   88 (387)
T d1qvra2          26 GRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGS   88 (387)
T ss_dssp             SCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC--
T ss_pred             CcHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhh
Confidence            35555555555442   3578999999999999999999888776321122345666665533

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.74  E-value=1.2e-05  Score=49.64  Aligned_cols=28  Identities=18%  Similarity=0.025  Sum_probs=23.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..++|.||||+|||+++..++......
T Consensus        37 G~~~~i~G~~GsGKT~lalq~~~~~~~~   64 (258)
T d1v5wa_          37 MAITEAFGEFRTGKTQLSHTLCVTAQLP   64 (258)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhh
Confidence            3478999999999999999998776543

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=97.72  E-value=1.2e-05  Score=49.62  Aligned_cols=23  Identities=22%  Similarity=0.345  Sum_probs=20.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.||+|+||||++..+..++
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~   24 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYL   24 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Confidence            36899999999999999988765

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.68  E-value=1.4e-05  Score=52.25  Aligned_cols=24  Identities=29%  Similarity=0.520  Sum_probs=21.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      ++++.||||+|||.++..++..+.
T Consensus        54 ~~lf~Gp~GvGKT~lak~la~~l~   77 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVTVQLSKALG   77 (315)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCcchhHHHHHHHHhhcc
Confidence            578999999999999999988763

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.68  E-value=4.2e-05  Score=48.34  Aligned_cols=24  Identities=33%  Similarity=0.313  Sum_probs=20.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +..++|.|++|||||++|..+-..
T Consensus        23 ~~pvlI~Ge~GtGK~~~A~~ih~~   46 (247)
T d1ny5a2          23 ECPVLITGESGVGKEVVARLIHKL   46 (247)
T ss_dssp             CSCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEECCCCcCHHHHHHHHHHh
Confidence            568999999999999998887653

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=97.66  E-value=8.9e-06  Score=49.96  Aligned_cols=28  Identities=18%  Similarity=0.230  Sum_probs=24.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..++|.|+||+|||+++..++..+...
T Consensus        34 G~l~~i~G~~G~GKT~~~l~~a~~~~~~   61 (258)
T d2i1qa2          34 QSVTEFAGVFGSGKTQIMHQSCVNLQNP   61 (258)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTCG
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            4578999999999999999999888665

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.65  E-value=4.1e-05  Score=47.14  Aligned_cols=35  Identities=14%  Similarity=0.289  Sum_probs=27.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEE
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIV   75 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~   75 (97)
                      +..++|.|+.|+||||.+..+...+...       +.++.++
T Consensus         3 G~lI~ieG~dGsGKsT~~~~L~~~L~~~-------g~~v~~~   37 (209)
T d1nn5a_           3 GALIVLEGVDRAGKSTQSRKLVEALCAA-------GHRAELL   37 (209)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHT-------TCCEEEE
T ss_pred             eeEEEEECCCCCCHHHHHHHHHHHHHHC-------CCcEEEE
Confidence            3456778999999999999998888776       5556554

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=97.61  E-value=2.5e-05  Score=48.12  Aligned_cols=25  Identities=20%  Similarity=0.428  Sum_probs=20.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..++|.||+|+|||++...++...
T Consensus         2 G~livi~GPSG~GK~tl~~~L~~~~   26 (205)
T d1s96a_           2 GTLYIVSAPSGAGKSSLIQALLKTQ   26 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhhC
Confidence            4578899999999999987776653

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.60  E-value=2.6e-05  Score=46.93  Aligned_cols=24  Identities=17%  Similarity=0.422  Sum_probs=19.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      ++.++|.||+|+|||++...++..
T Consensus         3 ~k~ivl~Gpsg~GK~tl~~~L~~~   26 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIKNTLITK   26 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHh
Confidence            356899999999999998776654

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.60  E-value=1.8e-05  Score=48.32  Aligned_cols=24  Identities=25%  Similarity=0.330  Sum_probs=20.1

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +-|.||+|+||||++..+...+-.
T Consensus         5 IgI~G~~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_           5 IGVSGGTASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTG
T ss_pred             EEEECCCCCCHHHHHHHHHHHhch
Confidence            458999999999999888877643

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=97.60  E-value=6.8e-05  Score=45.68  Aligned_cols=28  Identities=29%  Similarity=0.438  Sum_probs=24.0

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..++|.|+.|+||||.+..+...+...
T Consensus         2 gkfIviEG~dGsGKsT~~~~L~~~L~~~   29 (210)
T d4tmka_           2 SKYIVIEGLEGAGKTTARNVVVETLEQL   29 (210)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            4567889999999999999888888665

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=97.56  E-value=3.7e-05  Score=49.30  Aligned_cols=35  Identities=37%  Similarity=0.408  Sum_probs=27.7

Q ss_pred             HHHHHhc-C-----CceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         27 AYKAALT-R-----EFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        27 ~i~~~~~-~-----~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .++.++. +     ..+.+.||+|||||+++..++..+.+.
T Consensus        44 ~lD~~Lg~GGip~g~itei~G~~~sGKT~l~l~~~~~aqk~   84 (268)
T d1xp8a1          44 SLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKA   84 (268)
T ss_dssp             HHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             HHHHHhcCCCccCceEEEEecCCccchHHHHHHHHHHHHhC
Confidence            5555553 3     467899999999999999998887665

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.54  E-value=5e-05  Score=48.74  Aligned_cols=35  Identities=37%  Similarity=0.395  Sum_probs=27.5

Q ss_pred             HHHHHhc------CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         27 AYKAALT------REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        27 ~i~~~~~------~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .++.++.      +....+.||+|+|||+++..++......
T Consensus        47 ~lD~~lg~gG~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~   87 (269)
T d1mo6a1          47 ALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAA   87 (269)
T ss_dssp             HHHHHTSSSSBCSSSEEEEECSSSSSHHHHHHHHHHHHHHT
T ss_pred             HHHHhhccCCcccceeEEEecCCCcHHHHHHHHHHHHHhcC
Confidence            4555553      3578999999999999998888777665

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.53  E-value=3.1e-05  Score=48.81  Aligned_cols=24  Identities=33%  Similarity=0.588  Sum_probs=20.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +++.+.|.||+|+||||++..+..
T Consensus        25 ~Gei~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          25 EGEFVVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCChHHHHHHHHhc
Confidence            467899999999999999776643

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=97.53  E-value=7.3e-05  Score=47.32  Aligned_cols=35  Identities=20%  Similarity=0.375  Sum_probs=30.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      +.+++.|--|+||||++..++..+-+.       ++++|++.
T Consensus         9 ~~i~~sGKGGVGKTTvaa~lA~~lA~~-------G~rVLlvD   43 (296)
T d1ihua1           9 PYLFFTGKGGVGKTSISCATAIRLAEQ-------GKRVLLVS   43 (296)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             eEEEEECCCcChHHHHHHHHHHHHHHC-------CCCEEEEe
Confidence            467889999999999999999998776       77888877

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=97.52  E-value=2.6e-05  Score=47.93  Aligned_cols=26  Identities=27%  Similarity=0.367  Sum_probs=21.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++.+.|.||.|+||||++..++..+
T Consensus        26 ~Gei~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          26 KGNVVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhccc
Confidence            36788999999999999988876544

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.51  E-value=7.8e-05  Score=48.23  Aligned_cols=35  Identities=20%  Similarity=0.453  Sum_probs=25.9

Q ss_pred             EEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         38 IIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        38 ~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      -|.|++|+||||++..+...+.+...    ....+.+++
T Consensus        31 Gi~G~qGSGKSTl~~~l~~~L~~~~~----~~~~v~~iS   65 (286)
T d1odfa_          31 FFSGPQGSGKSFTSIQIYNHLMEKYG----GEKSIGYAS   65 (286)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHHHHHG----GGSCEEEEE
T ss_pred             EeECCCCCCHHHHHHHHHHHHHHHhC----CCcceEeec
Confidence            47899999999999988888766521    134566665

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.49  E-value=3.7e-05  Score=50.25  Aligned_cols=26  Identities=27%  Similarity=0.466  Sum_probs=22.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++++.||||+|||.++..++..+...
T Consensus        55 ~~lf~Gp~G~GKt~lak~la~~l~~~   80 (315)
T d1qvra3          55 SFLFLGPTGVGKTELAKTLAATLFDT   80 (315)
T ss_dssp             EEEEBSCSSSSHHHHHHHHHHHHHSS
T ss_pred             EEEEECCCcchHHHHHHHHHHHhcCC
Confidence            56888999999999999999988543

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=97.49  E-value=3.4e-05  Score=48.54  Aligned_cols=23  Identities=39%  Similarity=0.560  Sum_probs=19.3

Q ss_pred             cCCceEEeCCCCCchHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      +++.+.|.||+|+||||++..+.
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~   52 (230)
T d1l2ta_          30 EGEFVSIMGPSGSGKSTMLNIIG   52 (230)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCcchhhHhcc
Confidence            47799999999999999966553

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=97.46  E-value=4.2e-05  Score=48.37  Aligned_cols=25  Identities=40%  Similarity=0.521  Sum_probs=20.9

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +++.+.|.||+|+||||++..+...
T Consensus        28 ~Ge~~~liG~sGaGKSTll~~i~gl   52 (240)
T d1g2912          28 DGEFMILLGPSGCGKTTTLRMIAGL   52 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcC
Confidence            4678999999999999997776543

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=97.45  E-value=4.4e-05  Score=48.27  Aligned_cols=25  Identities=36%  Similarity=0.502  Sum_probs=20.8

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +++.+.|.||+|+||||++..+...
T Consensus        31 ~Ge~~~liGpsGaGKSTLl~~i~Gl   55 (239)
T d1v43a3          31 DGEFLVLLGPSGCGKTTTLRMIAGL   55 (239)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcC
Confidence            3678999999999999997766544

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=97.45  E-value=0.00016  Score=46.77  Aligned_cols=39  Identities=23%  Similarity=0.326  Sum_probs=31.2

Q ss_pred             HHHHHHHHHh---cCCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         23 IQFEAYKAAL---TREFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        23 ~Q~~~i~~~~---~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .-..+|+...   +++...|.||+|+|||+++..++......
T Consensus        29 ~~~r~ID~l~PigrGQr~~I~g~~g~GKT~l~~~i~~~~~~~   70 (289)
T d1xpua3          29 LTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYN   70 (289)
T ss_dssp             HHHHHHHHHSCCBTTCEEEEEECSSSSHHHHHHHHHHHHHHH
T ss_pred             ccceeeeecccccCCCeeeEeCCCCCCHHHHHHHHHHHHhhc
Confidence            3345666655   47899999999999999999998877655

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.45  E-value=0.00012  Score=44.23  Aligned_cols=32  Identities=19%  Similarity=0.349  Sum_probs=25.6

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEE
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIV   75 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~   75 (97)
                      ++|.|+.|+||||++..+...+...       +..+.++
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~-------g~~v~~~   34 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAA-------GRSVATL   34 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC-------CCCEEEE
Confidence            6789999999999999988887665       5555554

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=97.42  E-value=0.00011  Score=46.38  Aligned_cols=36  Identities=19%  Similarity=0.230  Sum_probs=29.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +.+++.|--|+||||++..++..+.+.       +++++++--
T Consensus        21 ~iii~sGKGGVGKTT~a~nLA~~lA~~-------G~rVllvD~   56 (279)
T d1ihua2          21 GLIMLMGKGGVGKTTMAAAIAVRLADM-------GFDVHLTTS   56 (279)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEES
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHC-------CCcEEEEeC
Confidence            466778999999999999999988766       677887653

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=97.42  E-value=5.7e-05  Score=43.40  Aligned_cols=21  Identities=19%  Similarity=0.284  Sum_probs=18.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|+||+|||+++..+..
T Consensus         2 kivlvG~~~vGKSsLi~~l~~   22 (160)
T d1r8sa_           2 RILMVGLDAAGKTTILYKLKL   22 (160)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            478999999999999887754

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.41  E-value=5.9e-05  Score=43.25  Aligned_cols=22  Identities=18%  Similarity=0.167  Sum_probs=18.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +.+++.|+||+|||+++..+..
T Consensus         1 ~KI~liG~~nvGKSSLln~l~~   22 (166)
T d2qtvb1           1 GKLLFLGLDNAGKTTLLHMLKN   22 (166)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            3578999999999999877654

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.40  E-value=5.1e-05  Score=48.21  Aligned_cols=25  Identities=32%  Similarity=0.466  Sum_probs=21.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..+...
T Consensus        39 ~Ge~vaivG~sGsGKSTLl~li~gl   63 (251)
T d1jj7a_          39 PGEVTALVGPNGSGKSTVAALLQNL   63 (251)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcc
Confidence            3679999999999999998777543

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=97.39  E-value=6.8e-05  Score=48.56  Aligned_cols=37  Identities=14%  Similarity=0.209  Sum_probs=25.1

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      +++.+-|.|++|+||||++..+...+-..       +.++.+++
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~~~~-------~v~~~iI~   39 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIFRRE-------GVKAVSIE   39 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHHH-------TCCEEEEE
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHhhc-------CCCeEEEe
Confidence            35678899999999999988887777554       44555554

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=97.39  E-value=4.5e-05  Score=48.26  Aligned_cols=24  Identities=17%  Similarity=0.216  Sum_probs=20.1

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +++.+.|.||+|+||||++..+..
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~G   53 (240)
T d3dhwc1          30 AGQIYGVIGASGAGKSTLIRCVNL   53 (240)
T ss_dssp             SSCEEEEEESTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcC
Confidence            467899999999999999766643

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=97.38  E-value=3.8e-05  Score=48.30  Aligned_cols=26  Identities=35%  Similarity=0.489  Sum_probs=21.5

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++.+.|.||+|+||||++..+....
T Consensus        25 ~Ge~~~liGpsGaGKSTll~~l~Gl~   50 (229)
T d3d31a2          25 SGEYFVILGPTGAGKTLFLELIAGFH   50 (229)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCc
Confidence            46789999999999999977776543

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=97.38  E-value=2.1e-05  Score=49.76  Aligned_cols=26  Identities=19%  Similarity=0.360  Sum_probs=20.9

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..+...+
T Consensus        27 ~Ge~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          27 PNSIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            36789999999999999977765443

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.37  E-value=4.3e-05  Score=48.60  Aligned_cols=25  Identities=24%  Similarity=0.311  Sum_probs=20.9

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||+|+||||++..++..
T Consensus        40 ~Ge~iaivG~sGsGKSTLl~ll~gl   64 (253)
T d3b60a1          40 AGKTVALVGRSGSGKSTIASLITRF   64 (253)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHTTT
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcc
Confidence            3679999999999999997777543

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.37  E-value=6.2e-05  Score=47.60  Aligned_cols=25  Identities=28%  Similarity=0.558  Sum_probs=19.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++.+.+.||+|+||||++..+...+
T Consensus        24 ~e~~~liGpnGaGKSTll~~i~Gl~   48 (240)
T d2onka1          24 RDYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CEEEEEECCCCChHHHHHHHHHcCC
Confidence            3567789999999999977776543

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.36  E-value=4.4e-05  Score=47.48  Aligned_cols=23  Identities=26%  Similarity=0.426  Sum_probs=18.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +..+|+|..|+||||++..++..
T Consensus         4 Pv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           4 AVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             EEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CEEEEeeCCCCCHHHHHHHHHhc
Confidence            35789999999999997777653

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=97.36  E-value=6e-05  Score=47.63  Aligned_cols=26  Identities=27%  Similarity=0.314  Sum_probs=21.7

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+.|.||+|+||||++..+...+
T Consensus        28 ~Ge~vaIvG~sGsGKSTLl~ll~gl~   53 (241)
T d2pmka1          28 QGEVIGIVGRSGSGKSTLTKLIQRFY   53 (241)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcC
Confidence            46789999999999999977776544

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.36  E-value=5.5e-05  Score=48.77  Aligned_cols=25  Identities=32%  Similarity=0.523  Sum_probs=20.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++.+.|.||+|+||||++..++..+
T Consensus        62 Ge~vaivG~nGsGKSTLl~~i~Gl~   86 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLMLILGEL   86 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCCC
Confidence            5688999999999999987776544

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.36  E-value=0.00058  Score=43.85  Aligned_cols=62  Identities=10%  Similarity=0.106  Sum_probs=41.2

Q ss_pred             HHHHHHh---cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe-CChHHHHHHHHHHHhh
Q psy16285         26 EAYKAAL---TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC-YTNHALDQFVEGVLKY   92 (97)
Q Consensus        26 ~~i~~~~---~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~-~~~~~~~~~~~~l~~~   92 (97)
                      .+|+...   ++++..|.|++|+|||+++..++....+..     ....|++.+ ....-+.++.+.+.+.
T Consensus        57 raID~l~pigkGQr~~If~~~g~GKt~l~~~i~~~~~~~~-----~~v~V~~~iGer~~ev~~~~~~~~~~  122 (276)
T d2jdid3          57 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAH-----GGYSVFAGVGERTREGNDLYHEMIES  122 (276)
T ss_dssp             HHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHHTTTC-----SSEEEEEEESCCHHHHHHHHHHHHHH
T ss_pred             eeeeeeccccCCCEEEeeCCCCCCHHHHHHHHHHHHHhhC-----CCeEEEEEeccChHHHHHHHHHHHhc
Confidence            3555544   578999999999999999999988764431     122333333 3555566677776653

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=97.29  E-value=3.9e-05  Score=48.60  Aligned_cols=25  Identities=36%  Similarity=0.287  Sum_probs=21.1

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +++.+.|.||+|+||||++..+...
T Consensus        30 ~Ge~~~iiG~sGsGKSTll~~i~gl   54 (242)
T d1oxxk2          30 NGERFGILGPSGAGKTTFMRIIAGL   54 (242)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHcC
Confidence            3679999999999999997777553

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=97.28  E-value=0.00017  Score=47.04  Aligned_cols=36  Identities=14%  Similarity=0.117  Sum_probs=25.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      .+-|.|++|+||||++..+...+.+..     .+.++.+++
T Consensus        82 iIGIaG~sgSGKSTla~~L~~lL~~~~-----~~~~v~~Is  117 (308)
T d1sq5a_          82 IISIAGSVAVGKSTTARVLQALLSRWP-----EHRRVELIT  117 (308)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHTTST-----TCCCEEEEE
T ss_pred             EEEEeCCCCCCCcHHHHHHHHHHhhhc-----CCCceEEEe
Confidence            456899999999999888877664321     245666665

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=97.27  E-value=9.1e-05  Score=45.73  Aligned_cols=25  Identities=24%  Similarity=0.578  Sum_probs=21.6

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ...+++.|||+||||.++.+++..+
T Consensus        53 kn~i~~~GP~~TGKS~f~~sl~~~l   77 (205)
T d1tuea_          53 KNCLVFCGPANTGKSYFGMSFIHFI   77 (205)
T ss_dssp             CSEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHh
Confidence            3578999999999999988887776

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=97.26  E-value=9e-05  Score=46.74  Aligned_cols=26  Identities=23%  Similarity=0.266  Sum_probs=21.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++.+.+.||.|+||||++..+...+
T Consensus        31 ~Gei~~liGpnGaGKSTl~~~i~Gl~   56 (240)
T d1ji0a_          31 RGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            46789999999999999988775443

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.25  E-value=0.00012  Score=44.05  Aligned_cols=22  Identities=32%  Similarity=0.453  Sum_probs=19.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +.++|.|+||+|||+++..+..
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~   25 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTT   25 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            5789999999999999877764

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.23  E-value=0.00012  Score=44.35  Aligned_cols=22  Identities=23%  Similarity=0.397  Sum_probs=18.8

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ++++|.|+||+|||+++..+..
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~   22 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLT   22 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHc
Confidence            3689999999999999877754

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.20  E-value=0.00012  Score=46.70  Aligned_cols=24  Identities=25%  Similarity=0.268  Sum_probs=20.7

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++.+.|.||+|+||||++..+..
T Consensus        27 ~GEi~~iiG~sGsGKSTLl~~i~G   50 (258)
T d1b0ua_          27 AGDVISIIGSSGSGKSTFLRCINF   50 (258)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHc
Confidence            467899999999999999887754

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=97.18  E-value=0.0001  Score=46.19  Aligned_cols=24  Identities=29%  Similarity=0.527  Sum_probs=20.8

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +++.+.|.||.|+||||++..+..
T Consensus        24 ~Gei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          24 AGEILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             TTCEEECBCCTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhC
Confidence            478899999999999999877765

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.18  E-value=0.00022  Score=44.54  Aligned_cols=33  Identities=24%  Similarity=0.352  Sum_probs=26.9

Q ss_pred             HHHHHHHHHhcCCceEEeCCCCCchHHHHHHHH
Q psy16285         23 IQFEAYKAALTREFAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        23 ~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      ...+.+...+++...++.|++|.|||+++.++.
T Consensus        84 ~g~~~L~~~l~~kt~~~~G~SGVGKSTLiN~L~  116 (225)
T d1u0la2          84 MGIEELKEYLKGKISTMAGLSGVGKSSLLNAIN  116 (225)
T ss_dssp             TTHHHHHHHHSSSEEEEECSTTSSHHHHHHHHS
T ss_pred             hhHhhHHHHhcCCeEEEECCCCCCHHHHHHhhc
Confidence            345566666778889999999999999988774

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=97.17  E-value=0.00014  Score=41.90  Aligned_cols=21  Identities=33%  Similarity=0.452  Sum_probs=18.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|+||+|||+++..+..
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~   27 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQV   27 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999887654

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=97.16  E-value=0.0001  Score=43.82  Aligned_cols=25  Identities=24%  Similarity=0.464  Sum_probs=22.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      .+++.|+-|+|||+++..++..+-.
T Consensus        35 ii~L~G~LGaGKTtfvr~~~~~lg~   59 (158)
T d1htwa_          35 MVYLNGDLGAGKTTLTRGMLQGIGH   59 (158)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             EEEEecCCCccHHHHHHHHHhhccc
Confidence            5788999999999999999988743

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=97.16  E-value=0.00053  Score=43.60  Aligned_cols=41  Identities=17%  Similarity=0.272  Sum_probs=28.6

Q ss_pred             CCCCHHHHHHHHHHh-c-----CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         18 LGLNTIQFEAYKAAL-T-----REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        18 ~~l~~~Q~~~i~~~~-~-----~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.-++...+.+...+ +     ...+.|.|..|.|||++|..+.+..
T Consensus        22 ~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~   68 (277)
T d2a5yb3          22 CYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKS   68 (277)
T ss_dssp             SCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             eeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhh
Confidence            334666665554443 1     2356799999999999999887653

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=97.13  E-value=0.00016  Score=43.59  Aligned_cols=23  Identities=35%  Similarity=0.495  Sum_probs=18.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +.-+++.|++|+|||+++..++.
T Consensus        14 g~gvl~~G~sG~GKStlal~l~~   36 (176)
T d1kkma_          14 GLGVLITGDSGVGKSETALELVQ   36 (176)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHH
Confidence            44678999999999999877654

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.10  E-value=7.6e-05  Score=47.50  Aligned_cols=24  Identities=25%  Similarity=0.241  Sum_probs=20.2

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++.+.|.||+|+||||++..+..
T Consensus        43 ~Ge~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          43 KGETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             TTCEEEEECSTTSSHHHHHTTTTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHh
Confidence            467999999999999999776643

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=97.10  E-value=0.00015  Score=42.16  Aligned_cols=20  Identities=20%  Similarity=0.262  Sum_probs=17.4

Q ss_pred             ceEEeCCCCCchHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      .+++.|++|+|||+++..+.
T Consensus         4 ki~ivG~~~~GKTsLi~~l~   23 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFN   23 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHc
Confidence            57899999999999987763

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=97.08  E-value=0.00032  Score=44.04  Aligned_cols=33  Identities=24%  Similarity=0.390  Sum_probs=27.5

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      +.|.|-=|+||||++..++..+-+.       +.+|+++=
T Consensus         4 Iai~gKGGvGKTT~a~nLA~~LA~~-------G~rVllID   36 (269)
T d1cp2a_           4 VAIYGKGGIGKSTTTQNLTSGLHAM-------GKTIMVVG   36 (269)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHTT-------TCCEEEEE
T ss_pred             EEEECCCcCCHHHHHHHHHHHHHhC-------CCcEEEEe
Confidence            5578989999999999999998765       67787764

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=97.08  E-value=0.00011  Score=43.00  Aligned_cols=23  Identities=17%  Similarity=0.187  Sum_probs=19.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ...+++.|++|+|||+++..+..
T Consensus        13 ~~kI~lvG~~~vGKTsLl~~l~~   35 (186)
T d1f6ba_          13 TGKLVFLGLDNAGKTTLLHMLKD   35 (186)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            34789999999999999777643

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.07  E-value=0.0002  Score=42.15  Aligned_cols=21  Identities=33%  Similarity=0.537  Sum_probs=17.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|++|+|||+++..++.
T Consensus         5 KivvvG~~~vGKTsli~r~~~   25 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTD   25 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHhc
Confidence            478999999999999877653

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=97.06  E-value=0.00036  Score=44.29  Aligned_cols=33  Identities=24%  Similarity=0.381  Sum_probs=27.3

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      +.|.|-=|+||||++..++..+.+.       +++||++=
T Consensus         5 IaisgKGGVGKTT~a~NLA~~LA~~-------G~rVLlID   37 (289)
T d2afhe1           5 CAIYGKGGIGKSTTTQNLVAALAEM-------GKKVMIVG   37 (289)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC-------CCCEEEEe
Confidence            4568889999999999999988765       77888764

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=97.06  E-value=0.00015  Score=43.30  Aligned_cols=18  Identities=39%  Similarity=0.455  Sum_probs=14.7

Q ss_pred             eEEeCCCCCchHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRI   54 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~   54 (97)
                      +-|+|++|+||||++..+
T Consensus         6 IgitG~~gSGKstva~~l   23 (191)
T d1uf9a_           6 IGITGNIGSGKSTVAALL   23 (191)
T ss_dssp             EEEEECTTSCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            348899999999997654

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=97.04  E-value=0.00018  Score=42.15  Aligned_cols=21  Identities=29%  Similarity=0.314  Sum_probs=18.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|.||+|||+++..+..
T Consensus        17 kI~vvG~~~~GKSsLi~rl~~   37 (177)
T d1zj6a1          17 KVIIVGLDNAGKTTILYQFSM   37 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            789999999999999877643

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=97.04  E-value=0.0002  Score=45.36  Aligned_cols=25  Identities=28%  Similarity=0.430  Sum_probs=21.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .++.+.|.||.|+||||++..+...
T Consensus        29 ~Gei~~liG~nGaGKSTLl~~i~Gl   53 (254)
T d1g6ha_          29 KGDVTLIIGPNGSGKSTLINVITGF   53 (254)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHCC
Confidence            3678999999999999998877544

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.00  E-value=0.00026  Score=41.27  Aligned_cols=21  Identities=19%  Similarity=0.305  Sum_probs=17.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|+||+|||+++..+..
T Consensus         4 Kv~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           4 KMVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            378999999999999877653

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=96.99  E-value=0.00024  Score=44.63  Aligned_cols=26  Identities=31%  Similarity=0.286  Sum_probs=21.1

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++.+-|.||.|+||||++..+...+
T Consensus        27 ~Gei~glvG~nGaGKSTLl~~l~G~~   52 (238)
T d1vpla_          27 EGEIFGLIGPNGAGKTTTLRIISTLI   52 (238)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            36688899999999999977775443

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=96.98  E-value=0.00024  Score=42.56  Aligned_cols=24  Identities=29%  Similarity=0.454  Sum_probs=19.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +.-+++.|++|+|||+++..++..
T Consensus        15 g~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          15 GVGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc
Confidence            456899999999999998776543

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=96.98  E-value=0.00021  Score=43.12  Aligned_cols=23  Identities=26%  Similarity=0.453  Sum_probs=19.1

Q ss_pred             CCceEEeCCCCCchHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +.-+++.|++|+|||+++..++.
T Consensus        15 g~gvli~G~sG~GKS~lal~l~~   37 (177)
T d1knxa2          15 GVGVLLTGRSGIGKSECALDLIN   37 (177)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHT
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH
Confidence            45678999999999999877654

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=96.93  E-value=0.00032  Score=40.84  Aligned_cols=21  Identities=24%  Similarity=0.115  Sum_probs=17.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..+..
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~   24 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIAS   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            478999999999999777643

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=96.92  E-value=0.00025  Score=42.45  Aligned_cols=21  Identities=14%  Similarity=0.232  Sum_probs=18.7

Q ss_pred             CceEEeCCCCCchHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      +.++|.|+||+|||+++.++.
T Consensus        24 ~~I~lvG~~n~GKSTLin~L~   44 (195)
T d1svia_          24 PEIALAGRSNVGKSSFINSLI   44 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHhc
Confidence            368999999999999988886

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.92  E-value=0.00034  Score=41.00  Aligned_cols=21  Identities=29%  Similarity=0.404  Sum_probs=17.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..+..
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~   27 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYAD   27 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHc
Confidence            378999999999999877654

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.91  E-value=0.00032  Score=41.62  Aligned_cols=20  Identities=30%  Similarity=0.370  Sum_probs=16.9

Q ss_pred             ceEEeCCCCCchHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      .++|.|++|+|||+++..++
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~   26 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYT   26 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHh
Confidence            47899999999999977654

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.90  E-value=0.00035  Score=41.14  Aligned_cols=21  Identities=24%  Similarity=0.449  Sum_probs=17.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..+..
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~   26 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTR   26 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999877654

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=96.90  E-value=7.9e-05  Score=43.94  Aligned_cols=25  Identities=20%  Similarity=0.376  Sum_probs=20.9

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      +..+|.||.|+|||+++.++...+.
T Consensus        25 ~~tvi~G~NGsGKStil~Ai~~~L~   49 (222)
T d1qhla_          25 LVTTLSGGNGAGKSTTMAAFVTALI   49 (222)
T ss_dssp             HHHHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhc
Confidence            4578999999999999888876664

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.89  E-value=0.00037  Score=40.67  Aligned_cols=21  Identities=33%  Similarity=0.419  Sum_probs=17.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|.+|+|||+++..++.
T Consensus         6 KivlvG~~~vGKTsli~~~~~   26 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTE   26 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999777654

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=96.88  E-value=0.00035  Score=40.91  Aligned_cols=21  Identities=29%  Similarity=0.523  Sum_probs=18.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|+||+|||+++.+++.
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            368999999999999888764

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.86  E-value=0.0004  Score=40.68  Aligned_cols=21  Identities=43%  Similarity=0.540  Sum_probs=17.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..++.
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHc
Confidence            378999999999999877653

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.86  E-value=0.00041  Score=40.63  Aligned_cols=21  Identities=29%  Similarity=0.460  Sum_probs=17.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..++.
T Consensus         4 Ki~lvG~~~vGKTsli~r~~~   24 (168)
T d2atva1           4 KLAIFGRAGVGKSALVVRFLT   24 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            478999999999999877664

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.85  E-value=0.00041  Score=40.42  Aligned_cols=21  Identities=24%  Similarity=0.517  Sum_probs=18.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|.+|+|||+++..++.
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~   25 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVT   25 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            578999999999999877754

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=96.85  E-value=0.00012  Score=43.92  Aligned_cols=23  Identities=26%  Similarity=0.238  Sum_probs=18.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .++|.|+.|+||||++..+...+
T Consensus        11 ~I~ieG~~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1          11 TVLIEGNIGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGGT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999977765543

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.82  E-value=0.00041  Score=40.53  Aligned_cols=21  Identities=33%  Similarity=0.542  Sum_probs=17.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|.+|+|||+++..++.
T Consensus         4 Ki~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           4 RVAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            478999999999999776653

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.80  E-value=0.0012  Score=40.08  Aligned_cols=32  Identities=25%  Similarity=0.363  Sum_probs=26.1

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEE
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIV   75 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~   75 (97)
                      .+..+-.|+||||++..++..+-+.       +.+++++
T Consensus         5 av~s~KGGvGKTtia~nlA~~la~~-------g~~Vlli   36 (232)
T d1hyqa_           5 TVASGKGGTGKTTITANLGVALAQL-------GHDVTIV   36 (232)
T ss_dssp             EEEESSSCSCHHHHHHHHHHHHHHT-------TCCEEEE
T ss_pred             EEECCCCCChHHHHHHHHHHHHHhC-------CCCEEEE
Confidence            3556889999999999999988765       6778776

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.78  E-value=0.00043  Score=40.52  Aligned_cols=21  Identities=19%  Similarity=0.507  Sum_probs=18.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|.+|+|||+++..++.
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~   27 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQ   27 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            589999999999999877764

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.78  E-value=0.00052  Score=39.79  Aligned_cols=21  Identities=29%  Similarity=0.441  Sum_probs=17.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|.+|+|||+++..++.
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~   24 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCA   24 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            378999999999999877754

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.77  E-value=0.00052  Score=40.03  Aligned_cols=21  Identities=33%  Similarity=0.438  Sum_probs=17.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|.+|+|||+++..++.
T Consensus         5 KivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            468999999999999877653

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.77  E-value=0.00043  Score=40.59  Aligned_cols=21  Identities=29%  Similarity=0.512  Sum_probs=17.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|.+|+|||+++..+..
T Consensus         7 KI~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999777653

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.77  E-value=0.00044  Score=40.30  Aligned_cols=21  Identities=19%  Similarity=0.564  Sum_probs=18.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..++.
T Consensus         5 Ki~viG~~~vGKTsli~~l~~   25 (166)
T d1ctqa_           5 KLVVVGAGGVGKSALTIQLIQ   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            478999999999999877754

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.77  E-value=0.00045  Score=40.22  Aligned_cols=20  Identities=35%  Similarity=0.695  Sum_probs=17.2

Q ss_pred             eEEeCCCCCchHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +++.|.+|+|||+++..++.
T Consensus         5 i~vvG~~~vGKTSli~~l~~   24 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVE   24 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68999999999999877653

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.77  E-value=0.00052  Score=40.14  Aligned_cols=21  Identities=29%  Similarity=0.515  Sum_probs=18.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|.+|+|||+++..++.
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999877754

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=96.76  E-value=0.00038  Score=40.76  Aligned_cols=20  Identities=20%  Similarity=0.300  Sum_probs=17.5

Q ss_pred             ceEEeCCCCCchHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      .+++.|++|+|||+++..+.
T Consensus        18 kI~vvG~~~vGKSsLi~~l~   37 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLA   37 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            68999999999999977663

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=96.75  E-value=0.00043  Score=42.00  Aligned_cols=18  Identities=33%  Similarity=0.383  Sum_probs=14.5

Q ss_pred             eEEeCCCCCchHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRI   54 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~   54 (97)
                      +-|+|++||||||++..+
T Consensus         5 IgITG~igSGKStv~~~l   22 (205)
T d1jjva_           5 VGLTGGIGSGKTTIANLF   22 (205)
T ss_dssp             EEEECSTTSCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            457999999999986543

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=96.75  E-value=0.00045  Score=42.06  Aligned_cols=18  Identities=33%  Similarity=0.468  Sum_probs=14.7

Q ss_pred             eEEeCCCCCchHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRI   54 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~   54 (97)
                      +-|+|++|+||||++..+
T Consensus         6 IgitG~igSGKStv~~~l   23 (208)
T d1vhta_           6 VALTGGIGSGKSTVANAF   23 (208)
T ss_dssp             EEEECCTTSCHHHHHHHH
T ss_pred             EEEECCCcCCHHHHHHHH
Confidence            458999999999986543

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.75  E-value=0.00046  Score=40.39  Aligned_cols=21  Identities=29%  Similarity=0.499  Sum_probs=18.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..++.
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999877764

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=96.75  E-value=0.00043  Score=39.88  Aligned_cols=20  Identities=25%  Similarity=0.456  Sum_probs=17.1

Q ss_pred             ceEEeCCCCCchHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      .+++.|+||+|||+++.++.
T Consensus         3 kI~lvG~~nvGKSsLin~l~   22 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALA   22 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            47899999999999977665

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.74  E-value=0.0012  Score=40.05  Aligned_cols=33  Identities=30%  Similarity=0.315  Sum_probs=26.0

Q ss_pred             eEEe-CCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEe
Q psy16285         37 AIIQ-GPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVC   76 (97)
Q Consensus        37 ~~v~-Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~   76 (97)
                      +.|. +-.|+||||++..++..+.+.       +.+++++=
T Consensus         5 Iav~~~kGGvGKTtia~nLA~~la~~-------g~~VlliD   38 (237)
T d1g3qa_           5 ISIVSGKGGTGKTTVTANLSVALGDR-------GRKVLAVD   38 (237)
T ss_dssp             EEEECSSTTSSHHHHHHHHHHHHHHT-------TCCEEEEE
T ss_pred             EEEECCCCCCcHHHHHHHHHHHHHhC-------CCCEEEEe
Confidence            3344 678999999999999988765       67787774

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.68  E-value=0.00065  Score=40.19  Aligned_cols=20  Identities=40%  Similarity=0.551  Sum_probs=17.3

Q ss_pred             eEEeCCCCCchHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ++|.|.+|+|||+++..++.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999877654

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.68  E-value=0.00064  Score=40.02  Aligned_cols=21  Identities=33%  Similarity=0.577  Sum_probs=18.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|.+|+|||+++..+..
T Consensus         9 Ki~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1           9 KILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999877654

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=96.68  E-value=0.00047  Score=40.52  Aligned_cols=21  Identities=24%  Similarity=0.404  Sum_probs=17.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|+||+|||++..++..
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~   22 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTG   22 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            468999999999999887753

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.68  E-value=0.00067  Score=39.78  Aligned_cols=21  Identities=33%  Similarity=0.441  Sum_probs=17.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|++|+|||+++..++.
T Consensus         8 KI~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            478999999999999877654

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.67  E-value=0.00041  Score=42.68  Aligned_cols=25  Identities=16%  Similarity=0.195  Sum_probs=21.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      ..++|.|+-|+||||++..+...+.
T Consensus         3 k~IviEG~~GsGKST~~~~L~~~l~   27 (241)
T d2ocpa1           3 RRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHh
Confidence            3678999999999999888887763

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.67  E-value=0.00058  Score=39.76  Aligned_cols=22  Identities=27%  Similarity=0.380  Sum_probs=18.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ..++|.|++|+|||+++..++.
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~   26 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVE   26 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHh
Confidence            3688999999999999877654

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.66  E-value=0.0007  Score=39.44  Aligned_cols=21  Identities=33%  Similarity=0.529  Sum_probs=18.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|.+|+|||+++..++.
T Consensus         6 Ki~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           6 KVCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            578999999999999877654

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.66  E-value=0.00059  Score=39.54  Aligned_cols=21  Identities=24%  Similarity=0.303  Sum_probs=17.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|.+|+|||+++..++.
T Consensus         2 Kv~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           2 KLVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999887653

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.65  E-value=0.00063  Score=39.98  Aligned_cols=21  Identities=19%  Similarity=0.506  Sum_probs=17.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|.+|+|||+++..++.
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~   28 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQ   28 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999776653

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.64  E-value=0.00061  Score=40.78  Aligned_cols=21  Identities=29%  Similarity=0.551  Sum_probs=17.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|++|+|||+++..+..
T Consensus         8 KivvvG~~~vGKTsli~~l~~   28 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSD   28 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHhh
Confidence            378999999999999777653

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.63  E-value=0.00074  Score=39.38  Aligned_cols=21  Identities=29%  Similarity=0.518  Sum_probs=17.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|.+|+|||+++..++.
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~   25 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVS   25 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999777653

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.62  E-value=0.00064  Score=39.98  Aligned_cols=21  Identities=24%  Similarity=0.256  Sum_probs=17.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|.+|+|||+++..++.
T Consensus         4 KivvvG~~~vGKTsLi~~~~~   24 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSK   24 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999776654

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.62  E-value=0.00067  Score=44.43  Aligned_cols=23  Identities=35%  Similarity=0.512  Sum_probs=19.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ++..+|+||.|+|||+++-++..
T Consensus        25 ~~l~~i~G~NGsGKS~ileAi~~   47 (427)
T d1w1wa_          25 SNFTSIIGPNGSGKSNMMDAISF   47 (427)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            45678999999999999888753

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.62  E-value=0.00077  Score=39.36  Aligned_cols=21  Identities=29%  Similarity=0.547  Sum_probs=17.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|++|+|||+++..++.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999776654

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.59  E-value=0.00014  Score=44.60  Aligned_cols=24  Identities=17%  Similarity=0.099  Sum_probs=20.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +.++|.|+-|+||||++..+...+
T Consensus         3 k~I~ieG~dGsGKST~~~~L~~~l   26 (241)
T d1p5zb_           3 KKISIEGNIAAGKSTFVNILKQLC   26 (241)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            467899999999999988877765

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=96.58  E-value=0.0059  Score=39.13  Aligned_cols=34  Identities=24%  Similarity=0.269  Sum_probs=26.3

Q ss_pred             HHHHHHh---cCCceEEeCCCCCchHHHHHHHHHHHH
Q psy16285         26 EAYKAAL---TREFAIIQGPPGTGKTYVALRIVEGFL   59 (97)
Q Consensus        26 ~~i~~~~---~~~~~~v~Gp~GtGKT~~~~~~~~~~~   59 (97)
                      .+|+...   +++...|.|++|+|||+++..++....
T Consensus        57 raID~l~pig~GQr~~If~~~g~GKt~ll~~~~~~~~   93 (285)
T d2jdia3          57 KAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQK   93 (285)
T ss_dssp             HHHHHHSCCBTTCBCEEEESTTSSHHHHHHHHHHHTH
T ss_pred             eEEecccCccCCCEEEeecCCCCChHHHHHHHHHhHH
Confidence            3555544   578999999999999999888876543

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.55  E-value=0.0008  Score=41.19  Aligned_cols=25  Identities=24%  Similarity=0.306  Sum_probs=21.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +..+++.|+-|+||||.+..+...+
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~~L   27 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYKKL   27 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHH
Confidence            4578899999999999988887766

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=96.55  E-value=0.00068  Score=39.89  Aligned_cols=22  Identities=27%  Similarity=0.502  Sum_probs=18.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +.++|.|.||+|||+++..++.
T Consensus         6 ~~I~lvG~~~~GKSSLin~l~~   27 (178)
T d1wf3a1           6 GFVAIVGKPNVGKSTLLNNLLG   27 (178)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            4689999999999999877653

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.54  E-value=0.00091  Score=39.54  Aligned_cols=21  Identities=19%  Similarity=0.333  Sum_probs=18.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|.+|+|||+++..++.
T Consensus         7 KivviG~~~vGKTsli~~~~~   27 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTT   27 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            579999999999999877654

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.53  E-value=0.00089  Score=39.10  Aligned_cols=21  Identities=29%  Similarity=0.438  Sum_probs=17.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..+..
T Consensus         3 Ki~lvG~~~vGKTsLi~~~~~   23 (168)
T d2gjsa1           3 KVLLLGAPGVGKSALARIFGG   23 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCcCHHHHHHHHhC
Confidence            368999999999999877643

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=96.53  E-value=0.00041  Score=40.97  Aligned_cols=19  Identities=37%  Similarity=0.559  Sum_probs=17.0

Q ss_pred             ceEEeCCCCCchHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRI   54 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~   54 (97)
                      .+++.|++|+|||+++..+
T Consensus        19 KI~lvG~~~vGKTsLi~~l   37 (182)
T d1moza_          19 RILILGLDGAGKTTILYRL   37 (182)
T ss_dssp             EEEEEEETTSSHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            6899999999999997765

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=96.52  E-value=0.00096  Score=38.99  Aligned_cols=21  Identities=29%  Similarity=0.488  Sum_probs=17.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|.+|+|||+++..++.
T Consensus         6 KivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999777653

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=96.52  E-value=0.00043  Score=40.63  Aligned_cols=20  Identities=20%  Similarity=0.343  Sum_probs=17.6

Q ss_pred             ceEEeCCCCCchHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      .+++.|+||+|||+++..+.
T Consensus        14 kIvlvG~~~vGKTSli~rl~   33 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLK   33 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            68999999999999987764

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=96.49  E-value=0.00093  Score=39.35  Aligned_cols=21  Identities=29%  Similarity=0.385  Sum_probs=18.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+.|.|.+|+|||+++.+++.
T Consensus        10 kV~iiG~~~~GKSTLin~l~~   30 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILN   30 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHC
Confidence            578999999999999877753

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=96.49  E-value=0.0011  Score=40.75  Aligned_cols=20  Identities=25%  Similarity=0.282  Sum_probs=16.9

Q ss_pred             eEEeCCCCCchHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +.|+|+.||||||++..+..
T Consensus         4 IgiTG~igSGKsTva~~l~e   23 (241)
T d1deka_           4 IFLSGVKRSGKDTTADFIMS   23 (241)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999777654

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.48  E-value=0.0011  Score=38.81  Aligned_cols=21  Identities=19%  Similarity=0.472  Sum_probs=17.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|.+|+|||+++..++.
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~   26 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQ   26 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            468999999999999877764

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.45  E-value=0.0011  Score=38.49  Aligned_cols=21  Identities=24%  Similarity=0.525  Sum_probs=17.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|.+|+|||+++..++.
T Consensus         5 KivvvG~~~vGKTsli~r~~~   25 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            478999999999999777654

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.42  E-value=0.001  Score=39.42  Aligned_cols=21  Identities=19%  Similarity=0.351  Sum_probs=17.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .++|.|.+|+|||+++..++.
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~   31 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAN   31 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhh
Confidence            478999999999999776653

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.41  E-value=0.001  Score=39.59  Aligned_cols=21  Identities=19%  Similarity=0.333  Sum_probs=17.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..++.
T Consensus         5 KvvllG~~~vGKTSli~r~~~   25 (191)
T d2ngra_           5 KCVVVGDGAVGKTCLLISYTT   25 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999776654

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.41  E-value=0.0012  Score=38.78  Aligned_cols=20  Identities=25%  Similarity=0.380  Sum_probs=17.2

Q ss_pred             ceEEeCCCCCchHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      .+++.|.+|+|||+++..+.
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~   24 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFA   24 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHH
Confidence            57899999999999977664

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.39  E-value=0.00054  Score=40.22  Aligned_cols=22  Identities=36%  Similarity=0.554  Sum_probs=8.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+++.|.+|+|||+++..++..
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEEECCCCC------------
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999998777643

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.34  E-value=0.00089  Score=42.35  Aligned_cols=22  Identities=32%  Similarity=0.453  Sum_probs=18.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +..+++||.|+|||+++.++..
T Consensus        25 ~lnvlvG~NgsGKS~iL~Ai~~   46 (308)
T d1e69a_          25 RVTAIVGPNGSGKSNIIDAIKW   46 (308)
T ss_dssp             SEEEEECCTTTCSTHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHH
Confidence            4678999999999999777643

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=96.32  E-value=0.001  Score=39.28  Aligned_cols=19  Identities=21%  Similarity=0.216  Sum_probs=16.5

Q ss_pred             ceEEeCCCCCchHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRI   54 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~   54 (97)
                      .+.|.|+|++|||+++.++
T Consensus         3 ~VaiiG~~nvGKSSLin~L   21 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVV   21 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHS
T ss_pred             eEEEECCCCCCHHHHHHHH
Confidence            4679999999999997766

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.30  E-value=0.00068  Score=39.73  Aligned_cols=22  Identities=36%  Similarity=0.495  Sum_probs=17.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+++.|++|+|||+++..++..
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC--
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999998766543

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.28  E-value=0.0014  Score=38.76  Aligned_cols=22  Identities=18%  Similarity=0.223  Sum_probs=18.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+++.|.+|+|||+++..++..
T Consensus         4 KivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3689999999999998777543

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=96.27  E-value=0.0012  Score=41.50  Aligned_cols=21  Identities=24%  Similarity=0.406  Sum_probs=18.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +++|.|.||+|||+++..++.
T Consensus        34 ~I~LvG~tg~GKSSliN~ilg   54 (257)
T d1h65a_          34 TILVMGKGGVGKSSTVNSIIG   54 (257)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCcHHHHHHHHhC
Confidence            789999999999999888764

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=96.27  E-value=0.0015  Score=41.54  Aligned_cols=23  Identities=35%  Similarity=0.404  Sum_probs=19.5

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+++.|||+||||+++..+...+
T Consensus       106 ~~~l~G~~~tGKS~f~~~i~~~l  128 (267)
T d1u0ja_         106 TIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHh
Confidence            57889999999999987776655

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.23  E-value=0.0015  Score=38.72  Aligned_cols=19  Identities=16%  Similarity=0.284  Sum_probs=17.0

Q ss_pred             ceEEeCCCCCchHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRI   54 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~   54 (97)
                      .+++.|.+|+|||+++..+
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4789999999999998877

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.22  E-value=0.0013  Score=38.28  Aligned_cols=21  Identities=29%  Similarity=0.558  Sum_probs=18.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|.||.|||+++.++..
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~   27 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLG   27 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            578999999999999877764

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=96.20  E-value=0.0029  Score=40.45  Aligned_cols=23  Identities=35%  Similarity=0.371  Sum_probs=19.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      +++...|.|++|+|||+++..++
T Consensus        66 ~GQr~~Ifg~~g~GKt~l~~~~~   88 (276)
T d1fx0a3          66 RGQRELIIGDRQTGKTAVATDTI   88 (276)
T ss_dssp             TTCBCBEEESSSSSHHHHHHHHH
T ss_pred             CCceEeeccCCCCChHHHHHHHH
Confidence            46789999999999999876643

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=96.19  E-value=0.0012  Score=38.79  Aligned_cols=20  Identities=20%  Similarity=0.255  Sum_probs=17.1

Q ss_pred             ceEEeCCCCCchHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      .+.+.|.||+|||+++..+.
T Consensus         3 ~VaivG~~nvGKSTLin~L~   22 (180)
T d1udxa2           3 DVGLVGYPNAGKSSLLAAMT   22 (180)
T ss_dssp             SEEEECCGGGCHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            47789999999999977764

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.11  E-value=0.00052  Score=39.48  Aligned_cols=22  Identities=27%  Similarity=0.487  Sum_probs=18.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+++.|.||+|||+++.++...
T Consensus         2 kI~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           2 RMVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3689999999999998887654

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.09  E-value=0.0023  Score=37.80  Aligned_cols=21  Identities=19%  Similarity=0.243  Sum_probs=18.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+++.|++|+|||+++..++.
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~   27 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLT   27 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            578999999999999876654

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=96.02  E-value=0.00044  Score=43.34  Aligned_cols=25  Identities=20%  Similarity=0.331  Sum_probs=20.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +++..++.|++|.|||+++.++...
T Consensus        96 ~~~~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          96 QDKTTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             TTSEEEEEESHHHHHHHHHHHHCC-
T ss_pred             ccceEEEECCCCccHHHHHHhhccH
Confidence            4567889999999999999888643

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.02  E-value=0.0067  Score=34.51  Aligned_cols=37  Identities=27%  Similarity=0.394  Sum_probs=29.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      ..-++.||=.+|||+-+...+......       +++++++-|.
T Consensus         3 ~L~li~GpMfsGKTt~Li~~~~~~~~~-------g~~v~~ikp~   39 (133)
T d1xbta1           3 QIQVILGPMFSGKSTELMRRVRRFQIA-------QYKCLVIKYA   39 (133)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHTT-------TCCEEEEEET
T ss_pred             EEEEEEecccCHHHHHHHHHHHHHHHc-------CCcEEEEecc
Confidence            346899999999999877777766554       6788888874

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=95.99  E-value=0.0075  Score=34.72  Aligned_cols=39  Identities=18%  Similarity=0.111  Sum_probs=30.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNH   80 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~   80 (97)
                      ..-++.||=.+|||+-+...+......       +++++++.|...
T Consensus         8 ~l~lI~GpMfSGKTteLi~~~~~~~~~-------g~~vl~i~~~~D   46 (141)
T d1xx6a1           8 WVEVIVGPMYSGKSEELIRRIRRAKIA-------KQKIQVFKPEID   46 (141)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEEEC--
T ss_pred             eEEEEEeccccHHHHHHHHHHHHhhhc-------CCcEEEEEeccc
Confidence            356899999999999888888776554       778999888654

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.98  E-value=0.0022  Score=39.19  Aligned_cols=22  Identities=14%  Similarity=0.279  Sum_probs=18.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      ...+++.|.+|+|||+++..+.
T Consensus         6 ~~KilllG~~~vGKTsll~~~~   27 (221)
T d1azta2           6 THRLLLLGAGESGKSTIVKQMR   27 (221)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHH
T ss_pred             cCEEEEECCCCCCHHHHHHHHh
Confidence            3468999999999999977763

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=95.98  E-value=0.00094  Score=38.93  Aligned_cols=22  Identities=14%  Similarity=0.116  Sum_probs=18.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      ...+++.|.|++|||+++.++.
T Consensus        16 ~~~I~lvG~~NvGKSSL~n~L~   37 (188)
T d1puia_          16 GIEVAFAGRSNAGKSSALNTLT   37 (188)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHh
Confidence            3568999999999999977663

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.92  E-value=0.0043  Score=38.59  Aligned_cols=26  Identities=27%  Similarity=0.218  Sum_probs=21.2

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      +..+|+||..+|||+.+..++...+-
T Consensus        42 ~~~iiTGpN~~GKSt~lk~i~l~~~l   67 (234)
T d1wb9a2          42 RMLIITGPNMGGKSTYMRQTALIALM   67 (234)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEeccCchhhHHHHHHHHHHHHH
Confidence            56899999999999998888655444

>d1c9ka_ c.37.1.11 (A:) Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.89  E-value=0.0039  Score=37.46  Aligned_cols=45  Identities=13%  Similarity=0.251  Sum_probs=29.1

Q ss_pred             eEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         37 AIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ++|+|+.++|||..|..++    ..       ..++++++.....-+++.++++++
T Consensus         2 iLVtGGarSGKS~~AE~l~----~~-------~~~~~YiAT~~~~D~em~~RI~~H   46 (180)
T d1c9ka_           2 ILVTGGARSGKSRHAEALI----GD-------APQVLYIATSQILDDEMAARIQHH   46 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHH----CS-------CSSEEEEECCCC------CHHHHH
T ss_pred             EEEECCCCccHHHHHHHHH----hc-------CCCcEEEEccCCCCHHHHHHHHHH
Confidence            6899999999999876542    22       567888887666666777777665

>d1bg2a_ c.37.1.9 (A:) Kinesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.87  E-value=0.0042  Score=40.15  Aligned_cols=24  Identities=25%  Similarity=0.192  Sum_probs=17.8

Q ss_pred             HHHhcCC--ceEEeCCCCCchHHHHH
Q psy16285         29 KAALTRE--FAIIQGPPGTGKTYVAL   52 (97)
Q Consensus        29 ~~~~~~~--~~~v~Gp~GtGKT~~~~   52 (97)
                      +.++++.  .++..|++|+|||+++.
T Consensus        69 ~~~l~G~n~~i~aYGqtgSGKTyT~~   94 (323)
T d1bg2a_          69 KDVLEGYNGTIFAYGQTSSGKTHTME   94 (323)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHHT
T ss_pred             HHHHcCCCcceeeecccCCCCceecc
Confidence            3334444  56789999999999864

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=95.78  E-value=0.01  Score=33.95  Aligned_cols=36  Identities=22%  Similarity=0.193  Sum_probs=28.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCC
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYT   78 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~   78 (97)
                      .-++.||=.+|||+=+...+..+...       +++++++-|.
T Consensus         4 L~~i~GpMfsGKTteLi~~~~~~~~~-------~~kv~~ikp~   39 (139)
T d2b8ta1           4 IEFITGPMFAGKTAELIRRLHRLEYA-------DVKYLVFKPK   39 (139)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHT-------TCCEEEEEEC
T ss_pred             EEEEEccccCHHHHHHHHHHHHHHHC-------CCcEEEEEEc
Confidence            45789999999999777777766554       6778888775

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=95.67  E-value=0.0022  Score=41.99  Aligned_cols=26  Identities=27%  Similarity=0.326  Sum_probs=21.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.|.|+-|+||||++..+...+...
T Consensus         7 rI~IEG~iGsGKSTl~~~L~~~l~~~   32 (331)
T d1osna_           7 RIYLDGAYGIGKTTAAEEFLHHFAIT   32 (331)
T ss_dssp             EEEEEESSSSCTTHHHHHHHHTTTTS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhc
Confidence            46899999999999998888777443

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.65  E-value=0.0083  Score=39.91  Aligned_cols=21  Identities=19%  Similarity=0.305  Sum_probs=18.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ++.|.|.||+|||+++.++..
T Consensus        58 ~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          58 NVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            689999999999999887753

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.64  E-value=0.0039  Score=36.58  Aligned_cols=22  Identities=14%  Similarity=0.104  Sum_probs=18.4

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+++.|..|+|||+++..+...
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999998877443

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=95.59  E-value=0.0074  Score=39.45  Aligned_cols=23  Identities=17%  Similarity=0.196  Sum_probs=19.8

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+.|-|+-|+||||++..+...+
T Consensus         8 rI~iEG~iGsGKSTl~~~L~~~l   30 (333)
T d1p6xa_           8 RIYLDGVYGIGKSTTGRVMASAA   30 (333)
T ss_dssp             EEEEECSTTSSHHHHHHHHHSGG
T ss_pred             EEEEECCccCCHHHHHHHHHHHh
Confidence            46889999999999988887765

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=95.55  E-value=0.006  Score=39.92  Aligned_cols=17  Identities=29%  Similarity=0.614  Sum_probs=14.3

Q ss_pred             ceEEeCCCCCchHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVAL   52 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~   52 (97)
                      .++..|++|+|||+++.
T Consensus        82 ti~aYG~tgSGKT~Tm~   98 (354)
T d1goja_          82 TVFAYGQTGAGKSYTMM   98 (354)
T ss_dssp             EEEEECSTTSSHHHHHT
T ss_pred             eEEecccCCCCcceeee
Confidence            46778999999999863

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=95.53  E-value=0.0043  Score=36.50  Aligned_cols=20  Identities=25%  Similarity=0.124  Sum_probs=17.9

Q ss_pred             ceEEeCCCCCchHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      ++.+.|.|++|||+++.++.
T Consensus         7 nIaiiG~~naGKSTL~n~L~   26 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLT   26 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHH
Confidence            67899999999999988775

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=95.47  E-value=0.0062  Score=40.06  Aligned_cols=23  Identities=22%  Similarity=0.238  Sum_probs=16.7

Q ss_pred             HHhcCC--ceEEeCCCCCchHHHHH
Q psy16285         30 AALTRE--FAIIQGPPGTGKTYVAL   52 (97)
Q Consensus        30 ~~~~~~--~~~v~Gp~GtGKT~~~~   52 (97)
                      .++++.  .++..|++|||||+++.
T Consensus       108 ~~l~G~n~tifaYGqTGSGKTyTm~  132 (362)
T d1v8ka_         108 TIFEGGKATCFAYGQTGSGKTHTMG  132 (362)
T ss_dssp             HHHTTCEEEEEEEESTTSSHHHHHH
T ss_pred             HHHhccCceEEeeccCCCCCceeee
Confidence            334454  45668999999999864

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=95.43  E-value=0.0084  Score=37.01  Aligned_cols=27  Identities=26%  Similarity=0.284  Sum_probs=21.4

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHh
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLK   60 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~   60 (97)
                      ++..+|+||..+|||+.+..++...+-
T Consensus        35 ~~~~iiTGpN~~GKSt~lk~i~l~~il   61 (224)
T d1ewqa2          35 HELVLITGPNMAGKSTFLRQTALIALL   61 (224)
T ss_dssp             SCEEEEESCSSSSHHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCccccchhhhhhHHHHHH
Confidence            456899999999999998887554443

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=95.41  E-value=0.0065  Score=39.96  Aligned_cols=24  Identities=25%  Similarity=0.419  Sum_probs=18.0

Q ss_pred             HHHHhcCC--ceEEeCCCCCchHHHH
Q psy16285         28 YKAALTRE--FAIIQGPPGTGKTYVA   51 (97)
Q Consensus        28 i~~~~~~~--~~~v~Gp~GtGKT~~~   51 (97)
                      +..++++.  .++..|++|||||+++
T Consensus        67 v~~~l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          67 VQSAVDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             HHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHhcCCceeeeccccCCCCccccc
Confidence            44445554  5677999999999986

>d1d0xa2 c.37.1.9 (A:2-33,A:80-759) Myosin S1, motor domain {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=95.40  E-value=0.013  Score=41.92  Aligned_cols=28  Identities=21%  Similarity=0.355  Sum_probs=24.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..++|.|.+|+|||.....++..+..-
T Consensus       125 nQsIiisGeSGaGKTe~~k~il~yL~~~  152 (712)
T d1d0xa2         125 NQSLLITGESGAGKTENTKKVIQYLASV  152 (712)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHH
T ss_pred             CceEEEeCCCCCCHHHHHHHHHHHHHHH
Confidence            4689999999999999999999888764

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=95.35  E-value=0.0075  Score=39.26  Aligned_cols=24  Identities=25%  Similarity=0.375  Sum_probs=17.5

Q ss_pred             HHHHhcCC--ceEEeCCCCCchHHHH
Q psy16285         28 YKAALTRE--FAIIQGPPGTGKTYVA   51 (97)
Q Consensus        28 i~~~~~~~--~~~v~Gp~GtGKT~~~   51 (97)
                      ++.++++.  .++..|++|||||+++
T Consensus        73 v~~~l~G~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          73 LDEVIMGYNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             HHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             HHHHhccCCceEEeeeeccccceEEe
Confidence            33444454  5678999999999886

>d1lkxa_ c.37.1.9 (A:) Myosin S1, motor domain {Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]

Probab=95.34  E-value=0.012  Score=41.82  Aligned_cols=28  Identities=29%  Similarity=0.381  Sum_probs=24.8

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++.+++.|.+|+|||..+..++..+..-
T Consensus        86 ~QsIiisGeSGsGKTe~~k~il~yL~~~  113 (684)
T d1lkxa_          86 NQCVIISGESGAGKTEASKKIMQFLTFV  113 (684)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHHH
Confidence            4689999999999999999999988654

>d1br2a2 c.37.1.9 (A:80-789) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=95.29  E-value=0.014  Score=41.55  Aligned_cols=28  Identities=18%  Similarity=0.271  Sum_probs=24.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++.++|.|.+|+|||.....++.++..-
T Consensus        91 ~Q~IiisGeSGaGKTe~~k~il~yL~~~  118 (710)
T d1br2a2          91 DQSILCTGESGAGKTENTKKVIQYLAVV  118 (710)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHH
Confidence            4689999999999999999999988754

>d2zfia1 c.37.1.9 (A:4-352) Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif1a [TaxId: 10090]

Probab=95.25  E-value=0.0093  Score=38.88  Aligned_cols=23  Identities=26%  Similarity=0.459  Sum_probs=17.2

Q ss_pred             HHhcCC--ceEEeCCCCCchHHHHH
Q psy16285         30 AALTRE--FAIIQGPPGTGKTYVAL   52 (97)
Q Consensus        30 ~~~~~~--~~~v~Gp~GtGKT~~~~   52 (97)
                      .+.++.  .++..|++|+|||+++.
T Consensus        81 ~~l~G~n~ti~aYGqTgSGKT~Tm~  105 (349)
T d2zfia1          81 HAFEGYNVCIFAYGQTGAGKSYTMM  105 (349)
T ss_dssp             HHHTTCCEEEEEECSTTSSHHHHHT
T ss_pred             HHHhccCceeeeeccCCCCCceeec
Confidence            334453  56789999999999863

>d2ncda_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.25  E-value=0.0079  Score=39.59  Aligned_cols=25  Identities=32%  Similarity=0.458  Sum_probs=18.8

Q ss_pred             HHHHHhcCC--ceEEeCCCCCchHHHH
Q psy16285         27 AYKAALTRE--FAIIQGPPGTGKTYVA   51 (97)
Q Consensus        27 ~i~~~~~~~--~~~v~Gp~GtGKT~~~   51 (97)
                      .+..+.++.  .++..|++|||||+++
T Consensus       116 lv~~vl~G~n~ti~aYGqtGSGKT~Tm  142 (368)
T d2ncda_         116 LIQSALDGYNICIFAYGQTGSGKTYTM  142 (368)
T ss_dssp             HHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcccceeEEeeccCCCccceEe
Confidence            455555554  5678999999999985

>d1g8fa3 c.37.1.15 (A:390-511) ATP sulfurylase C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.22  E-value=0.017  Score=32.52  Aligned_cols=39  Identities=10%  Similarity=0.090  Sum_probs=31.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCCh
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN   79 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~   79 (97)
                      .+++.|-.|+||++++.++...+++.+     .++++-++-.+|
T Consensus         8 ~i~~tg~~~~gk~~ia~al~~~l~q~~-----G~R~vtll~~~n   46 (122)
T d1g8fa3           8 SIVLGNSLTVSREQLSIALLSTFLQFG-----GGRYYKIFEHNN   46 (122)
T ss_dssp             EEEECTTCCSCHHHHHHHHHHHHTTSC-----SCCCEEECCCTT
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHHHHhc-----CCcceEEecCCC
Confidence            578899999999999999999998842     356777666554

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=95.20  E-value=0.0095  Score=36.40  Aligned_cols=25  Identities=20%  Similarity=0.142  Sum_probs=20.9

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++.+.|.|.|++|||+++.+++...
T Consensus         5 ~p~IaIiGh~d~GKSTL~~~L~~~~   29 (227)
T d1g7sa4           5 SPIVSVLGHVDHGKTTLLDHIRGSA   29 (227)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCccHHHHHHHHHhhc
Confidence            4558999999999999988887653

>d1j3ba1 c.91.1.1 (A:212-529) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Thermus thermophilus [TaxId: 274]

Probab=95.18  E-value=0.0047  Score=40.24  Aligned_cols=19  Identities=37%  Similarity=0.553  Sum_probs=16.1

Q ss_pred             CCceEEeCCCCCchHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVAL   52 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~   52 (97)
                      +...++.|.+||||||+..
T Consensus        14 ~~valffGLSGTGKTTLs~   32 (318)
T d1j3ba1          14 GDVAVFFGLSGTGKTTLST   32 (318)
T ss_dssp             CCEEEEEECTTSCHHHHTC
T ss_pred             CCEEEEEccCCCCcccccc
Confidence            4678999999999999753

>d2mysa2 c.37.1.9 (A:4-33,A:80-843) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=95.15  E-value=0.015  Score=42.00  Aligned_cols=28  Identities=29%  Similarity=0.455  Sum_probs=24.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++.++|.|.+|+|||.....++..+..-
T Consensus       123 ~QsIiisGeSGaGKTe~~K~il~yL~~~  150 (794)
T d2mysa2         123 NQSILITGESGAGKTVNTKRVIQYFATI  150 (794)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHHH
Confidence            4689999999999999999999888754

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.10  E-value=0.0087  Score=34.83  Aligned_cols=20  Identities=15%  Similarity=0.307  Sum_probs=17.1

Q ss_pred             ceEEeCCCCCchHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      .+++.|..|+|||+++..+.
T Consensus         4 KivllG~~~vGKTsl~~r~~   23 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMK   23 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            47899999999999977654

>d2olra1 c.91.1.1 (A:228-540) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Escherichia coli [TaxId: 562]

Probab=94.98  E-value=0.0069  Score=39.34  Aligned_cols=18  Identities=39%  Similarity=0.608  Sum_probs=15.6

Q ss_pred             CCceEEeCCCCCchHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVA   51 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~   51 (97)
                      +...++.|.+||||||+.
T Consensus        14 ~~~alfFGLSGTGKTTLs   31 (313)
T d2olra1          14 GDVAVFFGLSGTGKTTLS   31 (313)
T ss_dssp             SCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEEccCCCCcccce
Confidence            467899999999999975

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=94.96  E-value=0.0078  Score=39.29  Aligned_cols=23  Identities=35%  Similarity=0.349  Sum_probs=18.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      .+.|-|+=|+||||++..+...+
T Consensus         6 rI~IEG~iGsGKTTl~~~La~~l   28 (329)
T d1e2ka_           6 RVYIDGPHGMGKTTTTQLLVALG   28 (329)
T ss_dssp             EEEECSCTTSSHHHHHHHHTC--
T ss_pred             EEEEECCcCCCHHHHHHHHHHHh
Confidence            36789999999999988776655

>d1w7ja2 c.37.1.9 (A:63-792) Myosin S1, motor domain {Chicken (Gallus gallus), Va isoform [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), Va isoform [TaxId: 9031]

Probab=94.93  E-value=0.021  Score=40.78  Aligned_cols=28  Identities=29%  Similarity=0.347  Sum_probs=24.5

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      +..++|.|.+|+|||.....++..+..-
T Consensus        94 ~Q~IiisGeSGsGKTe~~k~il~~l~~~  121 (730)
T d1w7ja2          94 NQSIIVSGESGAGKTVSAKYAMRYFATV  121 (730)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHH
Confidence            5689999999999999999998888654

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=94.92  E-value=0.0077  Score=38.15  Aligned_cols=23  Identities=22%  Similarity=0.333  Sum_probs=19.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +++.|.|..|+||||++-+++..
T Consensus         3 RNv~iiGh~~~GKTtL~e~ll~~   25 (267)
T d2dy1a2           3 RTVALVGHAGSGKTTLTEALLYK   25 (267)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCcHHHHHHHHHHH
Confidence            46889999999999998877543

>d1ry6a_ c.37.1.9 (A:) Kinesin {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Malaria parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=94.81  E-value=0.0072  Score=39.14  Aligned_cols=17  Identities=41%  Similarity=0.671  Sum_probs=14.3

Q ss_pred             ceEEeCCCCCchHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVAL   52 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~   52 (97)
                      .++..|++|||||+++.
T Consensus        87 ~i~aYGqTGSGKTyTm~  103 (330)
T d1ry6a_          87 SCFAYGQTGSGKTYTML  103 (330)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEeeeccccccceeee
Confidence            46778999999999864

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=94.79  E-value=0.0097  Score=37.90  Aligned_cols=24  Identities=25%  Similarity=0.046  Sum_probs=20.6

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      +++.|.|..|+|||+++-+++...
T Consensus         7 Rni~i~gh~~~GKTtL~e~ll~~~   30 (276)
T d2bv3a2           7 RNIGIAAHIDAGKTTTTERILYYT   30 (276)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhc
Confidence            578999999999999988886544

>d1ii2a1 c.91.1.1 (A:201-523) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Trypanosoma cruzi [TaxId: 5693]

Probab=94.76  E-value=0.0089  Score=38.95  Aligned_cols=19  Identities=32%  Similarity=0.524  Sum_probs=16.3

Q ss_pred             CCceEEeCCCCCchHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVAL   52 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~   52 (97)
                      +...++.|-+||||||+..
T Consensus        14 gd~alfFGLSGTGKTTLs~   32 (323)
T d1ii2a1          14 GDVTVFFGLSGTGKTTLSA   32 (323)
T ss_dssp             CCEEEEECCTTSSHHHHHC
T ss_pred             CCEEEEEccCCCCccccee
Confidence            4678999999999999863

>d1kk8a2 c.37.1.9 (A:1-28,A:77-837) Myosin S1, motor domain {Bay scallop (Aequipecten irradians) [TaxId: 31199]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Bay scallop (Aequipecten irradians) [TaxId: 31199]

Probab=94.71  E-value=0.02  Score=41.25  Aligned_cols=28  Identities=25%  Similarity=0.368  Sum_probs=24.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++.++|.|.+|+|||..+..++..+..-
T Consensus       121 nQ~IiisGESGaGKTe~~K~il~yL~~~  148 (789)
T d1kk8a2         121 NQSCLITGESGAGKTENTKKVIMYLAKV  148 (789)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHH
Confidence            4689999999999999999999988754

>d1f5na2 c.37.1.8 (A:7-283) Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.66  E-value=0.0041  Score=39.63  Aligned_cols=41  Identities=24%  Similarity=0.284  Sum_probs=28.6

Q ss_pred             ccCCCCCHHHHHHHHHHhcCC--ceEEeCCCCCchHHHHHHHHH
Q psy16285         15 QEELGLNTIQFEAYKAALTRE--FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        15 ~~~~~l~~~Q~~~i~~~~~~~--~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ...+.++++-.+.+..+ +++  .+.|.||.+||||+++..+..
T Consensus        12 ~~~l~~~~e~l~~l~~~-~~~v~vvsi~G~~~sGKS~llN~l~~   54 (277)
T d1f5na2          12 NGRLMANPEALKILSAI-TQPMVVVAIVGLYRTGKSYLMNKLAG   54 (277)
T ss_dssp             TTEEEECHHHHHHHHTC-CSBEEEEEEEEBTTSSHHHHHHHHTT
T ss_pred             CCeEEECHHHHHHHHcC-CCCEEEEEEECCCCCCHHHHHHHHcC
Confidence            34567777666666553 333  557799999999999777653

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=94.51  E-value=0.013  Score=38.08  Aligned_cols=17  Identities=35%  Similarity=0.632  Sum_probs=14.5

Q ss_pred             ceEEeCCCCCchHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVAL   52 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~   52 (97)
                      .++..|++|||||+++.
T Consensus        85 ~i~aYGqtgSGKT~T~~  101 (342)
T d1f9va_          85 CIFAYGQTGSGKTFTML  101 (342)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             ceeeeeccCCccccccc
Confidence            56779999999999864

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=94.49  E-value=0.018  Score=34.72  Aligned_cols=23  Identities=17%  Similarity=-0.012  Sum_probs=19.6

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++.+.|-+++||||++-+++...
T Consensus         5 ni~iiGhvd~GKSTL~~~Ll~~~   27 (204)
T d2c78a3           5 NVGTIGHVDHGKTTLTAALTYVA   27 (204)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHh
Confidence            67899999999999988886543

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=92.59  E-value=0.69  Score=29.08  Aligned_cols=66  Identities=15%  Similarity=0.007  Sum_probs=42.1

Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         17 ELGLNTIQFEAYKAALTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        17 ~~~l~~~Q~~~i~~~~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      .+..-+.|.-......++  -+....+|-|||.++. +...+..-      .++.|.+++.+.-++.+=.+.+..
T Consensus        78 G~RhyDVQLiGgi~L~~G--~iaem~TGEGKTL~a~-l~a~l~al------~g~~vhvvTvNdyLA~RDae~m~~  143 (273)
T d1tf5a3          78 GMFPFKVQLMGGVALHDG--NIAEMKTGEGKTLTST-LPVYLNAL------TGKGVHVVTVNEYLASRDAEQMGK  143 (273)
T ss_dssp             SCCCCHHHHHHHHHHHTT--SEEECCTTSCHHHHHH-HHHHHHHT------TSSCEEEEESSHHHHHHHHHHHHH
T ss_pred             ceEEehhHHHHHHHHHhh--hheeecCCCcchhHHH-HHHHHHHh------cCCCceEEecCccccchhhhHHhH
Confidence            344556665554443333  4688999999997644 33344333      478999999888777665554443

>d1n0ua2 c.37.1.8 (A:3-343) Elongation factor 2 (eEF-2), N-terminal (G) domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor 2 (eEF-2), N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.47  E-value=0.055  Score=35.26  Aligned_cols=22  Identities=14%  Similarity=0.137  Sum_probs=19.4

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +++.|.|..|+|||+++-+++.
T Consensus        18 RNI~iiGhvd~GKTTL~d~Ll~   39 (341)
T d1n0ua2          18 RNMSVIAHVDHGKSTLTDSLVQ   39 (341)
T ss_dssp             EEEEEECCGGGTHHHHHHHHHH
T ss_pred             cEEEEEeCCCCcHHHHHHHHHH
Confidence            5799999999999999887764

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=92.46  E-value=0.16  Score=29.45  Aligned_cols=36  Identities=19%  Similarity=0.236  Sum_probs=29.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY   77 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~   77 (97)
                      +.+.|.-.+|=||||-|..++-...-.       +.+|+++-+
T Consensus         3 G~i~vytG~GKGKTTAAlG~alRA~G~-------G~rV~ivQF   38 (157)
T d1g5ta_           3 GIIIVFTGNGKGKTTAAFGTAARAVGH-------GKNVGVVQF   38 (157)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHT-------TCCEEEEES
T ss_pred             cEEEEEeCCCCCcHHHHHHHHHHHhcC-------CCEEEEEEE
Confidence            456677788999999998888877776       788888876

>d1em8a_ c.128.1.1 (A:) DNA polymerase III chi subunit {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: DNA polymerase III chi subunit
superfamily: DNA polymerase III chi subunit
family: DNA polymerase III chi subunit
domain: DNA polymerase III chi subunit
species: Escherichia coli [TaxId: 562]

Probab=91.79  E-value=0.28  Score=27.84  Aligned_cols=39  Identities=13%  Similarity=0.206  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         50 VALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        50 ~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      +++.+++...+.       +.+++|.|++.+.+..+-+.|..|..+
T Consensus        24 ~~crL~~K~~~~-------g~ri~I~~~d~~~~~~lD~~LWt~~~~   62 (147)
T d1em8a_          24 LVCEIAAERWRS-------GKRVLIACEDEKQAYRLDEALWARPAE   62 (147)
T ss_dssp             HHHHHHHHHHHT-------TCCEEEECSSHHHHHHHHHHHHHCSTT
T ss_pred             HHHHHHHHHHHC-------CCEEEEEeCCHHHHHHHHHHHhCCCCc
Confidence            466777777666       889999999999999999999988754

>d1e8ca3 c.72.2.1 (A:104-337) UDP-N-acetylmuramyl tripeptide synthetase MurE {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribokinase-like
superfamily: MurD-like peptide ligases, catalytic domain
family: MurCDEF
domain: UDP-N-acetylmuramyl tripeptide synthetase MurE
species: Escherichia coli [TaxId: 562]

Probab=91.46  E-value=0.086  Score=31.41  Aligned_cols=22  Identities=27%  Similarity=0.448  Sum_probs=13.9

Q ss_pred             EeCCCCC-chHHHHHHHHHHHHhc
Q psy16285         39 IQGPPGT-GKTYVALRIVEGFLKN   61 (97)
Q Consensus        39 v~Gp~Gt-GKT~~~~~~~~~~~~~   61 (97)
                      |.|=+|| ||||+ ..++.++++.
T Consensus         7 vI~ITGT~GKTTt-~~~l~~iL~~   29 (234)
T d1e8ca3           7 LVGVTGTNGKTTT-TQLLAQWSQL   29 (234)
T ss_dssp             EEEEESSSCHHHH-HHHHHHHHHH
T ss_pred             EEEEECCCcHHHH-HHHHHHHHHH
Confidence            4445564 99999 4555555554

>d1p3da3 c.72.2.1 (A:107-321) UDP-N-acetylmuramate-alanine ligase MurC {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: Ribokinase-like
superfamily: MurD-like peptide ligases, catalytic domain
family: MurCDEF
domain: UDP-N-acetylmuramate-alanine ligase MurC
species: Haemophilus influenzae [TaxId: 727]

Probab=91.32  E-value=0.15  Score=30.17  Aligned_cols=31  Identities=16%  Similarity=0.191  Sum_probs=17.3

Q ss_pred             HHHHHhcCC-ceEEeCCCCC-chHHHHHHHHHHHHhc
Q psy16285         27 AYKAALTRE-FAIIQGPPGT-GKTYVALRIVEGFLKN   61 (97)
Q Consensus        27 ~i~~~~~~~-~~~v~Gp~Gt-GKT~~~~~~~~~~~~~   61 (97)
                      .+....+.. .+.|+   || ||||+. .++.++++.
T Consensus         4 ~L~~~~r~~~~I~IT---GTnGKTTt~-~~l~~iL~~   36 (215)
T d1p3da3           4 MLAEIMRFRHGIAVA---GTHGKTTTT-AMISMIYTQ   36 (215)
T ss_dssp             HHHHHHHTSEEEEEE---SSSCHHHHH-HHHHHHHHH
T ss_pred             HHHHHHcCCCEEEEE---CCCCHHHHH-HHHHHHHHh
Confidence            344444444 34444   55 999994 555556555

>d1d2ea3 c.37.1.8 (A:55-250) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Cow (Bos taurus), mitochondrial [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Cow (Bos taurus), mitochondrial [TaxId: 9913]

Probab=91.21  E-value=0.12  Score=30.73  Aligned_cols=23  Identities=22%  Similarity=0.107  Sum_probs=19.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEGF   58 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~~   58 (97)
                      ++.+.|-+..||||++-++...+
T Consensus         5 ni~iiGHvd~GKSTL~~~l~~~~   27 (196)
T d1d2ea3           5 NVGTIGHVDHGKTTLTAAITKIL   27 (196)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHH
Confidence            67899999999999988887643

>d1jnya3 c.37.1.8 (A:4-227) Elongation factor eEF-1alpha, N-terminal (G) domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor eEF-1alpha, N-terminal (G) domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=91.17  E-value=0.091  Score=31.76  Aligned_cols=21  Identities=24%  Similarity=0.297  Sum_probs=18.1

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ++.+.|-.++||||++-+++.
T Consensus         5 Ni~viGHVd~GKTTL~~~Ll~   25 (224)
T d1jnya3           5 NLIVIGHVDHGKSTLVGRLLM   25 (224)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEecCCCCHHHHHHHHHH
Confidence            678999999999999877753

>d2qn6a3 c.37.1.8 (A:2-206) Initiation factor eIF2 gamma subunit, N-terminal (G) domain {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor eIF2 gamma subunit, N-terminal (G) domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=91.06  E-value=0.086  Score=31.30  Aligned_cols=20  Identities=25%  Similarity=0.182  Sum_probs=17.9

Q ss_pred             ceEEeCCCCCchHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIV   55 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~   55 (97)
                      ++.|.|.+.+||||++-+++
T Consensus        10 ni~iiGhVd~GKSTL~~~L~   29 (205)
T d2qn6a3          10 NIGVVGHVDHGKTTLVQAIT   29 (205)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEEEccCCcHHHHHHHHH
Confidence            68899999999999988775

>d1zunb3 c.37.1.8 (B:16-237) Sulfate adenylate transferase subunit cysN/C, EF-Tu domain G-like domain {Pseudomonas syringae pv. tomato [TaxId: 323]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Sulfate adenylate transferase subunit cysN/C, EF-Tu domain G-like domain
species: Pseudomonas syringae pv. tomato [TaxId: 323]

Probab=90.84  E-value=0.11  Score=31.57  Aligned_cols=21  Identities=19%  Similarity=0.224  Sum_probs=18.2

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ++++.|-+.+||||++-+++.
T Consensus        11 ~i~viGHVd~GKSTL~~~Ll~   31 (222)
T d1zunb3          11 RFLTCGNVDDGKSTLIGRLLH   31 (222)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEcCCCCCHHHHHHHHHH
Confidence            578999999999999887753

>d2c07a1 c.2.1.2 (A:54-304) beta-keto acyl carrier protein reductase {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: beta-keto acyl carrier protein reductase
species: Malaria parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=90.81  E-value=0.4  Score=29.27  Aligned_cols=51  Identities=14%  Similarity=0.264  Sum_probs=39.4

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +++.++|+|.++    -+..+++..+.+.       +.+|+++..+.+.++...+.+++++.
T Consensus         9 enKvalITGas~----GIG~a~a~~la~~-------Ga~V~~~~r~~~~l~~~~~~l~~~g~   59 (251)
T d2c07a1           9 ENKVALVTGAGR----GIGREIAKMLAKS-------VSHVICISRTQKSCDSVVDEIKSFGY   59 (251)
T ss_dssp             SSCEEEEESTTS----HHHHHHHHHHTTT-------SSEEEEEESSHHHHHHHHHHHHTTTC
T ss_pred             CCCEEEEeCCCC----HHHHHHHHHHHHc-------CCEEEEEECCHHHHHHHHHHHHhcCC
Confidence            567889998753    3666677777665       67888888888999999998887654

>d1jwyb_ c.37.1.8 (B:) Dynamin G domain {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Dynamin G domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=90.77  E-value=0.084  Score=33.17  Aligned_cols=22  Identities=27%  Similarity=0.383  Sum_probs=19.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +.++|.|..++|||+++.+++.
T Consensus        25 P~ivVvG~~ssGKSSliNaLlG   46 (306)
T d1jwyb_          25 PQIVVVGSQSSGKSSVLENIVG   46 (306)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHT
T ss_pred             CeEEEEeCCCCCHHHHHHHHhC
Confidence            4589999999999999888864

>d2akab1 c.37.1.8 (B:6-304) Dynamin G domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Dynamin G domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=90.48  E-value=0.084  Score=32.98  Aligned_cols=22  Identities=23%  Similarity=0.235  Sum_probs=19.0

Q ss_pred             CceEEeCCCCCchHHHHHHHHH
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +.++|.|.-++|||+++.+++.
T Consensus        27 P~ivvvG~~SsGKSsliNaLlg   48 (299)
T d2akab1          27 PQIAVVGGQSAGKSSVLENFVG   48 (299)
T ss_dssp             CEEEEEEBTTSCHHHHHHHHHT
T ss_pred             CeEEEEcCCCCCHHHHHHHHhC
Confidence            4589999999999999888865

>d1w6ua_ c.2.1.2 (A:) 2,4-dienoyl-CoA reductase, mitochondrial (DECR) {Human (Homo sapiens), [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: 2,4-dienoyl-CoA reductase, mitochondrial (DECR)
species: Human (Homo sapiens), [TaxId: 9606]

Probab=90.43  E-value=0.71  Score=28.46  Aligned_cols=50  Identities=12%  Similarity=0.060  Sum_probs=39.4

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      ++++.++|+|.+|    -+..+++..+.+.       +.+|+++..+...+++..+++.+.
T Consensus        23 l~gK~alITGas~----GIG~aiA~~la~~-------Ga~Vii~~r~~~~l~~~~~~l~~~   72 (294)
T d1w6ua_          23 FQGKVAFITGGGT----GLGKGMTTLLSSL-------GAQCVIASRKMDVLKATAEQISSQ   72 (294)
T ss_dssp             TTTCEEEEETTTS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCC----HHHHHHHHHHHHc-------CCEEEEEECCHHHHHHHHHHHHHh
Confidence            4578899999875    4667788888777       788999998888888888877654

>d1kk1a3 c.37.1.8 (A:6-200) Initiation factor eIF2 gamma subunit, N-terminal (G) domain {Archaeon Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor eIF2 gamma subunit, N-terminal (G) domain
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

Probab=90.11  E-value=0.12  Score=30.33  Aligned_cols=21  Identities=19%  Similarity=0.132  Sum_probs=18.0

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ++.+.|-+..||||++-++..
T Consensus         7 nIaiiGhvd~GKSTL~~~L~g   27 (195)
T d1kk1a3           7 NIGMVGHVDHGKTTLTKALTG   27 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHT
T ss_pred             EEEEEeccCCcHHHHHHHHHh
Confidence            578899999999999888753

>d1fmca_ c.2.1.2 (A:) 7-alpha-hydroxysteroid dehydrogenase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: 7-alpha-hydroxysteroid dehydrogenase
species: Escherichia coli [TaxId: 562]

Probab=90.10  E-value=0.5  Score=28.93  Aligned_cols=51  Identities=16%  Similarity=0.232  Sum_probs=38.8

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.++++.+++++.+.
T Consensus        10 ~gK~alITGas~----GIG~aia~~la~~-------Ga~V~~~~r~~~~~~~~~~~l~~~g~   60 (255)
T d1fmca_          10 DGKCAIITGAGA----GIGKEIAITFATA-------GASVVVSDINADAANHVVDEIQQLGG   60 (255)
T ss_dssp             TTCEEEETTTTS----HHHHHHHHHHHTT-------TCEEEEEESCHHHHHHHHHHHHHTTC
T ss_pred             CCCEEEEeCCCc----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHHcCC
Confidence            578889998763    3555666777665       77888888888888999888887654

>d1gg4a4 c.72.2.1 (A:99-312) UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribokinase-like
superfamily: MurD-like peptide ligases, catalytic domain
family: MurCDEF
domain: UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF
species: Escherichia coli [TaxId: 562]

Probab=89.98  E-value=0.083  Score=30.97  Aligned_cols=22  Identities=27%  Similarity=0.465  Sum_probs=14.1

Q ss_pred             EeCCCCC-chHHHHHHHHHHHHhc
Q psy16285         39 IQGPPGT-GKTYVALRIVEGFLKN   61 (97)
Q Consensus        39 v~Gp~Gt-GKT~~~~~~~~~~~~~   61 (97)
                      |.|=+|| |||++. .++.++++.
T Consensus         4 vI~VTGTnGKTTt~-~mi~~iL~~   26 (214)
T d1gg4a4           4 VVALTGSSGKTSVK-EMTAAILSQ   26 (214)
T ss_dssp             EEEEECSSCHHHHH-HHHHHHHTT
T ss_pred             EEEEeCCCcHHHHH-HHHHHHHHh
Confidence            3444566 999994 455666665

>d2rhca1 c.2.1.2 (A:5-261) beta-keto acyl carrier protein reductase {Streptomyces coelicolor [TaxId: 1902]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: beta-keto acyl carrier protein reductase
species: Streptomyces coelicolor [TaxId: 1902]

Probab=89.82  E-value=0.85  Score=27.73  Aligned_cols=50  Identities=14%  Similarity=0.207  Sum_probs=37.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ++..+|+|.++    -+..+++..+.++       +.+|+++..+.+.+++..+.+++.+.
T Consensus         2 gKValITGas~----GIG~aia~~la~~-------Ga~V~i~~r~~~~l~~~~~~l~~~g~   51 (257)
T d2rhca1           2 SEVALVTGATS----GIGLEIARRLGKE-------GLRVFVCARGEEGLRTTLKELREAGV   51 (257)
T ss_dssp             CCEEEEESCSS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCC----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHhcCC
Confidence            45678888763    3445667777666       77888888888889999988887654

>d1f60a3 c.37.1.8 (A:2-240) Elongation factor eEF-1alpha, N-terminal (G) domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor eEF-1alpha, N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.68  E-value=0.15  Score=31.34  Aligned_cols=21  Identities=14%  Similarity=0.256  Sum_probs=18.7

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ++.+.|-.++||||++-+++.
T Consensus         8 Ni~iiGHvD~GKsTl~~~ll~   28 (239)
T d1f60a3           8 NVVVIGHVDSGKSTTTGHLIY   28 (239)
T ss_dssp             EEEEEECTTSCHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHH
Confidence            788999999999999888864

>d1ni3a1 c.37.1.8 (A:11-306) YchF GTP-binding protein N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=89.66  E-value=0.098  Score=32.95  Aligned_cols=22  Identities=27%  Similarity=0.267  Sum_probs=18.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      .+=|.|-|.+||||+..++...
T Consensus        12 kiGivG~Pn~GKSTlfnalT~~   33 (296)
T d1ni3a1          12 KTGIVGMPNVGKSTFFRAITKS   33 (296)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            3568999999999998888753

>d2ae2a_ c.2.1.2 (A:) Tropinone reductase {Jimsonweed (Datura stramonium), II [TaxId: 4076]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Tropinone reductase
species: Jimsonweed (Datura stramonium), II [TaxId: 4076]

Probab=89.61  E-value=0.7  Score=28.25  Aligned_cols=52  Identities=13%  Similarity=0.114  Sum_probs=39.0

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ++++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.+++..+++.+.+.
T Consensus         6 L~GK~alITGas~----GIG~aia~~la~~-------Ga~V~~~~r~~~~l~~~~~~~~~~g~   57 (259)
T d2ae2a_           6 LEGCTALVTGGSR----GIGYGIVEELASL-------GASVYTCSRNQKELNDCLTQWRSKGF   57 (259)
T ss_dssp             CTTCEEEEESCSS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEeCCCC----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHhcCC
Confidence            3577889999763    4555677777776       67888888888888888888876543

>d1zema1 c.2.1.2 (A:3-262) Xylitol dehydrogenase {Gluconobacter oxydans [TaxId: 442]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Xylitol dehydrogenase
species: Gluconobacter oxydans [TaxId: 442]

Probab=89.43  E-value=0.86  Score=27.81  Aligned_cols=52  Identities=13%  Similarity=0.224  Sum_probs=38.2

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ++++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.+++..+.+.+.+.
T Consensus         3 L~gK~alITGas~----GIG~aia~~la~~-------Ga~V~~~~r~~~~l~~~~~~~~~~g~   54 (260)
T d1zema1           3 FNGKVCLVTGAGG----NIGLATALRLAEE-------GTAIALLDMNREALEKAEASVREKGV   54 (260)
T ss_dssp             TTTCEEEEETTTS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHTTTS
T ss_pred             CCCCEEEEeCCCC----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHhcCC
Confidence            3567889998763    3455667777666       77888888888888888888877653

>d2jfga3 c.72.2.1 (A:94-297) UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribokinase-like
superfamily: MurD-like peptide ligases, catalytic domain
family: MurCDEF
domain: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD
species: Escherichia coli [TaxId: 562]

Probab=89.27  E-value=0.2  Score=29.29  Aligned_cols=21  Identities=29%  Similarity=0.409  Sum_probs=13.2

Q ss_pred             eCCCCC-chHHHHHHHHHHHHhc
Q psy16285         40 QGPPGT-GKTYVALRIVEGFLKN   61 (97)
Q Consensus        40 ~Gp~Gt-GKT~~~~~~~~~~~~~   61 (97)
                      .|=+|| |||++. .++.++++.
T Consensus        14 I~VTGT~GKTTt~-~~l~~iL~~   35 (204)
T d2jfga3          14 VAITGSNGKSTVT-TLVGEMAKA   35 (204)
T ss_dssp             EEEECSSSHHHHH-HHHHHHHHH
T ss_pred             EEEECCCCHHHHH-HHHHHHHHh
Confidence            344455 899994 555555555

>d1ae1a_ c.2.1.2 (A:) Tropinone reductase {Jimsonweed (Datura stramonium), I [TaxId: 4076]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Tropinone reductase
species: Jimsonweed (Datura stramonium), I [TaxId: 4076]

Probab=89.00  E-value=0.89  Score=27.78  Aligned_cols=52  Identities=17%  Similarity=0.157  Sum_probs=38.2

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ++++.++|+|.++    -+..+++..+.++       +.+|+++..+...++...+.+.+.+.
T Consensus         4 L~gK~alITGas~----GIG~aia~~la~~-------G~~V~i~~r~~~~l~~~~~~~~~~~~   55 (258)
T d1ae1a_           4 LKGTTALVTGGSK----GIGYAIVEELAGL-------GARVYTCSRNEKELDECLEIWREKGL   55 (258)
T ss_dssp             CTTCEEEEESCSS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEeCCCC----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHhcCC
Confidence            3577889998762    3455667777666       67899988888888888888876653

>d1luaa1 c.2.1.7 (A:98-288) Methylene-tetrahydromethanopterin dehydrogenase {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Aminoacid dehydrogenase-like, C-terminal domain
domain: Methylene-tetrahydromethanopterin dehydrogenase
species: Methylobacterium extorquens [TaxId: 408]

Probab=88.70  E-value=0.86  Score=26.43  Aligned_cols=49  Identities=12%  Similarity=0.133  Sum_probs=36.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +++.++|+|.+|.    +...++..+.+.       +.++.+++.+.+.++++.+.+.+.
T Consensus        22 ~gK~vlItGasgG----IG~~ia~~la~~-------G~~V~~~~r~~~~~~~~~~~~~~~   70 (191)
T d1luaa1          22 KGKKAVVLAGTGP----VGMRSAALLAGE-------GAEVVLCGRKLDKAQAAADSVNKR   70 (191)
T ss_dssp             TTCEEEEETTTSH----HHHHHHHHHHHT-------TCEEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCHH----HHHHHHHHHHhh-------ccchhhcccchHHHHHHHHHHHhc
Confidence            4678999997643    344556666665       778999999988888888877654

>d1puja_ c.37.1.8 (A:) Probable GTPase YlqF {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase YlqF
species: Bacillus subtilis [TaxId: 1423]

Probab=88.70  E-value=0.14  Score=31.81  Aligned_cols=21  Identities=33%  Similarity=0.513  Sum_probs=17.9

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      .+.|.|-|.+|||+++..+..
T Consensus       114 ~v~vvG~PNvGKSsliN~L~~  134 (273)
T d1puja_         114 RALIIGIPNVGKSTLINRLAK  134 (273)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEEecCccchhhhhhhhhc
Confidence            479999999999999777753

>d1wxqa1 c.37.1.8 (A:1-319) GTP-binding protein PH0525 {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein PH0525
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=88.70  E-value=0.13  Score=32.39  Aligned_cols=20  Identities=20%  Similarity=0.189  Sum_probs=17.0

Q ss_pred             eEEeCCCCCchHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      +-+.|-|.+||||+..++..
T Consensus         3 v~lvG~pn~GKStlfn~lt~   22 (319)
T d1wxqa1           3 IGVVGKPNVGKSTFFSAATL   22 (319)
T ss_dssp             EEEEECTTSSHHHHHHHHHC
T ss_pred             EeEECCCCCCHHHHHHHHHC
Confidence            45899999999999888754

>d1r0ka2 c.2.1.3 (A:3-126,A:265-290) 1-deoxy-D-xylulose-5-phosphate reductoisomerase {Zymomonas mobilis [TaxId: 542]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
domain: 1-deoxy-D-xylulose-5-phosphate reductoisomerase
species: Zymomonas mobilis [TaxId: 542]

Probab=88.61  E-value=0.2  Score=28.83  Aligned_cols=49  Identities=14%  Similarity=0.301  Sum_probs=28.8

Q ss_pred             CceEEeCCCCC-chHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhcc
Q psy16285         35 EFAIIQGPPGT-GKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        35 ~~~~v~Gp~Gt-GKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~   94 (97)
                      +++.|.|.||+ |++++  .+++..-..       -+-+.+.|.+|  .+.+.++.++|..
T Consensus         3 K~I~IlGsTGSIG~~tL--~Vi~~~~d~-------f~v~~lsa~~N--~~~L~~q~~ef~P   52 (150)
T d1r0ka2           3 RTVTVLGATGSIGHSTL--DLIERNLDR-------YQVIALTANRN--VKDLADAAKRTNA   52 (150)
T ss_dssp             EEEEEETTTSHHHHHHH--HHHHHTGGG-------EEEEEEEESSC--HHHHHHHHHHTTC
T ss_pred             cEEEEECCCcHHHHHHH--HHHHcCCCC-------cEEEEEEeCCC--HHHHHHHHHhhcc
Confidence            57889999998 88865  333332111       22244444554  4666667776654

>d1j6ua3 c.72.2.1 (A:89-295) UDP-N-acetylmuramate-alanine ligase MurC {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Ribokinase-like
superfamily: MurD-like peptide ligases, catalytic domain
family: MurCDEF
domain: UDP-N-acetylmuramate-alanine ligase MurC
species: Thermotoga maritima [TaxId: 2336]

Probab=88.60  E-value=0.1  Score=30.86  Aligned_cols=25  Identities=32%  Similarity=0.409  Sum_probs=15.2

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~   61 (97)
                      .+.+.|+|-  .||||+ ..++.++++.
T Consensus        14 ~~~iAITGT--nGKTTt-~~~l~~iL~~   38 (207)
T d1j6ua3          14 KEEFAVTGT--DGKTTT-TAMVAHVLKH   38 (207)
T ss_dssp             CCEEEEECS--SSHHHH-HHHHHHHHHH
T ss_pred             CCEEEEECC--CCHHHH-HHHHHHHHHh
Confidence            345566543  289999 4555555554

>d1xkqa_ c.2.1.2 (A:) Hypothetical protein R05D8.7 {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Hypothetical protein R05D8.7
species: Caenorhabditis elegans [TaxId: 6239]

Probab=88.56  E-value=0.86  Score=27.97  Aligned_cols=51  Identities=16%  Similarity=0.194  Sum_probs=38.0

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ++++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.+++..+.+++.+
T Consensus         3 L~gK~alVTGas~----GIG~aia~~la~~-------Ga~V~l~~r~~~~l~~~~~~l~~~~   53 (272)
T d1xkqa_           3 FSNKTVIITGSSN----GIGRTTAILFAQE-------GANVTITGRSSERLEETRQIILKSG   53 (272)
T ss_dssp             TTTCEEEETTCSS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHTTT
T ss_pred             CCCCEEEEeCcCc----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHhcC
Confidence            3567888988753    4555667777666       7789888888888888888887653

>d1xg5a_ c.2.1.2 (A:) Putative dehydrogenase ARPG836 (MGC4172) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Putative dehydrogenase ARPG836 (MGC4172)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.98  E-value=1.3  Score=26.88  Aligned_cols=51  Identities=6%  Similarity=0.132  Sum_probs=39.0

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ++++.++|+|.+    +-+..+++..+.++       +.+|++...+...++++.+++.+.+
T Consensus         8 lk~Kv~lITGas----~GIG~aiA~~la~~-------G~~Vv~~~r~~~~l~~~~~~l~~~~   58 (257)
T d1xg5a_           8 WRDRLALVTGAS----GGIGAAVARALVQQ-------GLKVVGCARTVGNIEELAAECKSAG   58 (257)
T ss_dssp             GTTCEEEEESTT----SHHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHHTT
T ss_pred             CCCCEEEEeCCC----CHHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHhcC
Confidence            457889999876    24556677777776       7788888888888899888888754

>d1eg7a_ c.37.1.10 (A:) Formyltetrahydrofolate synthetase {Moorella thermoacetica [TaxId: 1525]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Formyltetrahydrofolate synthetase
species: Moorella thermoacetica [TaxId: 1525]

Probab=87.78  E-value=0.41  Score=32.97  Aligned_cols=28  Identities=18%  Similarity=0.489  Sum_probs=22.6

Q ss_pred             CCceEEeC----CCCCchHHHHHHHHHHHHhc
Q psy16285         34 REFAIIQG----PPGTGKTYVALRIVEGFLKN   61 (97)
Q Consensus        34 ~~~~~v~G----p~GtGKT~~~~~~~~~~~~~   61 (97)
                      ++.++|++    |.|-||||+...+...+.+-
T Consensus        51 gklilVTaitPTp~GEGKtTttiGL~~aL~~l   82 (549)
T d1eg7a_          51 GKLILVTAITPTPAGEGKTTTSVGLTDALARL   82 (549)
T ss_dssp             CEEEEEEESSCCTTCCCHHHHHHHHHHHHHHT
T ss_pred             ceEEEEEeCCCCCCCCCcceeHHhHHHHHHHh
Confidence            34667766    77999999999999999554

>d1p77a1 c.2.1.7 (A:102-272) Shikimate 5-dehydrogenase AroE {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Aminoacid dehydrogenase-like, C-terminal domain
domain: Shikimate 5-dehydrogenase AroE
species: Haemophilus influenzae [TaxId: 727]

Probab=87.34  E-value=0.47  Score=27.37  Aligned_cols=49  Identities=18%  Similarity=0.251  Sum_probs=35.8

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ++.+++|.|.=|++|+.+     ..+.+.       ..++.++..+.+.+..+.+++....
T Consensus        17 ~~k~vlIlGaGGaarai~-----~aL~~~-------~~~i~I~nR~~~~a~~l~~~~~~~~   65 (171)
T d1p77a1          17 PNQHVLILGAGGATKGVL-----LPLLQA-------QQNIVLANRTFSKTKELAERFQPYG   65 (171)
T ss_dssp             TTCEEEEECCSHHHHTTH-----HHHHHT-------TCEEEEEESSHHHHHHHHHHHGGGS
T ss_pred             CCCEEEEECCcHHHHHHH-----HHHccc-------CceeeeccchHHHHHHHHHHHhhcc
Confidence            356889998877777643     333333       5689999999999999999887553

>d2gc6a2 c.72.2.2 (A:1-296) Folylpolyglutamate synthetase {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: Ribokinase-like
superfamily: MurD-like peptide ligases, catalytic domain
family: Folylpolyglutamate synthetase
domain: Folylpolyglutamate synthetase
species: Lactobacillus casei [TaxId: 1582]

Probab=87.32  E-value=0.22  Score=31.20  Aligned_cols=25  Identities=28%  Similarity=0.166  Sum_probs=16.0

Q ss_pred             ceEEeCCCCC-chHHHHHHHHHHHHhc
Q psy16285         36 FAIIQGPPGT-GKTYVALRIVEGFLKN   61 (97)
Q Consensus        36 ~~~v~Gp~Gt-GKT~~~~~~~~~~~~~   61 (97)
                      .+=++|=+|| |||+++..+. .++..
T Consensus        38 ~lkvI~VTGTNGKtST~~~i~-~IL~~   63 (296)
T d2gc6a2          38 QGRYIHVTGTNGKGSAANAIA-HVLEA   63 (296)
T ss_dssp             SSCEEEEECSSSHHHHHHHHH-HHHHH
T ss_pred             hCCEEEEeccCcHHHHHHHHH-HHHHh
Confidence            3445666687 9999955554 44444

>d1nyta1 c.2.1.7 (A:102-271) Shikimate 5-dehydrogenase AroE {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Aminoacid dehydrogenase-like, C-terminal domain
domain: Shikimate 5-dehydrogenase AroE
species: Escherichia coli [TaxId: 562]

Probab=87.12  E-value=0.54  Score=26.92  Aligned_cols=49  Identities=10%  Similarity=0.074  Sum_probs=35.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ++.+++|.|.=|++|+.+.     .+.+.       +.++.++..+...++.+.+.+.+..
T Consensus        17 ~~k~vlIlGaGGaarai~~-----al~~~-------g~~i~I~nRt~~ka~~l~~~~~~~~   65 (170)
T d1nyta1          17 PGLRILLIGAGGASRGVLL-----PLLSL-------DCAVTITNRTVSRAEELAKLFAHTG   65 (170)
T ss_dssp             TTCEEEEECCSHHHHHHHH-----HHHHT-------TCEEEEECSSHHHHHHHHHHTGGGS
T ss_pred             CCCEEEEECCcHHHHHHHH-----Hhccc-------ceEEEeccchHHHHHHHHHHHhhcc
Confidence            3568999999999987542     23333       4468888888888888888776543

>d1xq1a_ c.2.1.2 (A:) Tropinone reductase {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Tropinone reductase
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=86.72  E-value=1.2  Score=27.14  Aligned_cols=50  Identities=16%  Similarity=0.133  Sum_probs=36.9

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +++.++|+|.++    -+..+++..+.+.       +.+|+++..+.+.+++..+++.+..
T Consensus         7 kgK~alVTGas~----GIG~aiA~~la~~-------Ga~V~~~~r~~~~l~~~~~~~~~~~   56 (259)
T d1xq1a_           7 KAKTVLVTGGTK----GIGHAIVEEFAGF-------GAVIHTCARNEYELNECLSKWQKKG   56 (259)
T ss_dssp             TTCEEEETTTTS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHHTT
T ss_pred             CCCEEEEeCCCC----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHhcC
Confidence            577889998763    4555677777666       6788888888888888888877654

>d1jala1 c.37.1.8 (A:1-278) YchF GTP-binding protein N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=86.71  E-value=0.23  Score=30.80  Aligned_cols=21  Identities=24%  Similarity=0.328  Sum_probs=17.1

Q ss_pred             eEEeCCCCCchHHHHHHHHHH
Q psy16285         37 AIIQGPPGTGKTYVALRIVEG   57 (97)
Q Consensus        37 ~~v~Gp~GtGKT~~~~~~~~~   57 (97)
                      +=|.|-|.+||||+..++...
T Consensus         5 ~GivG~Pn~GKSTlf~~lt~~   25 (278)
T d1jala1           5 CGIVGLPNVGKSTLFNALTKA   25 (278)
T ss_dssp             EEEECCTTSSHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHCC
Confidence            458999999999998877643

>d1r5ba3 c.37.1.8 (A:215-459) Eukaryotic peptide chain release factor ERF2, G domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Eukaryotic peptide chain release factor ERF2, G domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=86.51  E-value=0.19  Score=30.90  Aligned_cols=21  Identities=19%  Similarity=0.196  Sum_probs=18.3

Q ss_pred             ceEEeCCCCCchHHHHHHHHH
Q psy16285         36 FAIIQGPPGTGKTYVALRIVE   56 (97)
Q Consensus        36 ~~~v~Gp~GtGKT~~~~~~~~   56 (97)
                      ++++.|-.+.||||++-+++.
T Consensus        26 Ni~iiGHVD~GKSTL~~~Ll~   46 (245)
T d1r5ba3          26 NIVFIGHVDAGKSTLGGNILF   46 (245)
T ss_dssp             EEEEEECGGGTHHHHHHHHHH
T ss_pred             EEEEEeeCCCCHHHHHHHHHH
Confidence            688999999999999888753

>d1xu9a_ c.2.1.2 (A:) 11-beta-hydroxysteroid dehydrogenase 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: 11-beta-hydroxysteroid dehydrogenase 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.42  E-value=1.4  Score=26.82  Aligned_cols=51  Identities=14%  Similarity=0.231  Sum_probs=39.1

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ++++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.++++.+++....
T Consensus        12 L~GK~alITGass----GIG~aiA~~la~~-------G~~Vil~~r~~~~l~~~~~~~~~~~   62 (269)
T d1xu9a_          12 LQGKKVIVTGASK----GIGREMAYHLAKM-------GAHVVVTARSKETLQKVVSHCLELG   62 (269)
T ss_dssp             GTTCEEEESSCSS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHHHT
T ss_pred             cCCCEEEEeCCCc----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHhhhh
Confidence            5678899998873    2666677777776       7789999999888888888766543

>d1xhla_ c.2.1.2 (A:) Hypothetical protein F25D1.5 {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Hypothetical protein F25D1.5
species: Caenorhabditis elegans [TaxId: 6239]

Probab=86.33  E-value=1.5  Score=26.94  Aligned_cols=50  Identities=18%  Similarity=0.208  Sum_probs=37.6

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +++.++|+|.++    -+..+++..+.+.       +.+|+++..+.+.+++..+.+.+.+
T Consensus         3 ~gK~alITGas~----GIG~aia~~la~~-------Ga~V~~~~r~~~~l~~~~~~i~~~~   52 (274)
T d1xhla_           3 SGKSVIITGSSN----GIGRSAAVIFAKE-------GAQVTITGRNEDRLEETKQQILKAG   52 (274)
T ss_dssp             TTCEEEETTCSS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHHTT
T ss_pred             CCCEEEEeCCCc----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHHcC
Confidence            467788888763    3566677777776       7788888888888888888887653

>d1ulua_ c.2.1.2 (A:) Enoyl-ACP reductase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Enoyl-ACP reductase
species: Thermus thermophilus [TaxId: 274]

Probab=85.99  E-value=1.5  Score=26.46  Aligned_cols=37  Identities=8%  Similarity=0.203  Sum_probs=23.5

Q ss_pred             cCCceEEeCCCCC-chHHHHHHHHHHHHhchhhhhcCCCCEEEEeCCh
Q psy16285         33 TREFAIIQGPPGT-GKTYVALRIVEGFLKNKELARYMSGPILIVCYTN   79 (97)
Q Consensus        33 ~~~~~~v~Gp~Gt-GKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~   79 (97)
                      +++.++|+|.+|. |   +..+++..+.++       +.+|++...+.
T Consensus         7 ~gK~alITGas~~~G---IG~aiA~~la~~-------Ga~V~i~~~~~   44 (256)
T d1ulua_           7 SGKKALVMGVTNQRS---LGFAIAAKLKEA-------GAEVALSYQAE   44 (256)
T ss_dssp             TTCEEEEESCCCSSS---HHHHHHHHHHHT-------TCEEEEEESSG
T ss_pred             CCCEEEEECCCCCch---HHHHHHHHHHHC-------CCEEEEEeCcH
Confidence            5788999998753 4   344566666665       55665555443

>d1spxa_ c.2.1.2 (A:) Glucose dehydrogenase (5l265) {Nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Glucose dehydrogenase (5l265)
species: Nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=85.99  E-value=1.7  Score=26.38  Aligned_cols=51  Identities=16%  Similarity=0.209  Sum_probs=37.3

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      ++++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.+++..+++.+.+
T Consensus         3 l~gKvalVTGas~----GIG~aia~~la~~-------Ga~V~~~~r~~~~l~~~~~~l~~~~   53 (264)
T d1spxa_           3 FAEKVAIITGSSN----GIGRATAVLFARE-------GAKVTITGRHAERLEETRQQILAAG   53 (264)
T ss_dssp             TTTCEEEETTTTS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHHTT
T ss_pred             CCCCEEEEeCcCC----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHhcC
Confidence            3567888888763    3555667777666       7788888888888888888887653

>d1vl8a_ c.2.1.2 (A:) Gluconate 5-dehydrogenase {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Gluconate 5-dehydrogenase
species: Thermotoga maritima [TaxId: 2336]

Probab=85.32  E-value=2.1  Score=25.87  Aligned_cols=48  Identities=8%  Similarity=0.207  Sum_probs=35.2

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      +++.++|+|..+    -+..+++..+.++       +.+|+++..+.+.+++..+++.+
T Consensus         4 ~gK~~lITGas~----GIG~aia~~la~~-------Ga~V~i~~r~~~~~~~~~~~l~~   51 (251)
T d1vl8a_           4 RGRVALVTGGSR----GLGFGIAQGLAEA-------GCSVVVASRNLEEASEAAQKLTE   51 (251)
T ss_dssp             TTCEEEEETTTS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCC----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHH
Confidence            567889998763    3566677777776       67888888888777777776643

>d1npya1 c.2.1.7 (A:103-269) Shikimate 5-dehydrogenase-like protein HI0607 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Aminoacid dehydrogenase-like, C-terminal domain
domain: Shikimate 5-dehydrogenase-like protein HI0607
species: Haemophilus influenzae [TaxId: 727]

Probab=85.22  E-value=2  Score=24.29  Aligned_cols=46  Identities=15%  Similarity=0.086  Sum_probs=32.7

Q ss_pred             CCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         34 REFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        34 ~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      +..++|.|.=|++|+.+     ..+.+.      ...++.++..+.+.+.++.+.+.
T Consensus        17 ~~~vlIlGaGGaarai~-----~aL~~~------g~~~I~I~nR~~~ka~~L~~~~~   62 (167)
T d1npya1          17 NAKVIVHGSGGMAKAVV-----AAFKNS------GFEKLKIYARNVKTGQYLAALYG   62 (167)
T ss_dssp             TSCEEEECSSTTHHHHH-----HHHHHT------TCCCEEEECSCHHHHHHHHHHHT
T ss_pred             CCeEEEECCCHHHHHHH-----HHHHHC------CCCEEEEecccHHHHHHHHHhhh
Confidence            45799999999998854     233333      34678888888888887776553

>d1geea_ c.2.1.2 (A:) Glucose dehydrogenase {Bacillus megaterium [TaxId: 1404]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Glucose dehydrogenase
species: Bacillus megaterium [TaxId: 1404]

Probab=85.05  E-value=1.2  Score=27.22  Aligned_cols=52  Identities=12%  Similarity=0.210  Sum_probs=36.3

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCCh-HHHHHHHHHHHhhcc
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTN-HALDQFVEGVLKYTQ   94 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~-~~~~~~~~~l~~~~~   94 (97)
                      ++++.++|+|.++    -+..+++..+.++       +.+|+++..++ ..++.+.+.+++.+.
T Consensus         5 L~gK~alITGas~----GIG~aia~~la~~-------G~~Vv~~~r~~~~~~~~~~~~~~~~g~   57 (261)
T d1geea_           5 LEGKVVVITGSST----GLGKSMAIRFATE-------KAKVVVNYRSKEDEANSVLEEIKKVGG   57 (261)
T ss_dssp             GTTCEEEETTCSS----HHHHHHHHHHHHT-------TCEEEEEESSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEeCCCc----HHHHHHHHHHHHC-------CCEEEEEeCCcHHHHHHHHHHHHhcCC
Confidence            4677888888763    3556667777666       67788887664 467777777777653

>d1yb1a_ c.2.1.2 (A:) 17-beta-hydroxysteroid dehydrogenase type XI {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: 17-beta-hydroxysteroid dehydrogenase type XI
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.73  E-value=1.7  Score=26.30  Aligned_cols=51  Identities=18%  Similarity=0.234  Sum_probs=37.8

Q ss_pred             cCCceEEeCCCC-CchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         33 TREFAIIQGPPG-TGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        33 ~~~~~~v~Gp~G-tGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      .++.++|+|.++ -|+     .++..+.+.       +.+|+++..+.+.++++.+++.+.+.+
T Consensus         6 ~Gkv~lITGas~GIG~-----~ia~~la~~-------G~~V~l~~r~~~~l~~~~~~~~~~~~~   57 (244)
T d1yb1a_           6 TGEIVLITGAGHGIGR-----LTAYEFAKL-------KSKLVLWDINKHGLEETAAKCKGLGAK   57 (244)
T ss_dssp             TTCEEEEETTTSHHHH-----HHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHHTTCC
T ss_pred             CCCEEEEeCCCcHHHH-----HHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHhcCCc
Confidence            467788888763 454     456666565       778999999999999999888876543

>d1gega_ c.2.1.2 (A:) meso-2,3-butanediol dehydrogenase {Klebsiella pneumoniae [TaxId: 573]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: meso-2,3-butanediol dehydrogenase
species: Klebsiella pneumoniae [TaxId: 573]

Probab=84.27  E-value=1.9  Score=26.10  Aligned_cols=50  Identities=12%  Similarity=0.176  Sum_probs=35.3

Q ss_pred             CceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         35 EFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        35 ~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      +..+|+|.++    -+..+++..+.++       +.+|+++..+.+.++++.+.+.+.+.+
T Consensus         2 KValITGas~----GIG~aia~~la~~-------Ga~V~~~~r~~~~l~~~~~~i~~~g~~   51 (255)
T d1gega_           2 KVALVTGAGQ----GIGKAIALRLVKD-------GFAVAIADYNDATAKAVASEINQAGGH   51 (255)
T ss_dssp             CEEEEETTTS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHHTTCC
T ss_pred             CEEEEcCCcc----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHhcCCc
Confidence            3457887652    3445566677666       678888888888888888888876543

>d2b2na1 c.37.1.19 (A:26-333) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=83.68  E-value=1.3  Score=28.04  Aligned_cols=28  Identities=11%  Similarity=0.368  Sum_probs=24.6

Q ss_pred             CCCCEEEEeCChHHHHHHHHHHHhhccC
Q psy16285         68 MSGPILIVCYTNHALDQFVEGVLKYTQN   95 (97)
Q Consensus        68 ~~~~ilv~~~~~~~~~~~~~~l~~~~~~   95 (97)
                      ..++++++|++...++++.+.|..|..+
T Consensus        13 ~~~p~lvv~~~~~~A~~l~~~L~~~~~~   40 (308)
T d2b2na1          13 HAGPVVLIAPDMQNALRLHDEISQFTDQ   40 (308)
T ss_dssp             CSSCEEEEESSHHHHHHHHHHHHTTCSS
T ss_pred             hCCCEEEEcCCHHHHHHHHHHHHhcCCC
Confidence            3788999999999999999999887643

>d1g0oa_ c.2.1.2 (A:) 1,3,8-trihydroxynaphtalene reductase (THNR, naphtol reductase) {Rice blast fungus (Magnaporthe grisea) [TaxId: 148305]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: 1,3,8-trihydroxynaphtalene reductase (THNR, naphtol reductase)
species: Rice blast fungus (Magnaporthe grisea) [TaxId: 148305]

Probab=83.45  E-value=2.1  Score=25.99  Aligned_cols=52  Identities=10%  Similarity=0.191  Sum_probs=36.0

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeC-ChHHHHHHHHHHHhhcc
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCY-TNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~-~~~~~~~~~~~l~~~~~   94 (97)
                      ++++.++|+|.++    -+..+++..+.++       +.+|+++.. ..+.++.+.+.+++.+.
T Consensus        16 L~gK~~lITGas~----GIG~aia~~la~~-------Ga~Vvi~~~~~~~~~~~~~~~~~~~g~   68 (272)
T d1g0oa_          16 LEGKVALVTGAGR----GIGREMAMELGRR-------GCKVIVNYANSTESAEEVVAAIKKNGS   68 (272)
T ss_dssp             CTTCEEEETTTTS----HHHHHHHHHHHHT-------TCEEEEEESSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEeCCCC----HHHHHHHHHHHHc-------CCEEEEEeCCchHHHHHHHHHHHhhCC
Confidence            4578899999763    3455667777666       677777654 45677888888777654

>d1pr9a_ c.2.1.2 (A:) Carbonyl reductase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Carbonyl reductase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.13  E-value=1.9  Score=25.91  Aligned_cols=48  Identities=17%  Similarity=0.225  Sum_probs=35.9

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      ++++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.++++.+++.
T Consensus         5 L~GK~~lITGas~----GIG~aia~~la~~-------G~~V~~~~r~~~~l~~~~~~~~   52 (244)
T d1pr9a_           5 LAGRRVLVTGAGK----GIGRGTVQALHAT-------GARVVAVSRTQADLDSLVRECP   52 (244)
T ss_dssp             CTTCEEEEESTTS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHST
T ss_pred             CCCCEEEEeCCCC----HHHHHHHHHHHHc-------CCEEEEEECCHHHHHHHHHhcC
Confidence            3578899998763    4566677777776       7789998888888877776654

>d1yxma1 c.2.1.2 (A:7-303) Peroxisomal trans 2-enoyl CoA reductase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Peroxisomal trans 2-enoyl CoA reductase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.93  E-value=2.3  Score=26.41  Aligned_cols=49  Identities=18%  Similarity=0.245  Sum_probs=35.4

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      ++++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.++...+++..
T Consensus        10 L~gKvalITGas~----GIG~aia~~la~~-------Ga~Vvi~~r~~~~l~~~~~el~~   58 (297)
T d1yxma1          10 LQGQVAIVTGGAT----GIGKAIVKELLEL-------GSNVVIASRKLERLKSAADELQA   58 (297)
T ss_dssp             TTTCEEEEETTTS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCC----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHh
Confidence            4578889998653    2556667777666       67888888887777777777764

>d2bgka1 c.2.1.2 (A:11-278) Rhizome secoisolariciresinol dehydrogenase {Mayapple (Podophyllum peltatum) [TaxId: 35933]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Rhizome secoisolariciresinol dehydrogenase
species: Mayapple (Podophyllum peltatum) [TaxId: 35933]

Probab=82.34  E-value=3.2  Score=25.15  Aligned_cols=49  Identities=16%  Similarity=0.249  Sum_probs=35.0

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHh
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLK   91 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~   91 (97)
                      ++++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.++++.+.+..
T Consensus         4 L~gKvalITGas~----GIG~aia~~la~~-------Ga~V~i~~r~~~~~~~~~~~l~~   52 (268)
T d2bgka1           4 LQDKVAIITGGAG----GIGETTAKLFVRY-------GAKVVIADIADDHGQKVCNNIGS   52 (268)
T ss_dssp             TTTCEEEEESTTS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHCC
T ss_pred             CCCCEEEEeCCCc----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHhcC
Confidence            3567889988653    3556677777666       67788888888878877777654

>d1iy8a_ c.2.1.2 (A:) Levodione reductase {Corynebacterium aquaticum [TaxId: 144185]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Levodione reductase
species: Corynebacterium aquaticum [TaxId: 144185]

Probab=81.85  E-value=3.8  Score=24.78  Aligned_cols=50  Identities=14%  Similarity=0.154  Sum_probs=33.7

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhhc
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKYT   93 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~~   93 (97)
                      +++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.+++..+.+.+..
T Consensus         3 ~gK~alITGas~----GIG~aia~~la~~-------Ga~V~i~~r~~~~l~~~~~~~~~~~   52 (258)
T d1iy8a_           3 TDRVVLITGGGS----GLGRATAVRLAAE-------GAKLSLVDVSSEGLEASKAAVLETA   52 (258)
T ss_dssp             TTCEEEEETTTS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHHHHC
T ss_pred             CCCEEEEeCCCC----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHhhC
Confidence            467788888762    3445566666665       6778777777777777777766543

>d1q7ba_ c.2.1.2 (A:) beta-keto acyl carrier protein reductase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: beta-keto acyl carrier protein reductase
species: Escherichia coli [TaxId: 562]

Probab=81.79  E-value=2.7  Score=25.23  Aligned_cols=47  Identities=9%  Similarity=0.143  Sum_probs=33.3

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      +++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.++++.+.+.
T Consensus         3 ~gK~alITGas~----GIG~a~a~~l~~~-------G~~Vv~~~r~~~~l~~~~~~~~   49 (243)
T d1q7ba_           3 EGKIALVTGASR----GIGRAIAETLAAR-------GAKVIGTATSENGAQAISDYLG   49 (243)
T ss_dssp             TTCEEEESSCSS----HHHHHHHHHHHHT-------TCEEEEEESSHHHHHHHHHHHG
T ss_pred             CCCEEEEeCCCC----HHHHHHHHHHHHc-------CCEEEEEeCCHHHHHHHHHHhC
Confidence            467788888653    3455566777666       7788888888777877777664

>d1nffa_ c.2.1.2 (A:) Putative oxidoreductase Rv2002 {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Putative oxidoreductase Rv2002
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=81.69  E-value=2.9  Score=25.17  Aligned_cols=48  Identities=10%  Similarity=0.141  Sum_probs=33.1

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      ++++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.++.+.+++.
T Consensus         4 L~gK~alITGas~----GIG~aia~~la~~-------G~~V~~~~r~~~~~~~~~~~~~   51 (244)
T d1nffa_           4 LTGKVALVSGGAR----GMGASHVRAMVAE-------GAKVVFGDILDEEGKAMAAELA   51 (244)
T ss_dssp             TTTCEEEEETTTS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHTG
T ss_pred             cCCCEEEEeCCCC----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHhh
Confidence            3567889998763    3555667777666       6778888877777776666553

>d1zk4a1 c.2.1.2 (A:1-251) R-specific alcohol dehydrogenase {Lactobacillus brevis [TaxId: 1580]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: R-specific alcohol dehydrogenase
species: Lactobacillus brevis [TaxId: 1580]

Probab=80.84  E-value=3  Score=25.09  Aligned_cols=48  Identities=21%  Similarity=0.265  Sum_probs=33.4

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      ++++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.+++..+.+.
T Consensus         4 L~gK~alVTGas~----GIG~aia~~la~~-------Ga~V~~~~r~~~~~~~~~~~~~   51 (251)
T d1zk4a1           4 LDGKVAIITGGTL----GIGLAIATKFVEE-------GAKVMITGRHSDVGEKAAKSVG   51 (251)
T ss_dssp             TTTCEEEETTTTS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHC
T ss_pred             CCCCEEEEeCCCC----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHhC
Confidence            3567888888654    3555666777666       6778888877777777776664

>d1hxha_ c.2.1.2 (A:) 3beta/17beta hydroxysteroid dehydrogenase {Comamonas testosteroni [TaxId: 285]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: 3beta/17beta hydroxysteroid dehydrogenase
species: Comamonas testosteroni [TaxId: 285]

Probab=80.72  E-value=2.9  Score=25.23  Aligned_cols=48  Identities=19%  Similarity=0.216  Sum_probs=33.5

Q ss_pred             hcCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHH
Q psy16285         32 LTREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVL   90 (97)
Q Consensus        32 ~~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~   90 (97)
                      ++++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.++++.+++.
T Consensus         4 L~gK~alITGas~----GIG~aia~~la~~-------Ga~V~~~~~~~~~~~~~~~~~~   51 (253)
T d1hxha_           4 LQGKVALVTGGAS----GVGLEVVKLLLGE-------GAKVAFSDINEAAGQQLAAELG   51 (253)
T ss_dssp             TTTCEEEETTTTS----HHHHHHHHHHHHT-------TCEEEEECSCHHHHHHHHHHHC
T ss_pred             CCCCEEEEeCCCC----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHhC
Confidence            3567888988653    3555667777666       6778888877777777776653

>d2gdza1 c.2.1.2 (A:3-256) 15-hydroxyprostaglandin dehydrogenase, PGDH {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: 15-hydroxyprostaglandin dehydrogenase, PGDH
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.56  E-value=4  Score=24.52  Aligned_cols=49  Identities=14%  Similarity=0.168  Sum_probs=34.0

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHHHhh
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGVLKY   92 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l~~~   92 (97)
                      +++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.+++..+.+.+.
T Consensus         2 ~GKvalITGas~----GIG~aia~~la~~-------Ga~V~i~~r~~~~~~~~~~~l~~~   50 (254)
T d2gdza1           2 NGKVALVTGAAQ----GIGRAFAEALLLK-------GAKVALVDWNLEAGVQCKAALHEQ   50 (254)
T ss_dssp             TTCEEEEETTTS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHHTTT
T ss_pred             CCCEEEEeCCCC----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHHHHh
Confidence            467788988753    2455566666665       677888888877777777777543

>d1bdba_ c.2.1.2 (A:) Cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase {Pseudomonas sp., lb400 [TaxId: 306]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase
species: Pseudomonas sp., lb400 [TaxId: 306]

Probab=80.47  E-value=3.9  Score=24.88  Aligned_cols=46  Identities=13%  Similarity=0.234  Sum_probs=33.3

Q ss_pred             cCCceEEeCCCCCchHHHHHHHHHHHHhchhhhhcCCCCEEEEeCChHHHHHHHHHH
Q psy16285         33 TREFAIIQGPPGTGKTYVALRIVEGFLKNKELARYMSGPILIVCYTNHALDQFVEGV   89 (97)
Q Consensus        33 ~~~~~~v~Gp~GtGKT~~~~~~~~~~~~~~~~~~~~~~~ilv~~~~~~~~~~~~~~l   89 (97)
                      +++.++|+|.++    -+..+++..+.++       +.+|+++..+.+.+.++.+++
T Consensus         4 ~gK~alITGas~----GIG~aia~~la~~-------Ga~V~i~~r~~~~l~~~~~~~   49 (276)
T d1bdba_           4 KGEAVLITGGAS----GLGRALVDRFVAE-------GAKVAVLDKSAERLAELETDH   49 (276)
T ss_dssp             TTCEEEEETTTS----HHHHHHHHHHHHT-------TCEEEEEESCHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCC----HHHHHHHHHHHHC-------CCEEEEEECCHHHHHHHHHHc
Confidence            567889998763    3566677777776       778888888777777666554

>d1q0qa2 c.2.1.3 (A:1-125,A:275-300) 1-deoxy-D-xylulose-5-phosphate reductoisomerase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
domain: 1-deoxy-D-xylulose-5-phosphate reductoisomerase
species: Escherichia coli [TaxId: 562]

Probab=80.43  E-value=0.65  Score=26.56  Aligned_cols=47  Identities=21%  Similarity=0.325  Sum_probs=25.5

Q ss_pred             ceEEeCCCCC-chHHHHHHHHHHHHhchhhhhcCCCCEE-EEeCChHHHHHHHHHHHhhcc
Q psy16285         36 FAIIQGPPGT-GKTYVALRIVEGFLKNKELARYMSGPIL-IVCYTNHALDQFVEGVLKYTQ   94 (97)
Q Consensus        36 ~~~v~Gp~Gt-GKT~~~~~~~~~~~~~~~~~~~~~~~il-v~~~~~~~~~~~~~~l~~~~~   94 (97)
                      ++.|.|.||+ |++++-  +++.. .       +..++. +.+.+|  .+.+.++..+|..
T Consensus         3 ~I~IlGsTGSIG~~tL~--Vi~~~-~-------d~f~v~~Lsa~~N--~~~L~~q~~~f~p   51 (151)
T d1q0qa2           3 QLTILGSTGSIGCSTLD--VVRHN-P-------EHFRVVALVAGKN--VTRMVEQCLEFSP   51 (151)
T ss_dssp             EEEEETTTSHHHHHHHH--HHHHC-T-------TTEEEEEEEESSC--HHHHHHHHHHHCC
T ss_pred             eEEEEcCCcHHHHHHHH--HHHhC-C-------CCcEEEEEEecCc--HHHHHHHHHHHhh
Confidence            4678999998 888652  22221 0       122333 333343  4666666666654