Citrus Sinensis ID: 031713

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150----
Protein Sequence
MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE
Secondary Structure (PSIPRED)
ccccEEEEEEcccHHHHHHHHHHHHHHcccccccEEEEEEEcccccHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEEEccHHHHHHHHHHHccccEEEEcccccccccEEEEccHHHHHHccccccEEEEccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEEEcccHHHHHHHHHHHHHHHccccccEEEEEEEcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEEEccHHHHHHHHHHHccccEEEEEcccccHHHHHHEccHcHHHHccccccEEEEEcccc
Coil and Loop (DISEMBL)
MDKKKVMVAIDESECRHYALQWALENlgdaisksdliiftarptEFIYVQasmfgaappdlLMSIQENQKKAALALLGRAKEICAKHGVVAEtmtemgdpknVICEAAEKHKIQLLIVgshsrgpiqrAFLGSVSnycvhnakcpvlvvrkpve
Flexible Loop (DISEMBL)
MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCvhnakcpvlvvrkpve
Low Complexity Region (SEG)
MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKaalallGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE
Disordered region (IsUnstruct)
******MVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR****
Disordered Region (DISOPRED)
MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK***
Disordered Region (DISEMBL)
MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE
Disordered Region (DISPRO)
*DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE
Positional Conservation
no confident homologs detected

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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	154	2.2.26 [Sep-21-2011]
Q8LGG8	175	Universal stress protein	no	no	0.941	0.828	0.320	1e-14
P42297	148	Universal stress protein	yes	no	0.928	0.966	0.331	2e-10
Q57951	170	Universal stress protein	yes	no	0.571	0.517	0.386	2e-09
P74148	154	Universal stress protein	N/A	no	0.961	0.961	0.296	4e-09
P45680	146	Universal stress protein	yes	no	0.701	0.739	0.330	1e-06
P72745	108	Universal stress protein	N/A	no	0.649	0.925	0.259	8e-06
Q4L751	165	Putative universal stress	yes	no	0.857	0.8	0.279	3e-05
P64922	295	Universal stress protein	yes	no	0.246	0.128	0.526	6e-05
P64921	295	Universal stress protein	yes	no	0.246	0.128	0.526	6e-05
Q2FXL6	166	Putative universal stress	yes	no	0.545	0.506	0.372	6e-05

>sp|Q8LGG8|USPAL_ARATH Universal stress protein A-like protein OS=Arabidopsis thaliana GN=At3g01520 PE=1 SV=2

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 51/159 (32%), Positives = 81/159 (50%), Gaps = 14/159 (8%)

Query: 5   KVMVAIDESECRHY---------ALQWALENLGDAISKSD---LIIFTARPTEFIYVQAS 52
           KVMVA++ S  + Y         A +W LE +  + + SD   L++      E  +    
Sbjct: 7   KVMVAVNASTIKDYPNPSISCKRAFEWTLEKIVRS-NTSDFKILLLHVQVVDEDGFDDVD 65

Query: 53  MFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHK 112
              A+P D     Q N+ K  L LL      C + GV  E   + GDPK+VIC+  ++ +
Sbjct: 66  SIYASPEDFRDMRQSNKAKG-LHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVR 124

Query: 113 IQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK 151
              L+VGS   G  Q+ F+G+VS +CV +A+CPV+ +++
Sbjct: 125 PDFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVMTIKR 163

Arabidopsis thaliana (taxid: 3702)

>sp|P42297|YXIE_BACSU Universal stress protein YxiE OS=Bacillus subtilis (strain 168) GN=yxiE PE=3 SV=1

 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 49/148 (33%), Positives = 75/148 (50%), Gaps = 5/148 (3%)

Query: 5   KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAA--PPDLL 62
           K++VAID S+    AL  A+ +L         I+   R  E +   +S+ G    P   +
Sbjct: 4   KMLVAIDGSDMSAKALDAAV-HLAKEQQAELSILHVGR--EAVVTTSSLTGIVYVPEHFI 60

Query: 63  MSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHS 122
             I+   KK  L +L  AKE  A+ GV AET+   G+P + I   A++  + L++VGS  
Sbjct: 61  DEIRNEVKKEGLKILENAKEKAAEKGVQAETIYANGEPAHEILNHAKEKGVSLIVVGSRG 120

Query: 123 RGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
              ++   LGSVS+     + CPVL+VR
Sbjct: 121 ISGLKEMMLGSVSHKVSQLSTCPVLIVR 148

Bacillus subtilis (strain 168) (taxid: 224308)

>sp|Q57951|Y531_METJA Universal stress protein MJ0531 OS=Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) GN=MJ0531 PE=3 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 34/88 (38%), Positives = 49/88 (55%)

Query: 65  IQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRG 124
           I E  K+     L + K++  + GV   T    G P N I E AEK K  L+++G+  + 
Sbjct: 80  ISELLKEEGQEALKKVKKMAEEWGVKIHTEMLEGVPANEIVEFAEKKKADLIVMGTTGKT 139

Query: 125 PIQRAFLGSVSNYCVHNAKCPVLVVRKP 152
            ++R  LGSV+   + NA CPVLVV+KP
Sbjct: 140 GLERILLGSVAERVIKNAHCPVLVVKKP 167

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (taxid: 243232)

>sp|P74148|Y1388_SYNY3 Universal stress protein Sll1388 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=sll1388 PE=3 SV=1

 Score = 60.5 bits (145), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 46/155 (29%), Positives = 77/155 (49%), Gaps = 7/155 (4%)

Query: 1   MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARP--TEFIYVQASMFGAAP 58
           M   K++VA+D SE     LQ A+  LG   S S L++F   P  ++ + +  S +G A 
Sbjct: 1   MGYGKILVALDRSELAKEVLQQAI-ALGQKES-SQLMVFYCIPVDSQDLSIYPSFYGEAA 58

Query: 59  PDLLMSIQEN---QKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQL 115
                 I+E+   Q+  A   L    +   + GV  E   ++G+P   I + A+     L
Sbjct: 59  IGFSQIIKEHLEEQQTEAREWLQSIVQQVQEDGVACEWDVKVGEPGRWIRDMAKNWDADL 118

Query: 116 LIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
           +++G      +   FLGSVS+Y +H+ +C VL+V+
Sbjct: 119 VVLGRRGLKGLAEVFLGSVSSYVIHHVQCSVLIVQ 153

Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

>sp|P45680|USPA2_COXBU Universal stress protein A homolog 2 OS=Coxiella burnetii (strain RSA 493 / Nine Mile phase I) GN=uspA2 PE=1 SV=1

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 39/118 (33%), Positives = 59/118 (50%), Gaps = 10/118 (8%)

Query: 35  DLIIFTARPTEFIYVQASMFG-AAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAE- 92
           D  ++     E +    + +G AA  D+   + E  KK       R  EI ++  + ++ 
Sbjct: 33  DAQLYLIHAVEHLSSYGAAYGVAAGVDVEDMLLEEAKK-------RMNEIASQLNISSDH 85

Query: 93  TMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
            + ++G  K +I E A+   + L+IVGSH R  IQ   LGS SN  +H AKC VL VR
Sbjct: 86  QIVKVGPAKFLILEQAKNWGVDLIIVGSHGRHGIQ-LLLGSTSNAVLHGAKCDVLAVR 142

Involved in stress response.

Coxiella burnetii (strain RSA 493 / Nine Mile phase I) (taxid: 227377)

>sp|P72745|Y1101_SYNY3 Universal stress protein Slr1101 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=slr1101 PE=3 SV=1

 Score = 49.7 bits (117), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/104 (25%), Positives = 49/104 (47%), Gaps = 4/104 (3%)

Query: 53  MFGAAPPDLLMSIQENQ----KKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAA 108
           ++ A   +L M + + Q    ++  L  L + ++      +  +    +G P  +IC+ A
Sbjct: 4   IYPAVGNELTMEVWQQQWQTFEQEGLDTLEKRRQQALALDIECQAEQILGSPGKIICQRA 63

Query: 109 EKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP 152
           ++    +++VG   R  +    LGSV NY  H+A C V VV  P
Sbjct: 64  KQDNSDIIVVGHRGRWGLSEILLGSVGNYVFHHAHCCVFVVPTP 107

Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

>sp|Q4L751|Y1215_STAHJ Putative universal stress protein SH1215 OS=Staphylococcus haemolyticus (strain JCSC1435) GN=SH1215 PE=3 SV=1

 Score = 47.8 bits (112), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 43/154 (27%), Positives = 70/154 (45%), Gaps = 22/154 (14%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSD-----LIIFTARPTEFIYVQASMFGAAP 58
           K +++A+D S   H A +WA     D   ++D     + I  +R     Y    ++ A  
Sbjct: 5   KNILIAVDGS---HEA-EWAFNKAVDVAKRNDAKLTIVNIIDSR----TYSSYEVYDA-- 54

Query: 59  PDLLMSIQENQKKAALALLGRAKEICAKHGVV-AETMTEMGDPKNVICEA-AEKHKIQLL 116
                   E  +  +  LL   +E+  + GV   ET  E G PK +I +  A +  + L+
Sbjct: 55  -----QFTEKSRSFSEELLKGYQEVATRAGVTNVETRLEFGSPKAIIPKKLASELGVDLI 109

Query: 117 IVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
           + G+     ++R  +GSVS   V +A C VLVVR
Sbjct: 110 MCGTSGLNAVERFIVGSVSEAIVRHAPCDVLVVR 143

Staphylococcus haemolyticus (strain JCSC1435) (taxid: 279808)

>sp|P64922|Y2028_MYCBO Universal stress protein Mb2028c OS=Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) GN=Mb2028c PE=3 SV=1

 Score = 46.6 bits (109), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 20/38 (52%), Positives = 27/38 (71%)

Query: 114 QLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK 151
           QL++VGSH RG +    LGSVSN  +H A+ PV+V R+
Sbjct: 257 QLVVVGSHGRGGLTGMLLGSVSNAVLHAARVPVIVARQ 294

Mycobacterium bovis (taxid: 1765)

>sp|P64921|Y2005_MYCTU Universal stress protein Rv2005c/MT2061 OS=Mycobacterium tuberculosis GN=Rv2005c PE=1 SV=1

 Score = 46.6 bits (109), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 20/38 (52%), Positives = 27/38 (71%)

Query: 114 QLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK 151
           QL++VGSH RG +    LGSVSN  +H A+ PV+V R+
Sbjct: 257 QLVVVGSHGRGGLTGMLLGSVSNAVLHAARVPVIVARQ 294

Mycobacterium tuberculosis (taxid: 1773)

>sp|Q2FXL6|Y1819_STAA8 Putative universal stress protein SAOUHSC_01819 OS=Staphylococcus aureus (strain NCTC 8325) GN=SAOUHSC_01819 PE=3 SV=1

 Score = 46.6 bits (109), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 32/86 (37%), Positives = 44/86 (51%), Gaps = 2/86 (2%)

Query: 67  ENQKKAALALLGRAKEICAKHGVV-AETMTEMGDPKNVICEA-AEKHKIQLLIVGSHSRG 124
           E  K  A  LL   KE+    GV   ET  E G PK++I +  A +    L++ G+    
Sbjct: 58  EKSKHFAEELLNGYKEVATNAGVKDVETRLEFGSPKSIIPKKLAHEINADLIMSGTSGLN 117

Query: 125 PIQRAFLGSVSNYCVHNAKCPVLVVR 150
            ++R  +GSVS   V +A C VLVVR
Sbjct: 118 AVERFIVGSVSESIVRHAPCDVLVVR 143

Staphylococcus aureus (strain NCTC 8325) (taxid: 93061)

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	154
224108456	161	predicted protein [Populus trichocarpa]	0.980	0.937	0.677	1e-55
224101747	161	predicted protein [Populus trichocarpa]	0.980	0.937	0.677	4e-54
255572094	160	conserved hypothetical protein [Ricinus	0.980	0.943	0.684	3e-53
297737805	148	unnamed protein product [Vitis vinifera]	0.948	0.986	0.653	1e-50
297737803	148	unnamed protein product [Vitis vinifera]	0.948	0.986	0.653	2e-50
225424009	164	PREDICTED: universal stress protein A-li	0.941	0.884	0.650	5e-50
225424013	164	PREDICTED: universal stress protein A-li	0.941	0.884	0.650	8e-50
283970968	159	universal stress protein 23267 [Hordeum	0.941	0.911	0.588	1e-41
283970966	159	universal stress protein 23267 [Hordeum	0.941	0.911	0.588	2e-41
18408994	160	universal stress protein domain-containi	0.954	0.918	0.567	8e-41

>gi|224108456|ref|XP_002314854.1| predicted protein [Populus trichocarpa] gi|222863894|gb|EEF01025.1| predicted protein [Populus trichocarpa]

 Score =  220 bits (561), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 103/152 (67%), Positives = 125/152 (82%), Gaps = 1/152 (0%)

Query: 2   DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARP-TEFIYVQASMFGAAPPD 60
           +KKKVMVAID+SE  HY L+W L+ L D+I+ SD+IIFTA+P ++  Y+ AS FG AP D
Sbjct: 8   EKKKVMVAIDDSESSHYTLEWFLDKLRDSIADSDVIIFTAQPNSDLGYLYASTFGTAPAD 67

Query: 61  LLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGS 120
           L+ SIQEN+KK AL LL +AK+ICA+HGV  E MTE+GDPK  ICEA EK  +QLL++GS
Sbjct: 68  LVASIQENKKKIALILLDKAKDICARHGVDVEIMTEIGDPKEAICEAVEKLNVQLLVLGS 127

Query: 121 HSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP 152
           H RGP+QRAFLGSVSNYCVHNAKCPVLVV+KP
Sbjct: 128 HDRGPVQRAFLGSVSNYCVHNAKCPVLVVKKP 159

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224101747|ref|XP_002312405.1| predicted protein [Populus trichocarpa] gi|222852225|gb|EEE89772.1| predicted protein [Populus trichocarpa]

 Score =  215 bits (548), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 103/152 (67%), Positives = 126/152 (82%), Gaps = 1/152 (0%)

Query: 2   DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARP-TEFIYVQASMFGAAPPD 60
           +KKKVMVAIDESE  HYAL+WAL+ L + I+ SD+IIFTA+P ++  YV AS  G A  D
Sbjct: 8   EKKKVMVAIDESENSHYALEWALDKLRETIADSDVIIFTAQPNSDLGYVYASTLGVASMD 67

Query: 61  LLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGS 120
           L+ SIQEN KK A  LL +AK+ICAK+G+VAET+TE+GDPK  ICEA EK  I+LL++GS
Sbjct: 68  LITSIQENHKKVASFLLDKAKDICAKYGIVAETVTEIGDPKYAICEAVEKLNIELLVLGS 127

Query: 121 HSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP 152
           H+RGP+QRAFLGSVSNYCV+NAKCPVLVV+KP
Sbjct: 128 HNRGPVQRAFLGSVSNYCVNNAKCPVLVVKKP 159

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255572094|ref|XP_002526987.1| conserved hypothetical protein [Ricinus communis] gi|223533622|gb|EEF35359.1| conserved hypothetical protein [Ricinus communis]

 Score =  213 bits (541), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 104/152 (68%), Positives = 120/152 (78%), Gaps = 1/152 (0%)

Query: 3   KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARP-TEFIYVQASMFGAAPPDL 61
           K+KVMVAIDESE   YALQWAL +L   I  S L+IFT +  + F YV AS FGAAP  L
Sbjct: 9   KQKVMVAIDESEYSQYALQWALNHLKATIIHSQLVIFTVQNNSTFGYVYASSFGAAPATL 68

Query: 62  LMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSH 121
           +  IQENQKK ALALL RAK  CA HG+VA+T+TE+GDPK  IC+A EKH I LL++GSH
Sbjct: 69  IELIQENQKKVALALLQRAKNTCADHGIVAQTLTEIGDPKEAICDAVEKHNIHLLVLGSH 128

Query: 122 SRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPV 153
           SRG I+RAFLGSVSNYCVHNAKCPVLVV+KP+
Sbjct: 129 SRGAIKRAFLGSVSNYCVHNAKCPVLVVKKPL 160

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297737805|emb|CBI27006.3| unnamed protein product [Vitis vinifera]

 Score =  204 bits (518), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 96/147 (65%), Positives = 115/147 (78%), Gaps = 1/147 (0%)

Query: 7   MVAIDESECRHYALQWALENLGDAISKSDLIIFTARP-TEFIYVQASMFGAAPPDLLMSI 65
           MV IDESE  H+AL WALENL D++S   LI+FT +  ++F Y+ AS  G APPDL+ ++
Sbjct: 1   MVCIDESEYSHHALNWALENLRDSLSNFQLIVFTVQSLSDFTYIHASTLGVAPPDLITAV 60

Query: 66  QENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGP 125
           QE QKK A ALL RAKEICA+ G+VAET+TE+GDPK  IC+A EK  IQ L++GSH RG 
Sbjct: 61  QERQKKVAFALLERAKEICAQCGIVAETITEVGDPKEAICKAVEKLNIQFLVLGSHGRGA 120

Query: 126 IQRAFLGSVSNYCVHNAKCPVLVVRKP 152
             RAFLGSVSNYC+HNAKCPVLVVRKP
Sbjct: 121 FGRAFLGSVSNYCMHNAKCPVLVVRKP 147

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297737803|emb|CBI27004.3| unnamed protein product [Vitis vinifera]

 Score =  203 bits (517), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 96/147 (65%), Positives = 114/147 (77%), Gaps = 1/147 (0%)

Query: 7   MVAIDESECRHYALQWALENLGDAISKSDLIIFTARP-TEFIYVQASMFGAAPPDLLMSI 65
           MV IDESE  H+AL WALENL D++S   LI+FT +  ++F Y+ AS  G APPDL+  +
Sbjct: 1   MVCIDESEYSHHALNWALENLRDSLSNFQLIVFTVQSLSDFTYIHASTLGVAPPDLITEV 60

Query: 66  QENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGP 125
           QE QKK A ALL RAKEICA+ G+VAET+TE+GDPK  IC+A EK  IQ L++GSH RG 
Sbjct: 61  QERQKKVAFALLERAKEICAQCGIVAETITEVGDPKEAICKAVEKLNIQFLVLGSHGRGA 120

Query: 126 IQRAFLGSVSNYCVHNAKCPVLVVRKP 152
             RAFLGSVSNYC+HNAKCPVLVVRKP
Sbjct: 121 FGRAFLGSVSNYCMHNAKCPVLVVRKP 147

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225424009|ref|XP_002283390.1| PREDICTED: universal stress protein A-like protein [Vitis vinifera]

 Score =  202 bits (513), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 95/146 (65%), Positives = 114/146 (78%), Gaps = 1/146 (0%)

Query: 8   VAIDESECRHYALQWALENLGDAISKSDLIIFTARP-TEFIYVQASMFGAAPPDLLMSIQ 66
           V IDESE  H+AL WALENL D++S   LI+FT +  ++F Y+ AS  G APPDL+ ++Q
Sbjct: 18  VCIDESEYSHHALNWALENLRDSLSNFQLIVFTVQSLSDFTYIHASTLGVAPPDLITAVQ 77

Query: 67  ENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPI 126
           E QKK A ALL RAKEICA+ G+VAET+TE+GDPK  IC+A EK  IQ L++GSH RG  
Sbjct: 78  ERQKKVAFALLERAKEICAQCGIVAETITEVGDPKEAICKAVEKLNIQFLVLGSHGRGAF 137

Query: 127 QRAFLGSVSNYCVHNAKCPVLVVRKP 152
            RAFLGSVSNYC+HNAKCPVLVVRKP
Sbjct: 138 GRAFLGSVSNYCMHNAKCPVLVVRKP 163

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225424013|ref|XP_002283402.1| PREDICTED: universal stress protein A-like protein [Vitis vinifera]

 Score =  201 bits (511), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 95/146 (65%), Positives = 113/146 (77%), Gaps = 1/146 (0%)

Query: 8   VAIDESECRHYALQWALENLGDAISKSDLIIFTARP-TEFIYVQASMFGAAPPDLLMSIQ 66
           V IDESE  H+AL WALENL D++S   LI+FT +  ++F Y+ AS  G APPDL+  +Q
Sbjct: 18  VCIDESEYSHHALNWALENLRDSLSNFQLIVFTVQSLSDFTYIHASTLGVAPPDLITEVQ 77

Query: 67  ENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPI 126
           E QKK A ALL RAKEICA+ G+VAET+TE+GDPK  IC+A EK  IQ L++GSH RG  
Sbjct: 78  ERQKKVAFALLERAKEICAQCGIVAETITEVGDPKEAICKAVEKLNIQFLVLGSHGRGAF 137

Query: 127 QRAFLGSVSNYCVHNAKCPVLVVRKP 152
            RAFLGSVSNYC+HNAKCPVLVVRKP
Sbjct: 138 GRAFLGSVSNYCMHNAKCPVLVVRKP 163

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|283970968|gb|ADB54810.1| universal stress protein 23267 [Hordeum vulgare subsp. vulgare] gi|326507524|dbj|BAK03155.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 90/153 (58%), Positives = 115/153 (75%), Gaps = 8/153 (5%)

Query: 3   KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARP-TEFIYVQA-SMFGA--AP 58
           ++K+MVAIDESEC HYAL+WAL NL    +   L++FT +P +   Y+ A S  G   A 
Sbjct: 9   EQKMMVAIDESECSHYALEWALRNL----APRRLVLFTVQPFSPLSYLPAGSPLGPSVAS 64

Query: 59  PDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIV 118
           P+L+ S+ E+Q++ A AL+ +AK ICA HGV AET+ E+GDPK  ICEAA+K  + LLI+
Sbjct: 65  PELIRSVTEHQRQLAQALVDKAKAICADHGVDAETVIEVGDPKETICEAADKLNVDLLIL 124

Query: 119 GSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK 151
           GSHSRGPIQR FLGSVSNYC H+AKCPVLVV+K
Sbjct: 125 GSHSRGPIQRFFLGSVSNYCSHHAKCPVLVVKK 157

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|283970966|gb|ADB54809.1| universal stress protein 23267 [Hordeum vulgare subsp. vulgare]

 Score =  173 bits (439), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 90/153 (58%), Positives = 114/153 (74%), Gaps = 8/153 (5%)

Query: 3   KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARP-TEFIYVQA-SMFGA--AP 58
           ++K+MVAIDESEC HYAL+WAL NL    +   L++FT +P +   Y+ A S  G   A 
Sbjct: 9   EQKMMVAIDESECSHYALEWALRNL----APRRLVLFTVQPFSPLSYLPAGSPLGPSVAS 64

Query: 59  PDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIV 118
           P+L+ S+ E+Q++ A AL  +AK ICA HGV AET+ E+GDPK  ICEAA+K  + LLI+
Sbjct: 65  PELIRSVTEHQRQLAQALADKAKAICADHGVDAETVIEVGDPKETICEAADKLNVDLLIL 124

Query: 119 GSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK 151
           GSHSRGPIQR FLGSVSNYC H+AKCPVLVV+K
Sbjct: 125 GSHSRGPIQRFFLGSVSNYCSHHAKCPVLVVKK 157

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18408994|ref|NP_564927.1| universal stress protein domain-containing protein [Arabidopsis thaliana] gi|12325313|gb|AAG52594.1|AC016447_3 unknown protein; 44604-45347 [Arabidopsis thaliana] gi|21555126|gb|AAM63782.1| unknown [Arabidopsis thaliana] gi|28950695|gb|AAO63271.1| At1g68300 [Arabidopsis thaliana] gi|110736101|dbj|BAF00023.1| hypothetical protein [Arabidopsis thaliana] gi|332196657|gb|AEE34778.1| universal stress protein domain-containing protein [Arabidopsis thaliana]

 Score =  171 bits (434), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 84/148 (56%), Positives = 107/148 (72%), Gaps = 1/148 (0%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARP-TEFIYVQASMFGAAPPDLL 62
           K+VMVAIDESEC   ALQW L  L D+++ SD+I+FTA+P  +   V AS +GAAP +L+
Sbjct: 10  KQVMVAIDESECSKRALQWTLVYLKDSLADSDIILFTAQPHLDLSCVYASSYGAAPIELI 69

Query: 63  MSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHS 122
            S+QE+ K A L  L    +ICA+ GV    + E G+PK  ICEAAEK  + +L+VGSH 
Sbjct: 70  NSLQESHKNAGLNRLDEGTKICAETGVTPRKVLEFGNPKEAICEAAEKLGVDMLVVGSHG 129

Query: 123 RGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
           +G +QR FLGSVSNYCV+NAKCPVLVVR
Sbjct: 130 KGALQRTFLGSVSNYCVNNAKCPVLVVR 157

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

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	154
TAIR|locus:2199282	160	AT1G68300 "AT1G68300" [Arabido	0.954	0.918	0.547	4.3e-38
TAIR|locus:2076381	204	AT3G58450 "AT3G58450" [Arabido	0.987	0.745	0.420	1.8e-23
TAIR|locus:2024291	171	AT1G09740 "AT1G09740" [Arabido	0.961	0.865	0.389	1.3e-22
TAIR|locus:2081531	226	AT3G11930 "AT3G11930" [Arabido	0.844	0.575	0.309	1.4e-22
TAIR|locus:2043273	162	AT2G47710 "AT2G47710" [Arabido	0.954	0.907	0.360	3.9e-21
TAIR|locus:2096089	162	AT3G62550 "AT3G62550" [Arabido	0.987	0.938	0.316	8.3e-19
TAIR|locus:2092170	154	AT3G25930 "AT3G25930" [Arabido	0.889	0.889	0.345	4.9e-14
TAIR|locus:2084153	175	AT3G01520 "AT3G01520" [Arabido	0.941	0.828	0.301	1.3e-13
TAIR|locus:2222687	175	AT5G14680 "AT5G14680" [Arabido	0.967	0.851	0.279	1.6e-13
TAIR|locus:2086102	163	AT3G17020 "AT3G17020" [Arabido	0.935	0.883	0.292	6.4e-12

TAIR|locus:2199282 AT1G68300 "AT1G68300" [Arabidopsis thaliana (taxid:3702)]

 Score = 408 (148.7 bits), Expect = 4.3e-38, P = 4.3e-38
 Identities = 81/148 (54%), Positives = 104/148 (70%)

Query:     4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARP-TEFIYVQASMFGAAPPDLL 62
             K+VMVAIDESEC   ALQW L  L D+++ SD+I+FTA+P  +   V AS +GAAP +L+
Sbjct:    10 KQVMVAIDESECSKRALQWTLVYLKDSLADSDIILFTAQPHLDLSCVYASSYGAAPIELI 69

Query:    63 MSIQENQKKXXXXXXGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHS 122
              S+QE+ K           +ICA+ GV    + E G+PK  ICEAAEK  + +L+VGSH 
Sbjct:    70 NSLQESHKNAGLNRLDEGTKICAETGVTPRKVLEFGNPKEAICEAAEKLGVDMLVVGSHG 129

Query:   123 RGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
             +G +QR FLGSVSNYCV+NAKCPVLVVR
Sbjct:   130 KGALQRTFLGSVSNYCVNNAKCPVLVVR 157

GO:0003674 "molecular_function" evidence=ND

GO:0005737 "cytoplasm" evidence=ISM

GO:0002238 "response to molecule of fungal origin" evidence=RCA

TAIR|locus:2076381 AT3G58450 "AT3G58450" [Arabidopsis thaliana (taxid:3702)]

 Score = 270 (100.1 bits), Expect = 1.8e-23, P = 1.8e-23
 Identities = 69/164 (42%), Positives = 89/164 (54%)

Query:     3 KKKVMVAIDESECRHYALQWALENLGDAISKSD--------LIIFTARPTEFIYVQASMF 54
             K KVMVAIDES+    AL+WA+++L   IS           L +    PT   Y+  S  
Sbjct:    29 KLKVMVAIDESKNSFDALEWAVDHLRVVISAEPETGQEGGLLTLLHVHPTYLQYIYPSGG 88

Query:    55 GAAPPDLLMSIQENQKKXXXXXXG----RAKEICAKHGVVAETMTEMGDPKNVICEAAEK 110
              A+      S+ E  +K           RA EIC    V  ETM   GDPK +IC+A E+
Sbjct:    89 TASAVYATDSVPEPMRKAREESTTNLFTRALEICRGKMVKTETMILEGDPKEMICQAVEQ 148

Query:   111 HKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE 154
               + LL+VGS   G I+RAFLGSVS+YC  +AKCP+L+VR P E
Sbjct:   149 THVDLLVVGSRGLGMIKRAFLGSVSDYCAQHAKCPILIVRPPRE 192

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2024291 AT1G09740 "AT1G09740" [Arabidopsis thaliana (taxid:3702)]

 Score = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 62/159 (38%), Positives = 90/159 (56%)

Query:     6 VMVAIDESECRHYALQWALENLGDAISKSD--LIIFTARPTEFIYVQASM----FGAAP- 58
             V+VA+D SE    AL+WAL+NL  + S SD   ++   +P+  +    S     FG    
Sbjct:    10 VVVAVDGSEVSMEALRWALDNLKLSSSSSDSSFVVLHVQPSPSVAAGVSPGTIPFGGPSG 69

Query:    59 ---PDLLMSIQENQKKXXXXXXGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQL 115
                P    +I+++QK+        A +ICA+  V  +T   +GDPK  ICEA E     L
Sbjct:    70 LEVPAFTAAIEQHQKRITDTILEHASQICAEKSVNVKTQVVIGDPKYKICEAVENLHADL 129

Query:   116 LIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE 154
             L++GS + G I+R FLGSVSNYC ++A CPV+++ KP E
Sbjct:   130 LVMGSRAYGRIKRMFLGSVSNYCTNHAHCPVVII-KPKE 167

GO:0003674 "molecular_function" evidence=ND

GO:0005737 "cytoplasm" evidence=ISM

GO:0002238 "response to molecule of fungal origin" evidence=RCA

GO:0006826 "iron ion transport" evidence=RCA

GO:0010106 "cellular response to iron ion starvation" evidence=RCA

GO:0010167 "response to nitrate" evidence=RCA

GO:0015706 "nitrate transport" evidence=RCA

TAIR|locus:2081531 AT3G11930 "AT3G11930" [Arabidopsis thaliana (taxid:3702)]

 Score = 168 (64.2 bits), Expect = 1.4e-22, Sum P(2) = 1.4e-22
 Identities = 47/152 (30%), Positives = 77/152 (50%)

Query:     4 KKVMVAIDESECRHYALQWALENLGDAI-------SKSDL--IIFTARP-TEFIYVQASM 53
             K+++VAIDES+   YALQW +++  + +       ++S +  +I    P   F    A  
Sbjct:    33 KRMVVAIDESDSSFYALQWVIDHFSNLLLTTAAAEAESGMLTVIHVQSPFNHFAAFPAGP 92

Query:    54 FGA----APPDLLMSIQENQKKXXXXXXGRAKEICAKHGVVAETMTEMGDPKNVICEAAE 109
              GA    A   ++ S+++ Q++       RA ++C    +  ET+   G+ K +ICEA E
Sbjct:    93 GGATAVYASSSMIESVKKAQQETSAALLSRALQMCRAKQIRTETLVLEGEAKEMICEAVE 152

Query:   110 KHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHN 141
             K  + LL+VGS  RG      LG +  YC+ N
Sbjct:   153 KMHVDLLVVGS--RG------LGKIKRYCIIN 176

GO:0003674 "molecular_function" evidence=ND

GO:0005737 "cytoplasm" evidence=ISM

GO:0002238 "response to molecule of fungal origin" evidence=RCA

TAIR|locus:2043273 AT2G47710 "AT2G47710" [Arabidopsis thaliana (taxid:3702)]

 Score = 248 (92.4 bits), Expect = 3.9e-21, P = 3.9e-21
 Identities = 57/158 (36%), Positives = 83/158 (52%)

Query:     2 DKKKVMVA-IDESECRHYALQWALENLGDAISKS---DLIIFTARPTEFIYVQASMFGAA 57
             D K VMV  +D+SE   YAL+W L+      + +    L I  A+P     V   + G  
Sbjct:     5 DGKSVMVVGVDDSEQSTYALEWTLDRFFAPYAPNYPFKLFIVHAKPNAVSAV--GLAGPG 62

Query:    58 PPDLLMSIQENQKKXXXXXXGRAKEICAK---HGVVAETMTEMGDPKNVICEAAEKHKIQ 114
               +++  +  + K        +AK IC     HG V E     GD +N++CE  +KH   
Sbjct:    63 TAEVVPYVDADLKHTAAKVVEKAKAICQSRSVHGAVIEVFE--GDARNILCEVVDKHHAS 120

Query:   115 LLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP 152
             +L+VGSH  G I+RA LGS S+YC H+A C V++V+KP
Sbjct:   121 ILVVGSHGYGAIKRAVLGSTSDYCAHHAHCSVMIVKKP 158

GO:0003674 "molecular_function" evidence=ND

GO:0005773 "vacuole" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=IDA

GO:0002238 "response to molecule of fungal origin" evidence=RCA

GO:0005886 "plasma membrane" evidence=IDA

TAIR|locus:2096089 AT3G62550 "AT3G62550" [Arabidopsis thaliana (taxid:3702)]

 Score = 226 (84.6 bits), Expect = 8.3e-19, P = 8.3e-19
 Identities = 49/155 (31%), Positives = 84/155 (54%)

Query:     3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFG-AAPPDL 61
             ++K++VA+DESE    AL W+L+NL    S + LI+   +P   +Y      G     D 
Sbjct:     6 ERKIVVAVDESEESMEALSWSLDNLFPYGSNNTLILLYVKPPLPVYSSLDAAGFIVTGDP 65

Query:    62 LMSIQENQKKXXXXXXGRAKEICAKH--GVVAETMTEMGDPKNVICEAAEKHKIQLLIVG 119
             + ++++ + +       R++ +   +   +  E     GD K VIC A +K ++ +L++G
Sbjct:    66 VAALKKYEYELVESVMARSRTVYQDYESDINIERRVGRGDAKEVICNAVQKLRVDMLVMG 125

Query:   120 SHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE 154
             +H  G  +RA LGSVS YC    KCPV++V+K  +
Sbjct:   126 THDYGFFKRALLGSVSEYCAKRVKCPVVIVKKQAQ 160

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0005773 "vacuole" evidence=IDA

GO:0002238 "response to molecule of fungal origin" evidence=RCA

TAIR|locus:2092170 AT3G25930 "AT3G25930" [Arabidopsis thaliana (taxid:3702)]

 Score = 181 (68.8 bits), Expect = 4.9e-14, P = 4.9e-14
 Identities = 55/159 (34%), Positives = 76/159 (47%)

Query:     4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARP-TEFI--YVQASMFGAA--- 57
             K VM+ IDES   +  L WALEN  D I  S + IF  +P   F    V +S  G A   
Sbjct:     2 KNVMLIIDESNASYDLLIWALENQKDTIESSKVYIFAKQPQNSFTPPTVLSSSVGFAQIF 61

Query:    58 -P--P--DLLMSIQENQKKXXXXXXGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHK 112
              P  P  +L+   QE   K       +AK+IC  HG+ AET T+ GDPK++I +  ++  
Sbjct:    62 YPFSPNSELIRLAQEKNMKIALGILEKAKKICLNHGIKAETFTDDGDPKDLIRKIIQERN 121

Query:   113 IQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK 151
             I L++               S+   C  N  C +LVV+K
Sbjct:   122 INLIVTSDQQ----------SLKK-CTQNTDCSLLVVKK 149

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0000041 "transition metal ion transport" evidence=RCA

GO:0002238 "response to molecule of fungal origin" evidence=RCA

GO:0006826 "iron ion transport" evidence=RCA

GO:0010106 "cellular response to iron ion starvation" evidence=RCA

GO:0010167 "response to nitrate" evidence=RCA

GO:0015706 "nitrate transport" evidence=RCA

TAIR|locus:2084153 AT3G01520 "AT3G01520" [Arabidopsis thaliana (taxid:3702)]

 Score = 177 (67.4 bits), Expect = 1.3e-13, P = 1.3e-13
 Identities = 48/159 (30%), Positives = 79/159 (49%)

Query:     5 KVMVAIDESECRHY---------ALQWALENLGDAISKSD---LIIFTARPTEFIYVQAS 52
             KVMVA++ S  + Y         A +W LE +  + + SD   L++      E  +    
Sbjct:     7 KVMVAVNASTIKDYPNPSISCKRAFEWTLEKIVRS-NTSDFKILLLHVQVVDEDGFDDVD 65

Query:    53 MFGAAPPDLLMSIQENQKKXXXXXXGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHK 112
                A+P D     Q N+ K          + C + GV  E   + GDPK+VIC+  ++ +
Sbjct:    66 SIYASPEDFRDMRQSNKAKGLHLLEFFVNK-CHEIGVGCEAWIKTGDPKDVICQEVKRVR 124

Query:   113 IQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK 151
                L+VGS   G  Q+ F+G+VS +CV +A+CPV+ +++
Sbjct:   125 PDFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVMTIKR 163

GO:0003674 "molecular_function" evidence=ND

GO:0005737 "cytoplasm" evidence=ISM

GO:0005886 "plasma membrane" evidence=IDA

GO:0002238 "response to molecule of fungal origin" evidence=RCA

TAIR|locus:2222687 AT5G14680 "AT5G14680" [Arabidopsis thaliana (taxid:3702)]

 Score = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 45/161 (27%), Positives = 74/161 (45%)

Query:     5 KVMVAIDESECRHY---------ALQWALENL--GDAISKSDLIIFTARPTEFIYVQASM 53
             +VMVA++ES  + Y         A +W L+ +   +      L++      E  +     
Sbjct:     7 RVMVAVNESTLKGYPHASISSKKAFEWTLKKIVRSNTSGFKLLLLHVQVQDEDGFDDMDS 66

Query:    54 FGAAPPDLLMSIQENQKKXXXXXXGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKI 113
               A+P D     + N+ K         K+ C   GV  E     GDP  +IC    + + 
Sbjct:    67 IYASPDDFRQMRERNKAKGLHLLEFFVKK-CHDIGVGCEAWIRKGDPTELICHEVRRVRP 125

Query:   114 QLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE 154
               L+VGS   GP Q+ F+G+VS +CV +A+CPV+ +++  E
Sbjct:   126 DFLVVGSRGLGPFQKVFVGTVSEFCVKHAECPVITIKRTAE 166

GO:0003674 "molecular_function" evidence=ND

GO:0005737 "cytoplasm" evidence=ISM

GO:0002238 "response to molecule of fungal origin" evidence=RCA

TAIR|locus:2086102 AT3G17020 "AT3G17020" [Arabidopsis thaliana (taxid:3702)]

 Score = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 46/157 (29%), Positives = 75/157 (47%)

Query:     4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMF---GAAPPD 60
             +++ VA+D S+C   AL WA++N+   +   D +I      +  Y +  M        P 
Sbjct:     7 RRIGVAVDFSDCSKKALSWAIDNV---VRDGDHLILITIAHDMNYEEGEMQLWETVGSPF 63

Query:    61 LLMSIQEN---QKKXXXXXXGRAKEI---CAKHGVVAETMT-EMGDPKNVICEAAEKHKI 113
             + MS   +    KK          +I    A+   +   M    GDP+  IC AAE+  +
Sbjct:    64 IPMSEFSDAAVMKKYALKPDAETLDIVNTAARKKTITVVMKIYWGDPREKICAAAEQIPL 123

Query:   114 QLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
               L++G+   G ++R  +GSVSN+ V+N  CPV VV+
Sbjct:   124 SSLVMGNRGLGGLKRMIMGSVSNHVVNNVACPVTVVK 160

GO:0003674 "molecular_function" evidence=ND

GO:0005737 "cytoplasm" evidence=ISM

GO:0009409 "response to cold" evidence=IEP

GO:0005886 "plasma membrane" evidence=IDA

GO:0002238 "response to molecule of fungal origin" evidence=RCA

GO:0006623 "protein targeting to vacuole" evidence=RCA

---

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)
P42297	YXIE_BACSU	No assigned EC number	0.3310	0.9285	0.9662	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	154
cd00293	130	cd00293, USP_Like, Usp: Universal stress protein f	2e-31
pfam00582	139	pfam00582, Usp, Universal stress protein family	4e-31
COG0589	154	COG0589, UspA, Universal stress protein UspA and r	1e-21
cd01988	132	cd01988, Na_H_Antiporter_C, The C-terminal domain	7e-10
cd01989	146	cd01989, STK_N, The N-terminal domain of Eukaryoti	2e-07
PRK15005	144	PRK15005, PRK15005, universal stress protein F; Pr	5e-06

>gnl|CDD|238182 cd00293, USP_Like, Usp: Universal stress protein family

 Score =  109 bits (274), Expect = 2e-31
 Identities = 47/145 (32%), Positives = 71/145 (48%), Gaps = 15/145 (10%)

Query: 5   KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMS 64
           +++VA+D SE    AL+WA          ++L++                   PP     
Sbjct: 1   RILVAVDGSEESERALRWAARLARR--LGAELVLLHVVDP-------------PPSSAAE 45

Query: 65  IQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRG 124
           + E  ++ A ALL   +E  A+ GV  ET+   GDP   I EAAE+    L+++GS  R 
Sbjct: 46  LAELLEEEARALLEALREALAEAGVKVETVVLEGDPAEAILEAAEELGADLIVMGSRGRS 105

Query: 125 PIQRAFLGSVSNYCVHNAKCPVLVV 149
            ++R  LGSV+   + +A CPVLVV
Sbjct: 106 GLRRLLLGSVAERVLRHAPCPVLVV 130

The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae Usp reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, athough Usp lacks ATP-binding activity. Length = 130

>gnl|CDD|216006 pfam00582, Usp, Universal stress protein family

 Score =  108 bits (271), Expect = 4e-31
 Identities = 47/147 (31%), Positives = 71/147 (48%), Gaps = 10/147 (6%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
           K+++VA+D SE    AL+WALE        ++LI+        ++V       A  + L 
Sbjct: 3   KRILVAVDGSEESERALEWALELAKR--RGAELIL--------LHVIDPEPSGAASEALE 52

Query: 64  SIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSR 123
             +E + +   A            GVV E +   GDP   I E AE+    L+++GS  R
Sbjct: 53  EEEEEELEEEEAEAEALAAAAEAGGVVVEVVVRGGDPAEAILEVAEEEDADLIVMGSRGR 112

Query: 124 GPIQRAFLGSVSNYCVHNAKCPVLVVR 150
             ++R  LGSV+   + +A CPVLVVR
Sbjct: 113 SGLRRLLLGSVAEKVLRHAPCPVLVVR 139

The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, though UspA lacks ATP-binding activity. Length = 139

>gnl|CDD|223662 COG0589, UspA, Universal stress protein UspA and related nucleotide-binding proteins [Signal transduction mechanisms]

 Score = 84.6 bits (209), Expect = 1e-21
 Identities = 49/152 (32%), Positives = 69/152 (45%), Gaps = 7/152 (4%)

Query: 4   KKVMVAIDE-SECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLL 62
           KK++VA+D  SE    AL+ A+         + LI+            A +  A     +
Sbjct: 6   KKILVAVDVGSEAAEKALEEAVAL--AKRLGAPLILLVVIDPL--EPTALVSVALADAPI 61

Query: 63  MSIQENQKKAALALLGRAKEICAKHGV-VAETMTEMGDPK-NVICEAAEKHKIQLLIVGS 120
              +E  ++ A  LL  AK +    GV V ET    G P    I E AE+    L++VGS
Sbjct: 62  PLSEEELEEEAEELLAEAKALAEAAGVPVVETEVVEGSPSAEEILELAEEEDADLIVVGS 121

Query: 121 HSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP 152
             R  + R  LGSV+   + +A CPVLVVR  
Sbjct: 122 RGRSGLSRLLLGSVAEKVLRHAPCPVLVVRSE 153

Length = 154

>gnl|CDD|238946 cd01988, Na_H_Antiporter_C, The C-terminal domain of a subfamily of Na+ /H+ antiporter existed in bacteria and archea

 Score = 53.4 bits (129), Expect = 7e-10
 Identities = 26/95 (27%), Positives = 43/95 (45%), Gaps = 1/95 (1%)

Query: 57  APPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEM-GDPKNVICEAAEKHKIQL 115
            P     S  E   + A  LL +A+ I A  GV   T+  +  D  + I   A++ +  L
Sbjct: 38  VPNHSSPSQLEVNVQRARKLLRQAERIAASLGVPVHTIIRIDHDIASGILRTAKERQADL 97

Query: 116 LIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
           +I+G H    ++    G V +  + +A C V VV+
Sbjct: 98  IIMGWHGSTSLRDRLFGGVIDQVLESAPCDVAVVK 132

Na+/H+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na+ /H+ exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiports exchange Na+ for H+ in an electroneutral manner, and this activity is carried out by a family of Na+ /H+ exchangers, or NHEs, which are known to be present in both prokaryotic and eukaryotic cells. These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N-terminus and a large cytoplasmic region at the C-terminus. The transmembrane regions M3-M12 share identity wit h other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the region that is involved in the transport of sodium and hydrogen ions. The cytoplasmic region or C-terminal has homology with a family universal stress protein.Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. Length = 132

>gnl|CDD|238947 cd01989, STK_N, The N-terminal domain of Eukaryotic Serine Threonine kinases

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 38/151 (25%), Positives = 65/151 (43%), Gaps = 10/151 (6%)

Query: 5   KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMS 64
            V VA+D+ +    AL+WAL+NL        +++    P     + +    +   ++  +
Sbjct: 1   SVAVAVDKDKKSKNALKWALDNLATKGQT--IVLVHVHPP----ITSIPSSSGKLEVASA 54

Query: 65  IQENQKKAALALLGRAKEICAKHGVVAETM-TEMGDPKNVICEAAEKHKIQLLIVGSHSR 123
            ++ + K A  LL   +  C++ GV  E +  E  D    I E    H I  L++G+ S 
Sbjct: 55  YKQEEDKEAKELLLPYRCFCSRKGVQCEDVVLEDDDVAKAIVEYVADHGITKLVMGASSD 114

Query: 124 GPIQRAFLGS-VSNYCVHNAK--CPVLVVRK 151
                 F  S V++  +  A   C V VV K
Sbjct: 115 NHFSMKFKKSDVASSVLKEAPDFCTVYVVSK 145

The Serine Threonine kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. The N-terminal domain is homologous to the USP family which has a ATP binding fold. The N-terminal domain is predicted to be involved in ATP binding. Length = 146

>gnl|CDD|184967 PRK15005, PRK15005, universal stress protein F; Provisional

 Score = 43.3 bits (102), Expect = 5e-06
 Identities = 23/53 (43%), Positives = 31/53 (58%), Gaps = 1/53 (1%)

Query: 98  GDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
           G PK+ I E A+K    ++I+ SH R  I    LGS +   V +A+C VLVVR
Sbjct: 93  GSPKDRILELAKKIPADMIIIASH-RPDITTYLLGSNAAAVVRHAECSVLVVR 144

Length = 144

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	154
PRK15456	142	universal stress protein UspG; Provisional	99.97
PRK15005	144	universal stress protein F; Provisional	99.97
PRK09982	142	universal stress protein UspD; Provisional	99.97
cd01989	146	STK_N The N-terminal domain of Eukaryotic Serine T	99.97
PRK15118	144	universal stress global response regulator UspA; P	99.96
PRK10116	142	universal stress protein UspC; Provisional	99.95
PF00582	140	Usp: Universal stress protein family; InterPro: IP	99.95
PRK11175	305	universal stress protein UspE; Provisional	99.95
cd01988	132	Na_H_Antiporter_C The C-terminal domain of a subfa	99.94
cd01987	124	USP_OKCHK USP domain is located between the N-term	99.93
cd00293	130	USP_Like Usp: Universal stress protein family. The	99.91
PRK11175	305	universal stress protein UspE; Provisional	99.9
COG0589	154	UspA Universal stress protein UspA and related nuc	99.88
PRK12652	357	putative monovalent cation/H+ antiporter subunit E	99.78
PRK10490	895	sensor protein KdpD; Provisional	99.59
COG2205	890	KdpD Osmosensitive K+ channel histidine kinase [Si	99.53
cd01984	86	AANH_like Adenine nucleotide alpha hydrolases supe	98.75
PLN03159	832	cation/H(+) antiporter 15; Provisional	98.29
TIGR02432	189	lysidine_TilS_N tRNA(Ile)-lysidine synthetase, N-t	97.81
PF01171	182	ATP_bind_3: PP-loop family; InterPro: IPR011063 Th	97.64
cd01992	185	PP-ATPase N-terminal domain of predicted ATPase of	97.43
PLN03159	832	cation/H(+) antiporter 15; Provisional	97.4
PRK12342	254	hypothetical protein; Provisional	96.79
cd01993	185	Alpha_ANH_like_II This is a subfamily of Adenine n	96.74
PRK10696	258	tRNA 2-thiocytidine biosynthesis protein TtcA; Pro	96.52
COG0037	298	MesJ tRNA(Ile)-lysidine synthase MesJ [Cell cycle	96.28
PRK03359	256	putative electron transfer flavoprotein FixA; Revi	96.2
TIGR00591	454	phr2 photolyase PhrII. All proteins in this family	95.91
PF01012	164	ETF: Electron transfer flavoprotein domain; InterP	95.55
COG0041	162	PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) m	95.33
COG2086	260	FixA Electron transfer flavoprotein, beta subunit	95.33
PRK10660	436	tilS tRNA(Ile)-lysidine synthetase; Provisional	95.31
TIGR01162	156	purE phosphoribosylaminoimidazole carboxylase, Pur	95.09
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	94.97
PF00875	165	DNA_photolyase: DNA photolyase from Prosite.; Inte	94.87
COG0299	200	PurN Folate-dependent phosphoribosylglycinamide fo	94.79
PF00731	150	AIRC: AIR carboxylase; InterPro: IPR000031 Phospho	94.68
PRK05253	301	sulfate adenylyltransferase subunit 2; Provisional	94.5
PRK13820	394	argininosuccinate synthase; Provisional	94.39
PRK10867	433	signal recognition particle protein; Provisional	93.47
TIGR00268	252	conserved hypothetical protein TIGR00268. The N-te	93.44
TIGR02765	429	crypto_DASH cryptochrome, DASH family. Photolyases	93.02
TIGR00930	953	2a30 K-Cl cotransporter.	92.58
TIGR03556	471	photolyase_8HDF deoxyribodipyrimidine photo-lyase,	92.47
PRK07313	182	phosphopantothenoylcysteine decarboxylase; Validat	92.0
PF02601	319	Exonuc_VII_L: Exonuclease VII, large subunit; Inte	91.46
PRK14665	360	mnmA tRNA-specific 2-thiouridylase MnmA; Provision	90.97
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	90.96
COG1597	301	LCB5 Sphingosine kinase and enzymes related to euk	90.09
cd01985	181	ETF The electron transfer flavoprotein (ETF) serve	89.54
PRK05579	399	bifunctional phosphopantothenoylcysteine decarboxy	89.28
PRK08091	228	ribulose-phosphate 3-epimerase; Validated	89.2
COG1646	240	Predicted phosphate-binding enzymes, TIM-barrel fo	88.58
cd01995	169	ExsB ExsB is a transcription regulator related pro	88.45
TIGR00959	428	ffh signal recognition particle protein. This mode	88.38
PRK10674	472	deoxyribodipyrimidine photolyase; Provisional	88.35
PF04459	204	DUF512: Protein of unknown function (DUF512); Inte	88.26
COG1184	301	GCD2 Translation initiation factor 2B subunit, eIF	88.18
PRK00286	438	xseA exodeoxyribonuclease VII large subunit; Revie	88.14
PRK13982	475	bifunctional SbtC-like/phosphopantothenoylcysteine	88.05
TIGR02039	294	CysD sulfate adenylyltransferase, small subunit. I	87.95
PRK11914	306	diacylglycerol kinase; Reviewed	87.86
KOG1650	769	consensus Predicted K+/H+-antiporter [Inorganic io	87.43
PLN02948	577	phosphoribosylaminoimidazole carboxylase	87.26
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	87.05
COG0655	207	WrbA Multimeric flavodoxin WrbA [General function	86.93
cd01714	202	ETF_beta The electron transfer flavoprotein (ETF)	86.91
TIGR02113	177	coaC_strep phosphopantothenoylcysteine decarboxyla	86.85
cd01994	194	Alpha_ANH_like_IV This is a subfamily of Adenine n	86.74
PRK08745	223	ribulose-phosphate 3-epimerase; Provisional	86.72
PF03652	135	UPF0081: Uncharacterised protein family (UPF0081);	86.43
PRK00109	138	Holliday junction resolvase-like protein; Reviewed	86.37
cd01990	202	Alpha_ANH_like_I This is a subfamily of Adenine nu	86.33
cd05565	99	PTS_IIB_lactose PTS_IIB_lactose: subunit IIB of en	86.09
PRK14057	254	epimerase; Provisional	85.99
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	85.89
TIGR00237	432	xseA exodeoxyribonuclease VII, large subunit. This	85.72
PRK09722	229	allulose-6-phosphate 3-epimerase; Provisional	85.66
PRK06027	286	purU formyltetrahydrofolate deformylase; Reviewed	85.54
PLN00200	404	argininosuccinate synthase; Provisional	85.25
cd01713	173	PAPS_reductase This domain is found in phosphoaden	84.98
cd01986	103	Alpha_ANH_like Adenine nucleotide alpha hydrolases	84.75
), forming GARS-AIRS-GART. This entry represents the N-domain, which is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (IPR005481 from INTERPRO).; GO: 0004637 phosphoribosylamine-glycine ligase activity, 0009113 purine base biosynthetic process; PDB: 3MJF_A 2XD4_A 2XCL_A 2IP4_A 2YW2_B 2YYA_A 3LP8_A 1VKZ_A 2YS6_A 2YRX_A ...." target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF02844">PF02844	100	GARS_N: Phosphoribosylglycinamide synthetase, N do	84.48
PF05582	287	Peptidase_U57: YabG peptidase U57; InterPro: IPR00	84.32
cd08550	349	GlyDH-like Glycerol_dehydrogenase-like. Families o	84.23
TIGR02855	283	spore_yabG sporulation peptidase YabG. Members of	84.13
TIGR00655	280	PurU formyltetrahydrofolate deformylase. This mode	84.05
PRK13010	289	purU formyltetrahydrofolate deformylase; Reviewed	83.9
TIGR00853	95	pts-lac PTS system, lactose/cellobiose family IIB	83.65
PF10087	97	DUF2325: Uncharacterized protein conserved in bact	83.26
PRK08185	283	hypothetical protein; Provisional	82.58
PF01261	213	AP_endonuc_2: Xylose isomerase-like TIM barrel; In	82.4
COG1570	440	XseA Exonuclease VII, large subunit [DNA replicati	82.2
TIGR00521	390	coaBC_dfp phosphopantothenoylcysteine decarboxylas	82.17
PRK13337	304	putative lipid kinase; Reviewed	82.06
PRK13054	300	lipid kinase; Reviewed	82.04
PF04244	224	DPRP: Deoxyribodipyrimidine photo-lyase-related pr	81.7
TIGR00032	394	argG argininosuccinate synthase. argG in bacteria,	81.3
TIGR00250	130	RNAse_H_YqgF RNAse H-fold protein YqgF. This prote	81.29
PF00834	201	Ribul_P_3_epim: Ribulose-phosphate 3 epimerase fam	81.23
TIGR02699	174	archaeo_AfpA archaeoflavoprotein AfpA. The prototy	80.87
COG0415	461	PhrB Deoxyribodipyrimidine photolyase [DNA replica	80.84
COG1927	277	Mtd Coenzyme F420-dependent N(5),N(10)-methenyltet	80.82
cd02067	119	B12-binding B12 binding domain (B12-BD). This doma	80.68
PRK13059	295	putative lipid kinase; Reviewed	80.56
PRK11070	575	ssDNA exonuclease RecJ; Provisional	80.52
PRK12857	284	fructose-1,6-bisphosphate aldolase; Reviewed	80.42
COG0036	220	Rpe Pentose-5-phosphate-3-epimerase [Carbohydrate	80.2

>PRK15456 universal stress protein UspG; Provisional

Probab=99.97  E-value=1.2e-29  Score=161.55  Aligned_cols=140  Identities=19%  Similarity=0.203  Sum_probs=113.5

Q ss_pred             CCcEEEEEecCCc--hHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESE--CRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGR   79 (154)
Q Consensus         2 ~~~~iLv~vd~~~--~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~   79 (154)
                      ||++||||+|+|+  .+..++++|..+|+. +  ++++++||++......    .... ....+.+.+..++..++.+++
T Consensus         1 m~~~ILv~vD~S~~~~s~~al~~A~~la~~-~--~~l~llhv~~~~~~~~----~~~~-~~~~~~~~~~~~~~~~~~l~~   72 (142)
T PRK15456          1 MYKTIIMPVDVFEMELSDKAVRHAEFLAQD-D--GVIHLLHVLPGSASLS----LHRF-AADVRRFEEHLQHEAEERLQT   72 (142)
T ss_pred             CCccEEEeccCCchhHHHHHHHHHHHHHhc-C--CeEEEEEEecCccccc----cccc-ccchhhHHHHHHHHHHHHHHH
Confidence            5899999999995  899999999999986 3  5999999998753211    0000 011133445566667777777


Q ss_pred             HHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           80 AKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      +.+.+...+.++++.+..|++.+.|.+++++.++||||||+++++ +.++++||++++++++++||||+||
T Consensus        73 ~~~~~~~~~~~v~~~v~~G~~~~~I~~~a~~~~~DLIVmG~~g~~-~~~~llGS~a~~v~~~a~~pVLvV~  142 (142)
T PRK15456         73 MVSHFTIDPSRIKQHVRFGSVRDEVNELAEELGADVVVIGSRNPS-ISTHLLGSNASSVIRHANLPVLVVR  142 (142)
T ss_pred             HHHHhCCCCcceEEEEcCCChHHHHHHHHhhcCCCEEEEcCCCCC-ccceecCccHHHHHHcCCCCEEEeC
Confidence            777666567888999999999999999999999999999999976 7888999999999999999999996

>PRK15005 universal stress protein F; Provisional

Probab=99.97  E-value=2.4e-29  Score=160.40  Aligned_cols=142  Identities=25%  Similarity=0.295  Sum_probs=110.6

Q ss_pred             CCcEEEEEecCCch--HHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESEC--RHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGR   79 (154)
Q Consensus         2 ~~~~iLv~vd~~~~--~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~   79 (154)
                      ||++||||+|+|+.  +..++++|.++|+..+  ++++++||++....... ..+... ... . ..+..++..++.+++
T Consensus         1 m~~~ILv~~D~s~~~~~~~a~~~a~~la~~~~--~~l~ll~v~~~~~~~~~-~~~~~~-~~~-~-~~~~~~~~~~~~l~~   74 (144)
T PRK15005          1 MNRTILVPIDISDSELTQRVISHVEAEAKIDD--AEVHFLTVIPSLPYYAS-LGLAYS-AEL-P-AMDDLKAEAKSQLEE   74 (144)
T ss_pred             CCccEEEecCCCchhHHHHHHHHHHHHHhccC--CeEEEEEEEccCccccc-cccccc-ccc-h-HHHHHHHHHHHHHHH
Confidence            58999999999998  5799999999999977  99999999986432210 001000 000 0 112334445566666


Q ss_pred             HHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           80 AKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      +.+.+...+++++..+..|++.+.|.+++++.++||||||++ ++.+.++++||++++|+++++||||+||
T Consensus        75 ~~~~~~~~~~~~~~~v~~G~p~~~I~~~a~~~~~DLIV~Gs~-~~~~~~~llGS~a~~vl~~a~cpVlvVr  144 (144)
T PRK15005         75 IIKKFKLPTDRVHVHVEEGSPKDRILELAKKIPADMIIIASH-RPDITTYLLGSNAAAVVRHAECSVLVVR  144 (144)
T ss_pred             HHHHhCCCCCceEEEEeCCCHHHHHHHHHHHcCCCEEEEeCC-CCCchheeecchHHHHHHhCCCCEEEeC
Confidence            666666667788899999999999999999999999999998 4568899999999999999999999996

>PRK09982 universal stress protein UspD; Provisional

Probab=99.97  E-value=3.2e-29  Score=159.53  Aligned_cols=141  Identities=18%  Similarity=0.106  Sum_probs=109.7

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      |+|++||||+|+|+.+..++++|+.+|+..+  ++++++||.+.......+ .+.    ...+...+..++..++.++++
T Consensus         1 ~~~k~ILvavD~S~~s~~al~~A~~lA~~~~--a~l~llhV~~~~~~~~~~-~~~----~~~~~~~~~~~~~~~~~l~~~   73 (142)
T PRK09982          1 MAYKHIGVAISGNEEDALLVNKALELARHND--AHLTLIHIDDGLSELYPG-IYF----PATEDILQLLKNKSDNKLYKL   73 (142)
T ss_pred             CCceEEEEEecCCcchHHHHHHHHHHHHHhC--CeEEEEEEccCcchhchh-hhc----cchHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999999999999999977  999999998764322100 000    011223344455555666666


Q ss_pred             HHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCCC
Q 031713           81 KEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPV  153 (154)
Q Consensus        81 ~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~~  153 (154)
                      .+.+.  ...++..+..|+|.+.|+++|++.++||||||++ ++.+.+++ | ++++++++++||||+||..+
T Consensus        74 ~~~~~--~~~~~~~v~~G~p~~~I~~~A~~~~aDLIVmG~~-~~~~~~~~-~-va~~V~~~s~~pVLvv~~~~  141 (142)
T PRK09982         74 TKNIQ--WPKTKLRIERGEMPETLLEIMQKEQCDLLVCGHH-HSFINRLM-P-AYRGMINKMSADLLIVPFID  141 (142)
T ss_pred             HHhcC--CCcceEEEEecCHHHHHHHHHHHcCCCEEEEeCC-hhHHHHHH-H-HHHHHHhcCCCCEEEecCCC
Confidence            65553  2347788888999999999999999999999986 77788777 5 99999999999999998754

>cd01989 STK_N The N-terminal domain of Eukaryotic Serine Threonine kinases

Probab=99.97  E-value=2.7e-28  Score=155.90  Aligned_cols=142  Identities=25%  Similarity=0.384  Sum_probs=118.4

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEIC   84 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   84 (154)
                      +||||+|+|+.+..+++||+++|+..+  ++++++||.+......   . ...............++..++.++++.+.+
T Consensus         1 ~ILVavD~S~~s~~al~~a~~~a~~~~--~~l~ll~v~~~~~~~~---~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   74 (146)
T cd01989           1 SVAVAVDKDKKSKNALKWALDNLATKG--QTIVLVHVHPPITSIP---S-SSGKLEVASAYKQEEDKEAKELLLPYRCFC   74 (146)
T ss_pred             CEEEEecCccccHHHHHHHHHhccCCC--CcEEEEEeccCcccCC---C-CccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            589999999999999999999999877  8999999987643221   0 011112234455566677888888888888


Q ss_pred             HhcCCeEEEEEecC-ChhhHHHHHHHhcCCCEEEEecCCCCCccccccc-chhHHHhhcCC--CcEEEEcCC
Q 031713           85 AKHGVVAETMTEMG-DPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLG-SVSNYCVHNAK--CPVLVVRKP  152 (154)
Q Consensus        85 ~~~~~~~~~~v~~g-~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~g-s~~~~l~~~~~--~pvliv~~~  152 (154)
                      ...++.++..+..| ++.+.|++++++.++|+||||+++++.+.++++| |++.+++++++  |||++|++.
T Consensus        75 ~~~~~~~~~~~~~g~~~~~~I~~~a~~~~~dlIV~Gs~g~~~l~~~~~gssva~~Vi~~a~~~c~Vlvv~~~  146 (146)
T cd01989          75 SRKGVQCEDVVLEDDDVAKAIVEYVADHGITKLVMGASSDNHFSMKFKKSDVASSVLKEAPDFCTVYVVSKG  146 (146)
T ss_pred             hhcCCeEEEEEEeCCcHHHHHHHHHHHcCCCEEEEeccCCCceeecccCCchhHHHHhcCCCCceEEEEeCc
Confidence            88899999888886 8999999999999999999999999999999887 69999999999  999999863

The Serine Threonine kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. The N-terminal domain is homologous to the USP family which has a ATP binding fold. The N-terminal domain is predicted to be involved in ATP binding.

>PRK15118 universal stress global response regulator UspA; Provisional

Probab=99.96  E-value=3.8e-28  Score=154.92  Aligned_cols=140  Identities=18%  Similarity=0.171  Sum_probs=100.6

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      |+|++||||+|+|+.+..++++|..+|+..+  ++++++||..+......  ++.   ....+...+...+...+.+   
T Consensus         1 ~~~~~ILvavD~S~~s~~al~~a~~la~~~~--a~l~ll~v~~~~~~~~~--~~~---~~~~~~~~~~~~~~~~~~l---   70 (144)
T PRK15118          1 MAYKHILIAVDLSPESKVLVEKAVSMARPYN--AKVSLIHVDVNYSDLYT--GLI---DVNLGDMQKRISEETHHAL---   70 (144)
T ss_pred             CCceEEEEEccCChhHHHHHHHHHHHHHhhC--CEEEEEEEccChhhhhh--hhh---hcchHHHHHHHHHHHHHHH---
Confidence            8999999999999999999999999999877  89999999543221110  000   0011122222222233333   


Q ss_pred             HHHHHhcCCeE-EEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCCC
Q 031713           81 KEICAKHGVVA-ETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPV  153 (154)
Q Consensus        81 ~~~~~~~~~~~-~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~~  153 (154)
                      .......|+.+ ...+..|++.++|++++++.++||||||+++ +.+. . +||++++++++++||||+||.+.
T Consensus        71 ~~~~~~~~~~~~~~~~~~G~p~~~I~~~a~~~~~DLIV~Gs~~-~~~~-~-lgSva~~v~~~a~~pVLvv~~~~  141 (144)
T PRK15118         71 TELSTNAGYPITETLSGSGDLGQVLVDAIKKYDMDLVVCGHHQ-DFWS-K-LMSSARQLINTVHVDMLIVPLRD  141 (144)
T ss_pred             HHHHHhCCCCceEEEEEecCHHHHHHHHHHHhCCCEEEEeCcc-cHHH-H-HHHHHHHHHhhCCCCEEEecCCc
Confidence            33334557775 3455679999999999999999999999995 3333 3 58999999999999999998653

>PRK10116 universal stress protein UspC; Provisional

Probab=99.95  E-value=6.5e-27  Score=148.88  Aligned_cols=140  Identities=17%  Similarity=0.225  Sum_probs=107.9

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      |+|++|||++|+++.+..++++|..+|+.++  ++++++|+.+......      .......+...+...++.++.++++
T Consensus         1 ~~~~~ILv~~D~s~~s~~al~~A~~lA~~~~--a~l~ll~v~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~l~~~   72 (142)
T PRK10116          1 MSYSNILVAVAVTPESQQLLAKAVSIARPVN--GKISLITLASDPEMYN------QFAAPMLEDLRSVMQEETQSFLDKL   72 (142)
T ss_pred             CCCceEEEEccCCcchHHHHHHHHHHHHHhC--CEEEEEEEccCcccch------hhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999999999999999977  8999999987643211      1111222333334444444444443


Q ss_pred             HHHHHhcCCeE-EEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCCC
Q 031713           81 KEICAKHGVVA-ETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPV  153 (154)
Q Consensus        81 ~~~~~~~~~~~-~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~~  153 (154)
                      .   ...|+.. ...+..|++.+.|.+++++.++||||+|+++++.+.+++  +++++++++++||||+||..-
T Consensus        73 ~---~~~~~~~~~~~~~~G~~~~~I~~~a~~~~~DLiV~g~~~~~~~~~~~--s~a~~v~~~~~~pVLvv~~~~  141 (142)
T PRK10116         73 I---QDADYPIEKTFIAYGELSEHILEVCRKHHFDLVICGNHNHSFFSRAS--CSAKRVIASSEVDVLLVPLTG  141 (142)
T ss_pred             H---HhcCCCeEEEEEecCCHHHHHHHHHHHhCCCEEEEcCCcchHHHHHH--HHHHHHHhcCCCCEEEEeCCC
Confidence            3   3457664 356677999999999999999999999999988888754  789999999999999999754

>PF00582 Usp: Universal stress protein family; InterPro: IPR006016 The universal stress protein UspA P28242 from SWISSPROT [] is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents

Probab=99.95  E-value=8.5e-27  Score=146.97  Aligned_cols=140  Identities=32%  Similarity=0.439  Sum_probs=106.6

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      |+++||||+|+++.+..++++|..+|+..+  ++++++||.+.......       ........................
T Consensus         1 M~~~Ilv~~d~~~~~~~al~~a~~la~~~~--~~i~~l~v~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~   71 (140)
T PF00582_consen    1 MYKRILVAIDGSEESRRALRFALELAKRSG--AEITLLHVIPPPPQYSF-------SAAEDEESEEEAEEEEQARQAEAE   71 (140)
T ss_dssp             -TSEEEEEESSSHHHHHHHHHHHHHHHHHT--CEEEEEEEEESCHCHHH-------HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCHHHHHHHHHHHHHHHhhC--CeEEEEEeecccccccc-------ccccccccccccchhhhhhhHHHH
Confidence            689999999999999999999999999987  99999999998765430       111111111111111111111112


Q ss_pred             HHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           82 EICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        82 ~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      ......+......+..|++.+.|++++++.++|+||+|+++++.+.++++|+++++++++++|||+|||
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~dliv~G~~~~~~~~~~~~gs~~~~l~~~~~~pVlvv~  140 (140)
T PF00582_consen   72 EAEAEGGIVIEVVIESGDVADAIIEFAEEHNADLIVMGSRGRSGLERLLFGSVAEKLLRHAPCPVLVVP  140 (140)
T ss_dssp             HHHHHTTSEEEEEEEESSHHHHHHHHHHHTTCSEEEEESSSTTSTTTSSSHHHHHHHHHHTSSEEEEEE
T ss_pred             HHhhhccceeEEEEEeeccchhhhhccccccceeEEEeccCCCCccCCCcCCHHHHHHHcCCCCEEEeC
Confidence            233344666777888899999999999999999999999999999999999999999999999999997

UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA [] reveals an alpha/beta fold similar to that of the Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0577 protein, which binds ATP [], though UspA lacks ATP-binding activity.; GO: 0006950 response to stress; PDB: 3DLO_C 3QTB_A 2PFS_A 3TNJ_A 1JMV_D 3FH0_B 3FDX_B 3AB7_A 3AB8_A 2GM3_F ....

>PRK11175 universal stress protein UspE; Provisional

Probab=99.95  E-value=1.6e-26  Score=163.99  Aligned_cols=146  Identities=14%  Similarity=0.159  Sum_probs=117.5

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      |+|++||||+|+|+.+..++++|+.+|+..+  ++++++|+.+.......  .  .......+...+...+..++.++++
T Consensus         1 ~~~~~ILv~~D~s~~~~~al~~a~~lA~~~~--a~l~ll~v~~~~~~~~~--~--~~~~~~~~~~~~~~~~~~~~~l~~~   74 (305)
T PRK11175          1 AKYQNILVVIDPNQDDQPALRRAVYLAQRNG--GKITAFLPIYDFSYEMT--T--LLSPDEREAMRQGVISQRTAWIREQ   74 (305)
T ss_pred             CCcceEEEEcCCCccccHHHHHHHHHHHhcC--CCEEEEEeccCchhhhh--c--ccchhHHHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999999999999999987  89999999865432210  0  0111112222233334456667777


Q ss_pred             HHHHHhcCCeEEEEEec-CChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           81 KEICAKHGVVAETMTEM-GDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        81 ~~~~~~~~~~~~~~v~~-g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      ...+...|++++..+.. |++.+.|.+++++.++||||+|+++++.+.+.++|+++++|+++++||||+||+.
T Consensus        75 ~~~~~~~~~~~~~~v~~~g~~~~~i~~~a~~~~~DLiV~G~~~~~~~~~~~~gs~~~~l~~~~~~pvlvv~~~  147 (305)
T PRK11175         75 AKPYLDAGIPIEIKVVWHNRPFEAIIQEVIAGGHDLVVKMTHQHDKLESVIFTPTDWHLLRKCPCPVLMVKDQ  147 (305)
T ss_pred             HHHHhhcCCceEEEEecCCCcHHHHHHHHHhcCCCEEEEeCCCCcHHHhhccChhHHHHHhcCCCCEEEeccc
Confidence            77777778888887764 8999999999999999999999999999999999999999999999999999874

>cd01988 Na_H_Antiporter_C The C-terminal domain of a subfamily of Na+ /H+ antiporter existed in bacteria and archea

Probab=99.94  E-value=1.5e-25  Score=140.78  Aligned_cols=131  Identities=22%  Similarity=0.311  Sum_probs=111.5

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEIC   84 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   84 (154)
                      +||||+|+++++..++++|..+|+..+  ++++++|+.+......         ..    ......+..++.++.+.+.+
T Consensus         1 ~ILv~vd~s~~~~~~l~~a~~la~~~~--~~v~ll~v~~~~~~~~---------~~----~~~~~~~~~~~~~~~~~~~~   65 (132)
T cd01988           1 RILVPVANPNTARDLLELAAALARAQN--GEIIPLNVIEVPNHSS---------PS----QLEVNVQRARKLLRQAERIA   65 (132)
T ss_pred             CEEEecCCchhHHHHHHHHHHHhhcCC--CeEEEEEEEecCCCCC---------cc----hhHHHHHHHHHHHHHHHHHh
Confidence            699999999999999999999999866  8999999998653221         00    11123455677888888888


Q ss_pred             HhcCCeEEEEEec-CChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           85 AKHGVVAETMTEM-GDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        85 ~~~~~~~~~~v~~-g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      .+.|++++..+.. |++.+.|.+++++.++|+||||+++++.+.++++|+++.+++++++|||++++
T Consensus        66 ~~~g~~~~~~~~~~~~~~~~I~~~a~~~~~dlIV~G~~~~~~~~~~~lGs~~~~v~~~~~~pvlvv~  132 (132)
T cd01988          66 ASLGVPVHTIIRIDHDIASGILRTAKERQADLIIMGWHGSTSLRDRLFGGVIDQVLESAPCDVAVVK  132 (132)
T ss_pred             hhcCCceEEEEEecCCHHHHHHHHHHhcCCCEEEEecCCCCCccceecCchHHHHHhcCCCCEEEeC
Confidence            8889998888765 79999999999999999999999999998899999999999999999999985

Na+/H+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na+ /H+ exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiports exchange Na+ for H+ in an electroneutral manner, and this activity is carried out by a family of Na+ /H+ exchangers, or NHEs, which are known to be present in both prokaryotic and eukaryotic cells. These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N-terminus and a large cytoplasmic region at the C-terminus. The transmembrane regions M3-M12 share identity wit h other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the regio

>cd01987 USP_OKCHK USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family

Probab=99.93  E-value=4.3e-25  Score=137.44  Aligned_cols=123  Identities=17%  Similarity=0.201  Sum_probs=103.1

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEIC   84 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   84 (154)
                      +||||+|+++.+..++++|+.+|+..+  ++|+++||.+.....                    ..+..++.++.+.+.+
T Consensus         1 ~Ilv~vd~s~~s~~al~~a~~la~~~~--~~l~ll~v~~~~~~~--------------------~~~~~~~~l~~~~~~~   58 (124)
T cd01987           1 RILVCISGGPNAERLIRRAARLADRLK--APWYVVYVETPRLNR--------------------LSEAERRRLAEALRLA   58 (124)
T ss_pred             CEEEEECCCcchHHHHHHHHHHHHHhC--CCEEEEEEecCcccc--------------------CCHHHHHHHHHHHHHH
Confidence            699999999999999999999999977  899999998764321                    1122345566666666


Q ss_pred             HhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcC-CCcEEEEc
Q 031713           85 AKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNA-KCPVLVVR  150 (154)
Q Consensus        85 ~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~-~~pvliv~  150 (154)
                      ++.++++. .+..|++.+.|.+++++.++|+||||+++++.+.++++||++++|++++ +|||||++
T Consensus        59 ~~~~~~~~-~~~~~~~~~~I~~~~~~~~~dllviG~~~~~~~~~~~~Gs~~~~v~~~a~~~~v~v~~  124 (124)
T cd01987          59 EELGAEVV-TLPGDDVAEAIVEFAREHNVTQIVVGKSRRSRWRELFRGSLVDRLLRRAGNIDVHIVA  124 (124)
T ss_pred             HHcCCEEE-EEeCCcHHHHHHHHHHHcCCCEEEeCCCCCchHHHHhcccHHHHHHHhCCCCeEEEeC
Confidence            66676543 2345689999999999999999999999999999999999999999999 89999985

The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium transport. The USP domain is homologous to the universal stress protein Usp Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity.

>cd00293 USP_Like Usp: Universal stress protein family

Probab=99.91  E-value=1e-22  Score=126.86  Aligned_cols=130  Identities=35%  Similarity=0.495  Sum_probs=112.2

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEIC   84 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   84 (154)
                      +||||+|+++.+..++++|..+|+..+  ++++++|+.+......         .    ...+....+.++.++++...+
T Consensus         1 ~ilv~i~~~~~~~~~l~~a~~~a~~~~--~~i~~l~v~~~~~~~~---------~----~~~~~~~~~~~~~l~~~~~~~   65 (130)
T cd00293           1 RILVAVDGSEESERALRWAARLARRLG--AELVLLHVVDPPPSSA---------A----ELAELLEEEARALLEALREAL   65 (130)
T ss_pred             CEEEEeCCCHHHHHHHHHHHHHHHhcC--CEEEEEEEecCCCCcc---------h----hHHHHHHHHHHHHHHHHHHHH
Confidence            589999999999999999999999977  9999999987754332         0    223344555667778887777


Q ss_pred             HhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEE
Q 031713           85 AKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVV  149 (154)
Q Consensus        85 ~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv  149 (154)
                      ...+++++..+..|++.++|.+++++.++|++|+|+++++.+.+.++|+++.+++++++|||+++
T Consensus        66 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~~dlvvig~~~~~~~~~~~~~~~~~~ll~~~~~pvliv  130 (130)
T cd00293          66 AEAGVKVETVVLEGDPAEAILEAAEELGADLIVMGSRGRSGLRRLLLGSVAERVLRHAPCPVLVV  130 (130)
T ss_pred             hcCCCceEEEEecCCCHHHHHHHHHHcCCCEEEEcCCCCCccceeeeccHHHHHHhCCCCCEEeC
Confidence            67789999999899889999999999999999999999999989999999999999999999985

The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae Usp reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, athough Usp lacks ATP-binding activity.

>PRK11175 universal stress protein UspE; Provisional

Probab=99.90  E-value=1.2e-22  Score=144.19  Aligned_cols=142  Identities=20%  Similarity=0.288  Sum_probs=104.3

Q ss_pred             CCcEEEEEecCCchH-------HHHHHHHHHHcccC-CCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECR-------HYALQWALENLGDA-ISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAA   73 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~-------~~~l~~a~~la~~~-~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   73 (154)
                      .+++||+|+|+++.+       ..++++|..+|+.. +  ++++++||.+........ ...   ........+..++..
T Consensus       151 ~~~~Ilva~D~s~~~~~~~~~~~~al~~a~~la~~~~~--a~l~ll~v~~~~~~~~~~-~~~---~~~~~~~~~~~~~~~  224 (305)
T PRK11175        151 EGGKILVAVNVASEEPYHDALNEKLVEEAIDLAEQLNH--AEVHLVNAYPVTPINIAI-ELP---EFDPSVYNDAIRGQH  224 (305)
T ss_pred             CCCeEEEEeCCCCCccchhHHHHHHHHHHHHHHhhCcC--CceEEEEEecCcchhccc-ccc---ccchhhHHHHHHHHH
Confidence            368999999998753       67999999999987 6  899999998754322100 000   001112222222233


Q ss_pred             HHHHHHHHHHHHhcCCeE-EEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           74 LALLGRAKEICAKHGVVA-ETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        74 ~~~l~~~~~~~~~~~~~~-~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .+.++++   .+..+++. ...+..|++.+.|.+++++.++||||||+++++.+.++++||++++|+++++||||+||+.
T Consensus       225 ~~~l~~~---~~~~~~~~~~~~v~~G~~~~~I~~~a~~~~~DLIVmG~~~~~~~~~~llGS~a~~v~~~~~~pVLvv~~~  301 (305)
T PRK11175        225 LLAMKAL---RQKFGIDEEQTHVEEGLPEEVIPDLAEHLDAELVILGTVGRTGLSAAFLGNTAEHVIDHLNCDLLAIKPD  301 (305)
T ss_pred             HHHHHHH---HHHhCCChhheeeccCCHHHHHHHHHHHhCCCEEEECCCccCCCcceeecchHHHHHhcCCCCEEEEcCC
Confidence            3333333   33446653 4566789999999999999999999999999999999999999999999999999999764

>COG0589 UspA Universal stress protein UspA and related nucleotide-binding proteins [Signal transduction mechanisms]

Probab=99.88  E-value=1.2e-20  Score=121.00  Aligned_cols=148  Identities=32%  Similarity=0.370  Sum_probs=120.7

Q ss_pred             CCCcEEEEEec-CCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAID-ESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGR   79 (154)
Q Consensus         1 m~~~~iLv~vd-~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~   79 (154)
                      +++++||+++| +++.+..+++.+..++...+  +.+.+++|.+...........  .................++.++.
T Consensus         3 ~~~~~il~~~d~~s~~~~~a~~~a~~~~~~~~--~~~~~~~v~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~   78 (154)
T COG0589           3 AMYKKILVAVDVGSEAAEKALEEAVALAKRLG--APLILLVVIDPLEPTALVSVA--LADAPIPLSEEELEEEAEELLAE   78 (154)
T ss_pred             cccceEEEEeCCCCHHHHHHHHHHHHHHHhcC--CeEEEEEEecccccccccccc--cccchhhhhHHHHHHHHHHHHHH
Confidence            46899999999 99999999999999999977  899999998776543210000  00000233344455666778888


Q ss_pred             HHHHHHhcCCe-EEEEEecCCh-hhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           80 AKEICAKHGVV-AETMTEMGDP-KNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        80 ~~~~~~~~~~~-~~~~v~~g~~-~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      +.+.....++. +...+..|++ .+.|..++++.++|+||||+++++.+.++++||++++++++++|||+++|..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~g~~~~~~i~~~a~~~~adliV~G~~g~~~l~~~llGsvs~~v~~~~~~pVlvv~~~  153 (154)
T COG0589          79 AKALAEAAGVPVVETEVVEGSPSAEEILELAEEEDADLIVVGSRGRSGLSRLLLGSVAEKVLRHAPCPVLVVRSE  153 (154)
T ss_pred             HHHHHHHcCCCeeEEEEecCCCcHHHHHHHHHHhCCCEEEECCCCCccccceeeehhHHHHHhcCCCCEEEEccC
Confidence            88888888888 5889999988 7999999999999999999999999999999999999999999999999875

>PRK12652 putative monovalent cation/H+ antiporter subunit E; Reviewed

Probab=99.78  E-value=1.9e-17  Score=118.61  Aligned_cols=107  Identities=21%  Similarity=0.263  Sum_probs=81.0

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      |+|+|||||+|+|+.+.+|+++|+++|+..+.+++|+++||.+......        ..       .......++.++++
T Consensus         3 ~~ykkILVavDGSe~S~~Al~~AielA~~~g~~AeL~lL~Vv~~~~~~~--------~~-------~~~~~~~eelle~~   67 (357)
T PRK12652          3 MAANRLLVPVADSVTVRQTVAYAVESAEEAAETPTVHLVAAASGRAVDP--------EG-------QDELAAAEELLERV   67 (357)
T ss_pred             cccCeEEEEeCCCHHHHHHHHHHHHHHHhcCCCCEEEEEEEecCccccc--------ch-------hHHHHHHHHHHHHH
Confidence            6899999999999999999999999998842128999999988643221        01       11222333444444


Q ss_pred             HHHHHh------cCCeEEEEEec--------CChhhHHHHHHHhcCCCEEEEecCC
Q 031713           81 KEICAK------HGVVAETMTEM--------GDPKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        81 ~~~~~~------~~~~~~~~v~~--------g~~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      .+.+++      .|++++..+..        |+++++|+++|++.++|+||||..-
T Consensus        68 ~~~~~~~l~~~~~gV~ve~~vv~~~~~~~~~G~pae~Iv~~Aee~~aDLIVm~~~~  123 (357)
T PRK12652         68 EVWATEDLGDDASSVTIETALLGTDEYLFGPGDYAEVLIAYAEEHGIDRVVLDPEY  123 (357)
T ss_pred             HHHHHHhhhcccCCCceEEEEEeccccccCCCCHHHHHHHHHHHcCCCEEEECCCC
Confidence            444443      58988888865        8999999999999999999999864

>PRK10490 sensor protein KdpD; Provisional

Probab=99.59  E-value=5.7e-14  Score=112.05  Aligned_cols=124  Identities=11%  Similarity=0.078  Sum_probs=97.4

Q ss_pred             cEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEI   83 (154)
Q Consensus         4 ~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~   83 (154)
                      .+||||+++++.+..++++|.++|..++  ++++++||..+.....                   ..+..+...+. .+.
T Consensus       251 eriLV~v~~~~~~~~lIr~~~rlA~~~~--a~~~~l~V~~~~~~~~-------------------~~~~~~~l~~~-~~l  308 (895)
T PRK10490        251 DAILLCIGHNTGSEKLVRTAARLAARLG--SVWHAVYVETPRLHRL-------------------PEKKRRAILSA-LRL  308 (895)
T ss_pred             CeEEEEECCCcchHHHHHHHHHHHHhcC--CCEEEEEEecCCcCcC-------------------CHHHHHHHHHH-HHH
Confidence            5799999999999999999999999987  9999999987643221                   01112222333 356


Q ss_pred             HHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCC-CcEEEEcCC
Q 031713           84 CAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAK-CPVLVVRKP  152 (154)
Q Consensus        84 ~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~-~pvliv~~~  152 (154)
                      +++.|.++.. +..++++++|+++|++.+++.||||.++++.+  ++.||+++++++.++ ..|.||+..
T Consensus       309 A~~lGa~~~~-~~~~dva~~i~~~A~~~~vt~IViG~s~~~~~--~~~~s~~~~l~r~~~~idi~iv~~~  375 (895)
T PRK10490        309 AQELGAETAT-LSDPAEEKAVLRYAREHNLGKIIIGRRASRRW--WRRESFADRLARLGPDLDLVIVALD  375 (895)
T ss_pred             HHHcCCEEEE-EeCCCHHHHHHHHHHHhCCCEEEECCCCCCCC--ccCCCHHHHHHHhCCCCCEEEEeCC
Confidence            6777877432 33458999999999999999999999887765  557899999999998 999999743

>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]

Probab=99.53  E-value=3.2e-13  Score=103.60  Aligned_cols=126  Identities=17%  Similarity=0.213  Sum_probs=107.8

Q ss_pred             cEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEI   83 (154)
Q Consensus         4 ~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~   83 (154)
                      .+||||++.++.+...+++|.++|..++  ++++++||..+.....                    .+...+.+....+.
T Consensus       249 e~ilvcI~~~~~~e~liR~a~RlA~~~~--a~~~av~v~~~~~~~~--------------------~~~~~~~l~~~~~L  306 (890)
T COG2205         249 ERILVCISGSPGSEKLIRRAARLASRLH--AKWTAVYVETPELHRL--------------------SEKEARRLHENLRL  306 (890)
T ss_pred             ceEEEEECCCCchHHHHHHHHHHHHHhC--CCeEEEEEeccccccc--------------------cHHHHHHHHHHHHH
Confidence            5899999999999999999999999977  9999999988765432                    23345667777777


Q ss_pred             HHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCC-CcEEEEcCC
Q 031713           84 CAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAK-CPVLVVRKP  152 (154)
Q Consensus        84 ~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~-~pvliv~~~  152 (154)
                      +++.|.++.+.. .++.+++|.+||+++++.-||+|.+.++.|.+.|.|++++++++..+ ..|.+|+.+
T Consensus       307 ae~lGae~~~l~-~~dv~~~i~~ya~~~~~TkiViG~~~~~rw~~~~~~~l~~~L~~~~~~idv~ii~~~  375 (890)
T COG2205         307 AEELGAEIVTLY-GGDVAKAIARYAREHNATKIVIGRSRRSRWRRLFKGSLADRLAREAPGIDVHIVALD  375 (890)
T ss_pred             HHHhCCeEEEEe-CCcHHHHHHHHHHHcCCeeEEeCCCcchHHHHHhcccHHHHHHhcCCCceEEEeeCC
Confidence            777787665432 46999999999999999999999999999999999999999999998 999999864

>cd01984 AANH_like Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF)

Probab=98.75  E-value=7.5e-08  Score=55.81  Aligned_cols=84  Identities=14%  Similarity=0.160  Sum_probs=71.5

Q ss_pred             EEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            6 VMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICA   85 (154)
Q Consensus         6 iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   85 (154)
                      |||+++++..|..++.++.+++.. +  .++..+|+.                                           
T Consensus         1 ilv~~sgg~dS~~~l~~~~~~~~~-~--~~~~~~~~~-------------------------------------------   34 (86)
T cd01984           1 ILVALSGGLDSSVLLHLAKRLKSG-G--PEVVALVVV-------------------------------------------   34 (86)
T ss_pred             CEEEeeCCHHHHHHHHHHHHHHhc-C--CCEEEEEeH-------------------------------------------
Confidence            689999999999999999998743 3  688888883                                           


Q ss_pred             hcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCccccccc-chhHHHhhcCCCcEEE
Q 031713           86 KHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLG-SVSNYCVHNAKCPVLV  148 (154)
Q Consensus        86 ~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~g-s~~~~l~~~~~~pvli  148 (154)
                                   ...+.+.+.+++.++|+|+.|++.....+..+.| ++...+++.++|||+.
T Consensus        35 -------------~~~~~~~~~a~~~~~~~Iv~G~~~~d~~~~~~~~~~~~~~~~~~~~~~vl~   85 (86)
T cd01984          35 -------------AFVRILKRLAAEEGADVIILGHNADDVAGRRLGASANVLVVIKGAGIPVLT   85 (86)
T ss_pred             -------------HHHHHHHHHHHHcCCCEEEEcCCchhhhhhccCchhhhhhcccccCCceeC
Confidence                         5666777888889999999999988878877777 8999999999999873

The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide.

>PLN03159 cation/H(+) antiporter 15; Provisional

Probab=98.29  E-value=1.5e-05  Score=64.00  Aligned_cols=144  Identities=11%  Similarity=0.127  Sum_probs=84.9

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHH-HHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDL-LMSIQENQKKAALALLGRAKEI   83 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~   83 (154)
                      |||+|+...++....++.+-........+-.++++|+++...-..+  .+....... .....+......++.++.+...
T Consensus       460 riL~cv~~~~~v~~li~Lle~s~~t~~sp~~vy~lhLveL~~r~~~--~l~~h~~~~~~~~~~~~~~~~~~~i~~af~~~  537 (832)
T PLN03159        460 RMLVCVHTPRNVPTIINLLEASHPTKRSPICIYVLHLVELTGRASA--MLIVHNTRKSGRPALNRTQAQSDHIINAFENY  537 (832)
T ss_pred             eEEEEeccCCcHHHHHHHHHhcCCCCCCCceEEEEEEEeecCCCcc--ceeeeecccccccccccccccccHHHHHHHHH
Confidence            7999999988888888665432222223368999999885432110  000000000 0000000011123444444333


Q ss_pred             HHh-cCCeEEEEEec---CChhhHHHHHHHhcCCCEEEEecCCCCCccc------ccccchhHHHhhcCCCcEEEEc
Q 031713           84 CAK-HGVVAETMTEM---GDPKNVICEAAEKHKIQLLIVGSHSRGPIQR------AFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        84 ~~~-~~~~~~~~v~~---g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~------~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      -+. .++.++.....   .+..+.|++.|++.++++||++.|++....+      ..++.+..++++++||+|-|.=
T Consensus       538 ~~~~~~v~v~~~t~vs~~~~mh~dIc~~A~d~~~slIilpfhk~~~~dg~~~~~~~~~r~~n~~VL~~ApCsVgIlV  614 (832)
T PLN03159        538 EQHAGCVSVQPLTAISPYSTMHEDVCNLAEDKRVSLIIIPFHKQQTVDGGMEATNPAFRGVNQNVLANAPCSVGILV  614 (832)
T ss_pred             HhhcCceEEEEEEEEeCcccHHHHHHHHHHhcCCCEEEECCCCccCCCCCccccCchHHHHHHHHHccCCCCEEEEE
Confidence            322 25665543322   3789999999999999999999986433222      2566788999999999998763

>TIGR02432 lysidine_TilS_N tRNA(Ile)-lysidine synthetase, N-terminal domain

Probab=97.81  E-value=0.00082  Score=44.62  Aligned_cols=93  Identities=15%  Similarity=0.090  Sum_probs=66.3

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEIC   84 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   84 (154)
                      +|+|++++...|..++..+.+++...+  .++.++|+.......                        ..+..+.+...+
T Consensus         1 ~v~va~SGG~DS~~ll~ll~~~~~~~~--~~v~~v~vd~g~~~~------------------------~~~~~~~~~~~~   54 (189)
T TIGR02432         1 RILVAVSGGVDSMALLHLLLKLQPKLK--IRLIAAHVDHGLRPE------------------------SDEEAEFVQQFC   54 (189)
T ss_pred             CEEEEeCCCHHHHHHHHHHHHHHHHcC--CCEEEEEeCCCCChh------------------------HHHHHHHHHHHH
Confidence            589999999999999998888877766  689999997653211                        122345566666


Q ss_pred             HhcCCeEEEEEecC---------Chh--------hHHHHHHHhcCCCEEEEecCCC
Q 031713           85 AKHGVVAETMTEMG---------DPK--------NVICEAAEKHKIQLLIVGSHSR  123 (154)
Q Consensus        85 ~~~~~~~~~~v~~g---------~~~--------~~i~~~a~~~~~dlivlg~~~~  123 (154)
                      +..|+++...-...         +..        ..+.+.+++.+++.|+.|++..
T Consensus        55 ~~~gi~~~~~~~~~~~~~~~~~~~~~~~~r~~R~~~l~~~a~~~g~~~i~~Gh~~~  110 (189)
T TIGR02432        55 KKLNIPLEIKKVDVKALAKGKKKNLEEAAREARYDFFEEIAKKHGADYILTAHHAD  110 (189)
T ss_pred             HHcCCCEEEEEecchhhccccCCCHHHHHHHHHHHHHHHHHHHcCCCEEEEcCccH
Confidence            77788755433321         122        5677889999999999998753

The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This family describes a protein domain found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain archictecture of this protein family is variable; some, including characterized proteins of E. coli and B. subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family ( pfam01171). It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer).

>PF01171 ATP_bind_3: PP-loop family; InterPro: IPR011063 This entry represents the PP-loop motif superfamily [,]

Probab=97.64  E-value=0.003  Score=41.77  Aligned_cols=92  Identities=17%  Similarity=0.111  Sum_probs=60.9

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEIC   84 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   84 (154)
                      +|+|++.+...|..++..+..+....+  .++.++||...-....                        ....+.+.+.+
T Consensus         1 ki~va~SGG~DS~~Ll~~l~~~~~~~~--~~~~~~~vdh~~~~~s------------------------~~~~~~v~~~~   54 (182)
T PF01171_consen    1 KILVAVSGGKDSMALLHLLKELRRRNG--IKLIAVHVDHGLREES------------------------DEEAEFVEEIC   54 (182)
T ss_dssp             EEEEE--SSHHHHHHHHHHHHHHTTTT--TEEEEEEEE-STSCCH------------------------HHHHHHHHHHH
T ss_pred             CEEEEEcCCHHHHHHHHHHHHHHHhcC--CCeEEEEEecCCCccc------------------------chhHHHHHHHH
Confidence            699999999999999999999999876  6999999987654221                        23345667777


Q ss_pred             HhcCCeEEEEEec-----C-Chh--------hHHHHHHHhcCCCEEEEecCC
Q 031713           85 AKHGVVAETMTEM-----G-DPK--------NVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        85 ~~~~~~~~~~v~~-----g-~~~--------~~i~~~a~~~~~dlivlg~~~  122 (154)
                      +..|+++......     + +..        +.+.+.|++.+++.|++|++.
T Consensus        55 ~~~~i~~~~~~~~~~~~~~~~~e~~aR~~Ry~~l~~~a~~~g~~~i~~GHh~  106 (182)
T PF01171_consen   55 EQLGIPLYIVRIDEDRKKGSNIEECARELRYQFLREIAKEEGCNKIALGHHL  106 (182)
T ss_dssp             HHTT-EEEEEE--CHCCTTSTCHHHHHHHHHHHHHHHHHTTT-CEEE---BH
T ss_pred             HhcCCceEEEEeeeeecccCCHHHHHHHHHHHHHHHhhhcccccceeecCcC
Confidence            7888886554433     1 111        355578899999999999874

The PP-loop motif appears to be a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding []. Named PP-motif, since it appears to be a part of a previously uncharacterised ATP pyrophophatase domain. ATP sulfurylases, Escherichia coli NtrL, and Bacillus subtilis OutB consist of this domain alone. In other proteins, the pyrophosphatase domain is associated with amidotransferase domains (type I or type II), a putative citrulline-aspartate ligase domain or a nitrilase/amidase domain.; PDB: 3A2K_A 2E89_B 2E21_D 1WY5_B 1NI5_A.

>cd01992 PP-ATPase N-terminal domain of predicted ATPase of the PP-loop faimly implicated in cell cycle control [Cell division and chromosome partitioning]

Probab=97.43  E-value=0.0053  Score=40.53  Aligned_cols=93  Identities=16%  Similarity=0.125  Sum_probs=65.2

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEIC   84 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   84 (154)
                      +|+|++++...|..++..+.+.....+  .++.++|+.......                        ..+..+.+.+.+
T Consensus         1 ~v~v~~SGG~DS~vl~~l~~~~~~~~~--~~v~~v~id~~~~~~------------------------~~~~~~~~~~~~   54 (185)
T cd01992           1 KILVAVSGGPDSMALLHLLSELKPRLG--LRLVAVHVDHGLRPE------------------------SDEEAAFVADLC   54 (185)
T ss_pred             CEEEEeCCCHHHHHHHHHHHHHHHHcC--CcEEEEEecCCCCch------------------------HHHHHHHHHHHH
Confidence            589999999999999998888776655  689999996653211                        133445566666


Q ss_pred             HhcCCeEEEE--E-ecCChh-----------hHHHHHHHhcCCCEEEEecCCC
Q 031713           85 AKHGVVAETM--T-EMGDPK-----------NVICEAAEKHKIQLLIVGSHSR  123 (154)
Q Consensus        85 ~~~~~~~~~~--v-~~g~~~-----------~~i~~~a~~~~~dlivlg~~~~  123 (154)
                      ...|++....  . ..+...           ..+.+++++.+++.|+.|++..
T Consensus        55 ~~~~i~~~~~~~~~~~~~~~~~~~~~r~~r~~~l~~~a~~~~~~~i~~Gh~~d  107 (185)
T cd01992          55 AKLGIPLYILVVALAPKPGGNLEAAAREARYDFFAEIAKEHGADVLLTAHHAD  107 (185)
T ss_pred             HHcCCcEEEEeeccccCCCCCHHHHHHHHHHHHHHHHHHHcCCCEEEEcCCcH
Confidence            6678876554  1 111111           4577789999999999998753

This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This domain has a strongly conserved motif SGGXD at the N terminus.

>PLN03159 cation/H(+) antiporter 15; Provisional

Probab=97.40  E-value=0.003  Score=51.20  Aligned_cols=115  Identities=16%  Similarity=0.082  Sum_probs=64.4

Q ss_pred             cEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCC-CCch---HHHHHHHHHHHHHHHHHHHH
Q 031713            4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFG-AAPP---DLLMSIQENQKKAALALLGR   79 (154)
Q Consensus         4 ~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~-~~~~---~~~~~~~~~~~~~~~~~l~~   79 (154)
                      .+|.++.-+.+.+..|+.+|.++|++.+  -.++++|..+............ ....   .......+..++.-++.+++
T Consensus       631 ~~v~~~F~GG~DDREALa~a~rma~~p~--v~lTVirf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~D~~~~~e  708 (832)
T PLN03159        631 HHVAVLFFGGPDDREALAYAWRMSEHPG--ITLTVMRFIPGEDAAPTASQPASSPSDPRIPTVETDGKKERQLDEEYINE  708 (832)
T ss_pred             eeEEEEecCCcchHHHHHHHHHHhcCCC--eEEEEEEEEcccccccccccccccccccccccccccchhHHHHHHHHHHH
Confidence            4899999999999999999999999965  8999999987533221000000 0000   00000011122233555666


Q ss_pred             HHHHHHh-cCCeEEEEEe-cC-ChhhHHHHHHHhcCCCEEEEecCC
Q 031713           80 AKEICAK-HGVVAETMTE-MG-DPKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        80 ~~~~~~~-~~~~~~~~v~-~g-~~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      +...... ..+.+.-+++ .| +....|....+  ++||+|+|+++
T Consensus       709 f~~~~~~~~~v~y~E~~V~~~~e~~~~l~~~~~--~ydL~iVGr~~  752 (832)
T PLN03159        709 FRARNAGNESIVYTEKVVSNGEETVAAIRSMDS--AHDLFIVGRGQ  752 (832)
T ss_pred             HHHhcCCCCceEEEEEecCCHHHHHHHHHHhhc--cCcEEEEecCC
Confidence            6655532 2344433333 34 23344444433  69999999753

>PRK12342 hypothetical protein; Provisional

Probab=96.79  E-value=0.024  Score=39.61  Aligned_cols=101  Identities=16%  Similarity=0.106  Sum_probs=64.7

Q ss_pred             cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCe
Q 031713           11 DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVV   90 (154)
Q Consensus        11 d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~   90 (154)
                      ..++++..|++.|+++. ..|  .+++++++=+.....                         ...+.++.    ..|..
T Consensus        32 ~iNp~D~~AlE~AlrLk-~~g--~~Vtvls~Gp~~a~~-------------------------~~l~r~al----amGaD   79 (254)
T PRK12342         32 KISQFDLNAIEAASQLA-TDG--DEIAALTVGGSLLQN-------------------------SKVRKDVL----SRGPH   79 (254)
T ss_pred             cCChhhHHHHHHHHHHh-hcC--CEEEEEEeCCChHhH-------------------------HHHHHHHH----HcCCC
Confidence            45788999999999999 566  899999997663211                         11112222    23554


Q ss_pred             EEEEE----ecC-Ch---hhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEE
Q 031713           91 AETMT----EMG-DP---KNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVL  147 (154)
Q Consensus        91 ~~~~v----~~g-~~---~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvl  147 (154)
                      --+.+    ..| ++   +..|..+++..++|||+.|...-. .   -.|.+.-.+......|.+
T Consensus        80 ~avli~d~~~~g~D~~ata~~La~~i~~~~~DLVl~G~~s~D-~---~tgqvg~~lA~~Lg~P~v  140 (254)
T PRK12342         80 SLYLVQDAQLEHALPLDTAKALAAAIEKIGFDLLLFGEGSGD-L---YAQQVGLLLGELLQLPVI  140 (254)
T ss_pred             EEEEEecCccCCCCHHHHHHHHHHHHHHhCCCEEEEcCCccc-C---CCCCHHHHHHHHhCCCcE
Confidence            32333    234 55   788888999889999999975422 2   234555666666666643

>cd01993 Alpha_ANH_like_II This is a subfamily of Adenine nucleotide alpha hydrolases superfamily

Probab=96.74  E-value=0.053  Score=35.64  Aligned_cols=94  Identities=14%  Similarity=0.069  Sum_probs=59.4

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEIC   84 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   84 (154)
                      +|+|++.+...|..++..+.++......+.++.++|+........                        ....+.+.+.+
T Consensus         1 ~v~v~~SGG~DS~~ll~~l~~~~~~~~~~~~~~~~~~d~~~~~~~------------------------~~~~~~~~~~~   56 (185)
T cd01993           1 RILVALSGGKDSLVLLHVLKKLQRRYPYGFELEALTVDEGIPGYR------------------------DESLEVVERLA   56 (185)
T ss_pred             CEEEEeCCCHHHHHHHHHHHHHHhhcCCCeEEEEEEEECCCCCCc------------------------HHHHHHHHHHH
Confidence            589999999999988888777665441125889999876532211                        11223334445


Q ss_pred             HhcCCeEEEEEec-------------C---------ChhhHHHHHHHhcCCCEEEEecCC
Q 031713           85 AKHGVVAETMTEM-------------G---------DPKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        85 ~~~~~~~~~~v~~-------------g---------~~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      ...|+++...-..             +         -....+.+.+++.+++.|+.|++.
T Consensus        57 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~r~~~l~~~a~~~g~~~l~~Gh~~  116 (185)
T cd01993          57 EELGIELEIVSFKEEYTDDIEVKKRGGKSPCSLCGVLRRGLLNKIAKELGADKLATGHNL  116 (185)
T ss_pred             HHcCCceEEEehhhhcchhhhhhccCCCCCCCccHHHHHHHHHHHHHHcCCCEEEEcCCh
Confidence            5556664433221             0         012456678999999999999874

Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily of proteins is predicted to bind ATP. This domainhas a strongly conserved motif SGGKD at the N terminus.

>PRK10696 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional

Probab=96.52  E-value=0.13  Score=36.09  Aligned_cols=93  Identities=15%  Similarity=0.128  Sum_probs=59.7

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKE   82 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~   82 (154)
                      -.+|+|++.+...|..++..+..+.+..+..-++..+|+........                        ++   .+.+
T Consensus        29 ~~kilVa~SGG~DS~~LL~ll~~l~~~~~~~~~l~av~vd~g~~~~~------------------------~~---~~~~   81 (258)
T PRK10696         29 GDRVMVCLSGGKDSYTLLDILLNLQKRAPINFELVAVNLDQKQPGFP------------------------EH---VLPE   81 (258)
T ss_pred             CCEEEEEecCCHHHHHHHHHHHHHHHhCCCCeEEEEEEecCCCCCCC------------------------HH---HHHH
Confidence            35899999999999988888777665432224788888765421110                        01   1345


Q ss_pred             HHHhcCCeEEEEEec-----------CC---------hhhHHHHHHHhcCCCEEEEecCC
Q 031713           83 ICAKHGVVAETMTEM-----------GD---------PKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        83 ~~~~~~~~~~~~v~~-----------g~---------~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      .|++.|+++...-..           +.         ....+.+++++.++|.|++|++.
T Consensus        82 ~~~~lgI~~~v~~~~~~~~~~~~~~~~~~~c~~c~~~R~~~l~~~a~~~g~~~Ia~GH~~  141 (258)
T PRK10696         82 YLESLGVPYHIEEQDTYSIVKEKIPEGKTTCSLCSRLRRGILYRTARELGATKIALGHHR  141 (258)
T ss_pred             HHHHhCCCEEEEEecchhhhhhhhccCCChhHHHHHHHHHHHHHHHHHcCCCEEEEcCch
Confidence            566678775443211           11         12455678999999999999875

>COG0037 MesJ tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]

Probab=96.28  E-value=0.13  Score=36.56  Aligned_cols=93  Identities=14%  Similarity=0.139  Sum_probs=59.6

Q ss_pred             cEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEI   83 (154)
Q Consensus         4 ~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~   83 (154)
                      .+|+|++.+...|..++..+..+...    .++.++||........                        ....+.+...
T Consensus        22 ~~ilVavSGGkDS~~ll~~L~~l~~~----~~~~a~~Vd~~~~~~~------------------------~~~~~~~~~~   73 (298)
T COG0037          22 YKILVAVSGGKDSLALLHLLKELGRR----IEVEAVHVDHGLRGYS------------------------DQEAELVEKL   73 (298)
T ss_pred             CeEEEEeCCChHHHHHHHHHHHhccC----ceEEEEEecCCCCCcc------------------------chHHHHHHHH
Confidence            68999999999999888777666554    3899999987754321                        2223344444


Q ss_pred             HHhcCCeEEE---EEecCC---------------hhhHHHHHHHhcCCCEEEEecCCCC
Q 031713           84 CAKHGVVAET---MTEMGD---------------PKNVICEAAEKHKIQLLIVGSHSRG  124 (154)
Q Consensus        84 ~~~~~~~~~~---~v~~g~---------------~~~~i~~~a~~~~~dlivlg~~~~~  124 (154)
                      +...+++...   ....+.               ....+.+.+++.++|.|+.|++...
T Consensus        74 ~~~~~~~~~v~~~~~~~~~~~~~~~~~c~~c~~~R~~~l~~~a~~~g~~~i~tgH~~dD  132 (298)
T COG0037          74 CEKLGIPLIVERVTDDLGRETLDGKSICAACRRLRRGLLYKIAKELGADKIATGHHLDD  132 (298)
T ss_pred             HHHhCCceEEEEEEeeccccccCCCChhHHHHHHHHHHHHHHHHHcCCCeEEeccCcHH
Confidence            4444543211   111111               1234667799999999999987633

>PRK03359 putative electron transfer flavoprotein FixA; Reviewed

Probab=96.20  E-value=0.08  Score=37.08  Aligned_cols=106  Identities=12%  Similarity=0.027  Sum_probs=63.9

Q ss_pred             cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCe
Q 031713           11 DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVV   90 (154)
Q Consensus        11 d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~   90 (154)
                      -.++++..|++.|+++..+.+. .+++++++=+.....                         ...+.++..+-.+.++-
T Consensus        33 ~iN~~D~~AlE~Alrlke~~~g-~~Vtvvs~Gp~~a~~-------------------------~~~lr~aLAmGaD~avl   86 (256)
T PRK03359         33 KISQYDLNAIEAACQLKQQAAE-AQVTALSVGGKALTN-------------------------AKGRKDVLSRGPDELIV   86 (256)
T ss_pred             ccChhhHHHHHHHHHHhhhcCC-CEEEEEEECCcchhh-------------------------HHHHHHHHHcCCCEEEE
Confidence            3578899999999999997521 699999997764221                         12223222222222222


Q ss_pred             EEEEEecC-C---hhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcE
Q 031713           91 AETMTEMG-D---PKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPV  146 (154)
Q Consensus        91 ~~~~v~~g-~---~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pv  146 (154)
                      +.-....| +   .+..|..++++.++|||+.|......    -.|.+.-.+......|.
T Consensus        87 i~d~~~~g~D~~~tA~~La~ai~~~~~DLVl~G~~s~D~----~tgqvg~~lAe~Lg~P~  142 (256)
T PRK03359         87 VIDDQFEQALPQQTASALAAAAQKAGFDLILCGDGSSDL----YAQQVGLLVGEILNIPA  142 (256)
T ss_pred             EecCcccCcCHHHHHHHHHHHHHHhCCCEEEEcCccccC----CCCcHHHHHHHHhCCCc
Confidence            32222223 3   47778888998899999999764222    23445555666666553

>TIGR00591 phr2 photolyase PhrII

Probab=95.91  E-value=0.22  Score=37.84  Aligned_cols=91  Identities=14%  Similarity=0.046  Sum_probs=66.5

Q ss_pred             cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCe
Q 031713           11 DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVV   90 (154)
Q Consensus        11 d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~   90 (154)
                      |..-....+|..|++.|...+  .+|..+++.++.....                .........+-|..+.+.+++.|+.
T Consensus        32 DLRl~DN~aL~~A~~~a~~~~--~~vl~vyi~dp~~~~~----------------~~~r~~Fl~esL~~L~~~L~~~g~~   93 (454)
T TIGR00591        32 DQRVQDNWALIAAQTLALKKK--LPLHVCFCLVDFFLAA----------------TRRHYFFMLGGLDEVANECERLIIP   93 (454)
T ss_pred             chhccCCHHHHHHHHHHHHcC--CCEEEEEEeCCCcccc----------------cHHHHHHHHHHHHHHHHHHHHcCCc
Confidence            344456778888888766544  5899999987643211                1244555666777788888777766


Q ss_pred             EEEEEecCChhhHHHHHHHhcCCCEEEEecC
Q 031713           91 AETMTEMGDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        91 ~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      .  .+..|++.+.|.+++++.+++.|+....
T Consensus        94 L--~v~~g~~~~~l~~l~~~~~i~~V~~~~~  122 (454)
T TIGR00591        94 F--HLLDGPPKELLPYFVDLHAAAAVVTDFS  122 (454)
T ss_pred             e--EEeecChHHHHHHHHHHcCCCEEEEecc
Confidence            5  4568999999999999999999999875

All proteins in this family for which functions are known are DNA-photolyases used for the direct repair of UV irradiation induced DNA damage. Some repair 6-4 photoproducts while others repair cyclobutane pyrimidine dimers. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF01012 ETF: Electron transfer flavoprotein domain; InterPro: IPR014730 Electron transfer flavoproteins (ETFs) serve as specific electron acceptors for primary dehydrogenases, transferring the electrons to terminal respiratory systems

Probab=95.55  E-value=0.19  Score=32.55  Aligned_cols=87  Identities=16%  Similarity=0.106  Sum_probs=58.0

Q ss_pred             EEEEEecCC-----chHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDES-----ECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGR   79 (154)
Q Consensus         5 ~iLv~vd~~-----~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~   79 (154)
                      +|||-++..     +.+..++..|.++++..|  .+++++.+=+....                             .+.
T Consensus         1 ~ilv~~e~~~~~l~~~~~e~l~~A~~La~~~g--~~v~av~~G~~~~~-----------------------------~~~   49 (164)
T PF01012_consen    1 NILVFAEHRDGRLNPVSLEALEAARRLAEALG--GEVTAVVLGPAEEA-----------------------------AEA   49 (164)
T ss_dssp             EEEEEE-EETCEE-HHHHHHHHHHHHHHHCTT--SEEEEEEEETCCCH-----------------------------HHH
T ss_pred             CEEEEEECCCCccCHHHHHHHHHHHHHHhhcC--CeEEEEEEecchhh-----------------------------HHH
Confidence            456666544     789999999999999987  89999987632211                             234


Q ss_pred             HHHHHHhcCCeEEEEEecC--------ChhhHHHHHHHhcCCCEEEEecCC
Q 031713           80 AKEICAKHGVVAETMTEMG--------DPKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~g--------~~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      +.+.+..+|.+--+.+...        ...+.|.+.+++.++|+|++|+..
T Consensus        50 l~~~l~~~G~d~v~~~~~~~~~~~~~~~~a~~l~~~~~~~~~~lVl~~~t~  100 (164)
T PF01012_consen   50 LRKALAKYGADKVYHIDDPALAEYDPEAYADALAELIKEEGPDLVLFGSTS  100 (164)
T ss_dssp             HHHHHHSTTESEEEEEE-GGGTTC-HHHHHHHHHHHHHHHT-SEEEEESSH
T ss_pred             HhhhhhhcCCcEEEEecCccccccCHHHHHHHHHHHHHhcCCCEEEEcCcC
Confidence            4445555777633433221        145678888999999999999753

They can be functionally classified into constitutive, "housekeeping" ETFs, mainly involved in the oxidation of fatty acids (Group I), and ETFs produced by some prokaryotes under specific growth conditions, receiving electrons only from the oxidation of specific substrates (Group II) []. ETFs are heterodimeric proteins composed of an alpha and beta subunit, and contain an FAD cofactor and AMP [, , , , ]. ETF consists of three domains: domains I and II are formed by the N- and C-terminal portions of the alpha subunit, respectively, while domain III is formed by the beta subunit. Domains I and III share an almost identical alpha-beta-alpha sandwich fold, while domain II forms an alpha-beta-alpha sandwich similar to that of bacterial flavodoxins. FAD is bound in a cleft between domains II and III, while domain III binds the AMP molecule. Interactions between domains I and III stabilise the protein, forming a shallow bowl where domain II resides. This entry represents the N-terminal domain of both the alpha and beta subunits from Group I and Group II ETFs.; PDB: 1EFP_B 3FET_B 3IH5_B 2A1T_S 1EFV_B 1T9G_S 2A1U_B 1O96_E 1O94_C 3CLU_C ....

>COG0041 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]

Probab=95.33  E-value=0.31  Score=31.19  Aligned_cols=69  Identities=20%  Similarity=0.270  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHhcCCeEEEEEecC-ChhhHHHHH---HHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           76 LLGRAKEICAKHGVVAETMTEMG-DPKNVICEA---AEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        76 ~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~---a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      .++++.+.+++.|++++.++..- ..-+.+.+|   +++.+++.||-|+.+...+.+        -+...++.||+=||-
T Consensus        17 ~mk~Aa~~L~~fgi~ye~~VvSAHRTPe~m~~ya~~a~~~g~~viIAgAGgAAHLPG--------mvAa~T~lPViGVPv   88 (162)
T COG0041          17 TMKKAAEILEEFGVPYEVRVVSAHRTPEKMFEYAEEAEERGVKVIIAGAGGAAHLPG--------MVAAKTPLPVIGVPV   88 (162)
T ss_pred             HHHHHHHHHHHcCCCeEEEEEeccCCHHHHHHHHHHHHHCCCeEEEecCcchhhcch--------hhhhcCCCCeEeccC
Confidence            34566677778899999999885 445555554   567888899999887554443        355677899999886


Q ss_pred             C
Q 031713          152 P  152 (154)
Q Consensus       152 ~  152 (154)
                      +
T Consensus        89 ~   89 (162)
T COG0041          89 Q   89 (162)
T ss_pred             c
Confidence            5

>COG2086 FixA Electron transfer flavoprotein, beta subunit [Energy production and conversion]

Probab=95.33  E-value=0.31  Score=34.24  Aligned_cols=102  Identities=16%  Similarity=0.142  Sum_probs=66.4

Q ss_pred             EecCCchHHHHHHHHHHHcc-cCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 031713            9 AIDESECRHYALQWALENLG-DAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKH   87 (154)
Q Consensus         9 ~vd~~~~~~~~l~~a~~la~-~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   87 (154)
                      +...++.+..|++.|+++.. ..+  .+++++++=++...                           ..+..    +-..
T Consensus        32 ~~~in~~D~~AvEeAlrLke~~~~--~eV~vlt~Gp~~a~---------------------------~~lr~----aLAm   78 (260)
T COG2086          32 PLSINPFDLNAVEEALRLKEKGYG--GEVTVLTMGPPQAE---------------------------EALRE----ALAM   78 (260)
T ss_pred             CcccChhhHHHHHHHHHhhccCCC--ceEEEEEecchhhH---------------------------HHHHH----HHhc
Confidence            44557889999999999999 566  89999999665321                           11222    3334


Q ss_pred             CCeEEEEEe----cC-C---hhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEE
Q 031713           88 GVVAETMTE----MG-D---PKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVL  147 (154)
Q Consensus        88 ~~~~~~~v~----~g-~---~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvl  147 (154)
                      |.+--..+.    .+ +   .+..|...++..+.|||++|...- ..   -.|.+...+......|.+
T Consensus        79 GaDraili~d~~~~~~d~~~ta~~Laa~~~~~~~~LVl~G~qa~-D~---~t~qvg~~lAe~Lg~P~~  142 (260)
T COG2086          79 GADRAILITDRAFAGADPLATAKALAAAVKKIGPDLVLTGKQAI-DG---DTGQVGPLLAELLGWPQV  142 (260)
T ss_pred             CCCeEEEEecccccCccHHHHHHHHHHHHHhcCCCEEEEecccc-cC---CccchHHHHHHHhCCcee
Confidence            666333333    23 2   577888889999999999997642 22   234555556666666644

>PRK10660 tilS tRNA(Ile)-lysidine synthetase; Provisional

Probab=95.31  E-value=0.41  Score=36.29  Aligned_cols=66  Identities=11%  Similarity=0.053  Sum_probs=46.9

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHc-ccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENL-GDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la-~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      -++|+|++.+...|..++.....+. ...+  -+++++||.......                        .++..+.+.
T Consensus        15 ~~~ilvavSGG~DS~~Ll~~l~~~~~~~~~--~~l~a~hvnhglr~~------------------------s~~~~~~~~   68 (436)
T PRK10660         15 SRQILVAFSGGLDSTVLLHLLVQWRTENPG--VTLRAIHVHHGLSPN------------------------ADSWVKHCE   68 (436)
T ss_pred             CCeEEEEecCCHHHHHHHHHHHHHHHhcCC--CeEEEEEEeCCCCcc------------------------hHHHHHHHH
Confidence            3789999999999998888776654 2234  689999997664321                        233445667


Q ss_pred             HHHHhcCCeEEEE
Q 031713           82 EICAKHGVVAETM   94 (154)
Q Consensus        82 ~~~~~~~~~~~~~   94 (154)
                      +.|++.|+++...
T Consensus        69 ~~~~~l~i~~~~~   81 (436)
T PRK10660         69 QVCQQWQVPLVVE   81 (436)
T ss_pred             HHHHHcCCcEEEE
Confidence            7788888886553

>TIGR01162 purE phosphoribosylaminoimidazole carboxylase, PurE protein

Probab=95.09  E-value=0.43  Score=30.78  Aligned_cols=69  Identities=20%  Similarity=0.302  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHH---HhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           76 LLGRAKEICAKHGVVAETMTEMG-DPKNVICEAA---EKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        76 ~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a---~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      ..+++...+++.|++++..+..- ...+.+.+++   ++.+++.+|.++...+.+.        .-+...++.||+-||.
T Consensus        13 ~~~~a~~~L~~~gi~~dv~V~SaHRtp~~~~~~~~~a~~~g~~viIa~AG~aa~Lp--------gvva~~t~~PVIgvP~   84 (156)
T TIGR01162        13 TMKKAADILEEFGIPYELRVVSAHRTPELMLEYAKEAEERGIKVIIAGAGGAAHLP--------GMVAALTPLPVIGVPV   84 (156)
T ss_pred             HHHHHHHHHHHcCCCeEEEEECcccCHHHHHHHHHHHHHCCCeEEEEeCCccchhH--------HHHHhccCCCEEEecC
Confidence            45667777788899999998775 4445555554   5567899888886544333        4466778899999886


Q ss_pred             C
Q 031713          152 P  152 (154)
Q Consensus       152 ~  152 (154)
                      +
T Consensus        85 ~   85 (156)
T TIGR01162        85 P   85 (156)
T ss_pred             C
Confidence            4

Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, an N5-CAIR mutase.

>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=94.97  E-value=0.68  Score=31.10  Aligned_cols=112  Identities=14%  Similarity=0.109  Sum_probs=63.4

Q ss_pred             EEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            6 VMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICA   85 (154)
Q Consensus         6 iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   85 (154)
                      ++|.-.+.-=...+...|.++... +  .++.++.........                            .++++..++
T Consensus         5 ~lvGptGvGKTTt~aKLAa~~~~~-~--~~v~lis~D~~R~ga----------------------------~eQL~~~a~   53 (196)
T PF00448_consen    5 ALVGPTGVGKTTTIAKLAARLKLK-G--KKVALISADTYRIGA----------------------------VEQLKTYAE   53 (196)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHT-T----EEEEEESTSSTHH----------------------------HHHHHHHHH
T ss_pred             EEECCCCCchHhHHHHHHHHHhhc-c--ccceeecCCCCCccH----------------------------HHHHHHHHH
Confidence            344455555566677788877776 5  788888864443222                            345555555


Q ss_pred             hcCCeEEEEEecCChhhHH---HHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhc-CCCcEEEE
Q 031713           86 KHGVVAETMTEMGDPKNVI---CEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHN-AKCPVLVV  149 (154)
Q Consensus        86 ~~~~~~~~~v~~g~~~~~i---~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~-~~~pvliv  149 (154)
                      ..|+++...-...++.+.+   ++..+..++|+|++.+.|++........... .++.. .+..+++|
T Consensus        54 ~l~vp~~~~~~~~~~~~~~~~~l~~~~~~~~D~vlIDT~Gr~~~d~~~~~el~-~~~~~~~~~~~~LV  120 (196)
T PF00448_consen   54 ILGVPFYVARTESDPAEIAREALEKFRKKGYDLVLIDTAGRSPRDEELLEELK-KLLEALNPDEVHLV  120 (196)
T ss_dssp             HHTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE-SSSSTHHHHHHHHH-HHHHHHSSSEEEEE
T ss_pred             HhccccchhhcchhhHHHHHHHHHHHhhcCCCEEEEecCCcchhhHHHHHHHH-HHhhhcCCccceEE
Confidence            5576654422223455544   3445567899999999998877654444443 33333 34445444

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 ....

>PF00875 DNA_photolyase: DNA photolyase from Prosite

Probab=94.87  E-value=0.35  Score=31.36  Aligned_cols=115  Identities=17%  Similarity=0.102  Sum_probs=68.2

Q ss_pred             CchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCeEE
Q 031713           13 SECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAE   92 (154)
Q Consensus        13 ~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~   92 (154)
                      .-....+|..|+    ..+  .++..+++.++.....        .     ...........+-+..+.+.+++.|+.  
T Consensus        10 Rl~DN~aL~~A~----~~~--~~v~~vfv~d~~~~~~--------~-----~~~~~r~~Fl~~sL~~L~~~L~~~g~~--   68 (165)
T PF00875_consen   10 RLHDNPALHAAA----QNG--DPVLPVFVFDPEEFHP--------Y-----RIGPRRRRFLLESLADLQESLRKLGIP--   68 (165)
T ss_dssp             SSTT-HHHHHHH----HTT--SEEEEEEEE-HHGGTT--------C-----SSCHHHHHHHHHHHHHHHHHHHHTTS---
T ss_pred             chhhhHHHHHHH----HcC--CCeEEEEEeccccccc--------c-----cCcchHHHHHHHHHHHHHHHHHhcCcc--
Confidence            334556777663    223  5899999988862110        0     001234445566677777777777755  


Q ss_pred             EEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           93 TMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        93 ~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      ..+..|++.+.+.+++++.+++.|+....- +...... .....+.+...++++..+.
T Consensus        69 L~v~~g~~~~~l~~l~~~~~~~~V~~~~~~-~~~~~~r-d~~v~~~l~~~~i~~~~~~  124 (165)
T PF00875_consen   69 LLVLRGDPEEVLPELAKEYGATAVYFNEEY-TPYERRR-DERVRKALKKHGIKVHTFD  124 (165)
T ss_dssp             EEEEESSHHHHHHHHHHHHTESEEEEE----SHHHHHH-HHHHHHHHHHTTSEEEEE-
T ss_pred             eEEEecchHHHHHHHHHhcCcCeeEecccc-CHHHHHH-HHHHHHHHHhcceEEEEEC
Confidence            567789999999999999999999988653 3333222 2233445555567766554

; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....

>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]

Probab=94.79  E-value=0.5  Score=31.60  Aligned_cols=82  Identities=17%  Similarity=0.172  Sum_probs=56.9

Q ss_pred             cEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEI   83 (154)
Q Consensus         4 ~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~   83 (154)
                      ++|.|-+.++-+...++--|+. ....+  +++.++-......                                ...++
T Consensus         1 ~ki~VlaSG~GSNlqaiida~~-~~~~~--a~i~~Visd~~~A--------------------------------~~ler   45 (200)
T COG0299           1 KKIAVLASGNGSNLQAIIDAIK-GGKLD--AEIVAVISDKADA--------------------------------YALER   45 (200)
T ss_pred             CeEEEEEeCCcccHHHHHHHHh-cCCCC--cEEEEEEeCCCCC--------------------------------HHHHH
Confidence            4788999999998888888886 33323  6777665544432                                22344


Q ss_pred             HHhcCCeEEEEEecCC-----hhhHHHHHHHhcCCCEEEEec
Q 031713           84 CAKHGVVAETMTEMGD-----PKNVICEAAEKHKIQLLIVGS  120 (154)
Q Consensus        84 ~~~~~~~~~~~v~~g~-----~~~~i~~~a~~~~~dlivlg~  120 (154)
                      +++.|++....-..+-     ..++|.+..++.++|+||+.-
T Consensus        46 A~~~gIpt~~~~~k~~~~r~~~d~~l~~~l~~~~~dlvvLAG   87 (200)
T COG0299          46 AAKAGIPTVVLDRKEFPSREAFDRALVEALDEYGPDLVVLAG   87 (200)
T ss_pred             HHHcCCCEEEeccccCCCHHHHHHHHHHHHHhcCCCEEEEcc
Confidence            4567888654443332     678899999999999999964

>PF00731 AIRC: AIR carboxylase; InterPro: IPR000031 Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE

Probab=94.68  E-value=0.52  Score=30.25  Aligned_cols=70  Identities=11%  Similarity=0.121  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHHhc---CCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           75 ALLGRAKEICAKHGVVAETMTEMG-DPKNVICEAAEKH---KIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        75 ~~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~~~---~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      ...+++...+++.|+.++..+..- ...+.+.+++++.   +++.+|.++...+.+        ..-+...++.||+-||
T Consensus        14 ~~~~~a~~~L~~~gi~~~~~V~saHR~p~~l~~~~~~~~~~~~~viIa~AG~~a~L--------pgvva~~t~~PVIgvP   85 (150)
T PF00731_consen   14 PIAEEAAKTLEEFGIPYEVRVASAHRTPERLLEFVKEYEARGADVIIAVAGMSAAL--------PGVVASLTTLPVIGVP   85 (150)
T ss_dssp             HHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHTTTTTESEEEEEEESS--H--------HHHHHHHSSS-EEEEE
T ss_pred             HHHHHHHHHHHHcCCCEEEEEEeccCCHHHHHHHHHHhccCCCEEEEEECCCcccc--------hhhheeccCCCEEEee
Confidence            345677777888899999988775 4566777776654   578888887644333        3446667789999998


Q ss_pred             CC
Q 031713          151 KP  152 (154)
Q Consensus       151 ~~  152 (154)
                      ..
T Consensus        86 ~~   87 (150)
T PF00731_consen   86 VS   87 (150)
T ss_dssp             E-
T ss_pred             cC
Confidence            54

PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain []. The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme [].; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process; PDB: 3TRH_O 2YWX_A 2NSL_A 1D7A_A 2NSJ_A 1QCZ_A 2ATE_A 2NSH_A 3RG8_C 3RGG_D ....

>PRK05253 sulfate adenylyltransferase subunit 2; Provisional

Probab=94.50  E-value=1.1  Score=32.37  Aligned_cols=93  Identities=10%  Similarity=0.039  Sum_probs=59.2

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKE   82 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~   82 (154)
                      +.+++|++.+...|..++..+.......+  .++.++|+.......                          +.++-..+
T Consensus        27 f~~~vv~~SGGKDS~VLL~La~ka~~~~~--~~~~vl~iDTG~~Fp--------------------------Et~ef~d~   78 (301)
T PRK05253         27 FENPVMLYSIGKDSSVMLHLARKAFYPGK--LPFPLLHVDTGWKFP--------------------------EMIEFRDR   78 (301)
T ss_pred             CCCEEEEecCCHHHHHHHHHHHHhhcccC--CCeeEEEEeCCCCCH--------------------------HHHHHHHH
Confidence            57899999999999988888876554323  478899997654211                          11112223


Q ss_pred             HHHhcCCeEEEEEe-----cC-Ch-------------hhHHHHHHHhcCCCEEEEecCCC
Q 031713           83 ICAKHGVVAETMTE-----MG-DP-------------KNVICEAAEKHKIQLLIVGSHSR  123 (154)
Q Consensus        83 ~~~~~~~~~~~~v~-----~g-~~-------------~~~i~~~a~~~~~dlivlg~~~~  123 (154)
                      .++..|+++.+...     .| .+             ...+.++++++++|.++.|.+..
T Consensus        79 ~a~~~gl~l~v~~~~~~i~~g~~~~~~~~~~cC~~lK~~pL~~al~e~g~da~~~G~RrD  138 (301)
T PRK05253         79 RAKELGLELIVHSNPEGIARGINPFRHGSAKHTNAMKTEGLKQALEKYGFDAAFGGARRD  138 (301)
T ss_pred             HHHHhCCCEEEEeChHHHhcCCCCCCCChHHHHHHHHHHHHHHHHHHcCCCEEEeccccc
Confidence            34455776544321     12 11             14566788889999999999753

>PRK13820 argininosuccinate synthase; Provisional

Probab=94.39  E-value=1.5  Score=32.81  Aligned_cols=38  Identities=18%  Similarity=0.038  Sum_probs=29.1

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCC-eEEEEEeccC
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKS-DLIIFTARPT   44 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~-~l~~l~v~~~   44 (154)
                      ++++|+|++.+.-.|..++.++.+   .+|  . +++.+|+...
T Consensus         1 ~~~kVvvA~SGGvDSsvll~lL~e---~~g--~~~Viav~vd~g   39 (394)
T PRK13820          1 MMKKVVLAYSGGLDTSVCVPLLKE---KYG--YDEVITVTVDVG   39 (394)
T ss_pred             CCCeEEEEEeCcHHHHHHHHHHHH---hcC--CCEEEEEEEECC
Confidence            468999999999888888877643   234  4 8999999654

>PRK10867 signal recognition particle protein; Provisional

Probab=93.47  E-value=2.6  Score=32.04  Aligned_cols=91  Identities=15%  Similarity=0.112  Sum_probs=52.0

Q ss_pred             EecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 031713            9 AIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHG   88 (154)
Q Consensus         9 ~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~   88 (154)
                      ...++-=+..+...|..+++..|  .++.++........                            ..+++....+..|
T Consensus       107 G~~GsGKTTtaakLA~~l~~~~G--~kV~lV~~D~~R~a----------------------------a~eQL~~~a~~~g  156 (433)
T PRK10867        107 GLQGAGKTTTAGKLAKYLKKKKK--KKVLLVAADVYRPA----------------------------AIEQLKTLGEQIG  156 (433)
T ss_pred             CCCCCcHHHHHHHHHHHHHHhcC--CcEEEEEccccchH----------------------------HHHHHHHHHhhcC
Confidence            33444446667777777766534  57777765443211                            1233344445567


Q ss_pred             CeEEEEEecCChhh---HHHHHHHhcCCCEEEEecCCCCCcccc
Q 031713           89 VVAETMTEMGDPKN---VICEAAEKHKIQLLIVGSHSRGPIQRA  129 (154)
Q Consensus        89 ~~~~~~v~~g~~~~---~i~~~a~~~~~dlivlg~~~~~~~~~~  129 (154)
                      +++...-...+|..   ..++.++..++|+||+.+.|+......
T Consensus       157 v~v~~~~~~~dp~~i~~~a~~~a~~~~~DvVIIDTaGrl~~d~~  200 (433)
T PRK10867        157 VPVFPSGDGQDPVDIAKAALEEAKENGYDVVIVDTAGRLHIDEE  200 (433)
T ss_pred             CeEEecCCCCCHHHHHHHHHHHHHhcCCCEEEEeCCCCcccCHH
Confidence            77544322234433   334566777899999999987765443

>TIGR00268 conserved hypothetical protein TIGR00268

Probab=93.44  E-value=1.9  Score=30.19  Aligned_cols=89  Identities=17%  Similarity=0.142  Sum_probs=54.4

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      .+++++|++++.-.|..++..+.+.    |  .++..+|+......                          ....+.+.
T Consensus        11 ~~~~vlVa~SGGvDSs~ll~la~~~----g--~~v~av~~~~~~~~--------------------------~~e~~~a~   58 (252)
T TIGR00268        11 EFKKVLIAYSGGVDSSLLAAVCSDA----G--TEVLAITVVSPSIS--------------------------PRELEDAI   58 (252)
T ss_pred             hcCCEEEEecCcHHHHHHHHHHHHh----C--CCEEEEEecCCCCC--------------------------HHHHHHHH
Confidence            3578999999998888777766553    5  57888988643211                          01122334


Q ss_pred             HHHHhcCCeEEEEEec------------------CChhhHHHHHHHhcCCCEEEEecCC
Q 031713           82 EICAKHGVVAETMTEM------------------GDPKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        82 ~~~~~~~~~~~~~v~~------------------g~~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      +.++..|++....-..                  ......+.+.|++.+++.|+.|++.
T Consensus        59 ~~a~~lgi~~~ii~~~~~~~~~~~n~~~~c~~ck~~~~~~l~~~A~~~g~~~I~~G~n~  117 (252)
T TIGR00268        59 IIAKEIGVNHEFVKIDKMINPFRANVEERCYFCKKMVLSILVKEAEKRGYDVVVDGTNA  117 (252)
T ss_pred             HHHHHcCCCEEEEEcHHHHHHHHhCCCcccchhhHHHHHHHHHHHHHcCCCEEEECCCC
Confidence            4444556554332211                  0123345678889999999999753

The N-terminal region of the model shows similarity to Argininosuccinate synthase proteins using PSI-blast and using the recognize protein identification server.

>TIGR02765 crypto_DASH cryptochrome, DASH family

Probab=93.02  E-value=2.8  Score=31.71  Aligned_cols=97  Identities=16%  Similarity=0.091  Sum_probs=61.7

Q ss_pred             cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCe
Q 031713           11 DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVV   90 (154)
Q Consensus        11 d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~   90 (154)
                      |..-....+|..|++.    +  .+|..++|.++......  ... ..    ............+-++++.+.+++.|++
T Consensus        10 DLRl~DN~aL~~A~~~----~--~~vl~vfi~dp~~~~~~--~~~-~~----~~~~~~r~~Fl~esL~~L~~~L~~~g~~   76 (429)
T TIGR02765        10 DLRVHDNPALYKASSS----S--DTLIPLYCFDPRQFKLT--HFF-GF----PKTGPARGKFLLESLKDLRTSLRKLGSD   76 (429)
T ss_pred             CCccccHHHHHHHHhc----C--CeEEEEEEECchHhccc--ccc-cc----CCCCHHHHHHHHHHHHHHHHHHHHcCCC
Confidence            4444566778777642    2  37888999886432200  000 00    0011233444556677777778777766


Q ss_pred             EEEEEecCChhhHHHHHHHhcCCCEEEEecCC
Q 031713           91 AETMTEMGDPKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        91 ~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      .  .+..|++.+.|.+.+++.+++.|+.....
T Consensus        77 L--~v~~G~~~~vl~~L~~~~~~~~V~~~~~~  106 (429)
T TIGR02765        77 L--LVRSGKPEDVLPELIKELGVRTVFLHQEV  106 (429)
T ss_pred             e--EEEeCCHHHHHHHHHHHhCCCEEEEeccC
Confidence            5  45679999999999999999999998753

Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.

>TIGR00930 2a30 K-Cl cotransporter

Probab=92.58  E-value=5.4  Score=33.61  Aligned_cols=95  Identities=17%  Similarity=0.082  Sum_probs=65.3

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEIC   84 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   84 (154)
                      ++||.+........+++++-.+.+..|   -..+.||...+...                    ..++.+...+++.+.+
T Consensus       577 qiLvl~~~p~~~~~Ll~f~~~l~~~~g---l~i~~~v~~~~~~~--------------------~~~~~~~~~~~~~~~~  633 (953)
T TIGR00930       577 QCLVLTGPPVCRPALLDFASQFTKGKG---LMICGSVIQGPRLE--------------------CVKEAQAAEAKIQTWL  633 (953)
T ss_pred             eEEEEeCCCcCcHHHHHHHHHhccCCc---EEEEEEEecCchhh--------------------hHHHHHHHHHHHHHHH
Confidence            689999988889999999999997654   78888998764221                    1222233344455556


Q ss_pred             HhcCCeEEEEEecC-ChhhHHHHHHHh-----cCCCEEEEecCC
Q 031713           85 AKHGVVAETMTEMG-DPKNVICEAAEK-----HKIQLLIVGSHS  122 (154)
Q Consensus        85 ~~~~~~~~~~v~~g-~~~~~i~~~a~~-----~~~dlivlg~~~  122 (154)
                      +..+++.-..+..+ +..+.+....+.     .+++.+++|.+.
T Consensus       634 ~~~~~~~f~~~~~~~~~~~g~~~l~q~~GlG~l~PNtv~lg~~~  677 (953)
T TIGR00930       634 EKNKVKAFYAVVVADDLREGVRHLIQASGLGRMKPNTLVMGYKK  677 (953)
T ss_pred             HHhCCCeEEEEecCCCHHHHHHHHHHhcCCCCCCCCEEEecCcc
Confidence            66777744444444 777777777664     468899999864

>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type

Probab=92.47  E-value=1.4  Score=33.84  Aligned_cols=90  Identities=11%  Similarity=0.101  Sum_probs=59.8

Q ss_pred             cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCe
Q 031713           11 DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVV   90 (154)
Q Consensus        11 d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~   90 (154)
                      |..-....||..|+.    .+  .+|.++++.++......       .      .........-+-+.++.+.+++.|++
T Consensus        10 DLRl~DN~AL~~A~~----~~--~~vl~vfi~dp~~~~~~-------~------~~~~r~~Fl~esL~~L~~~L~~~G~~   70 (471)
T TIGR03556        10 DLRLSDNIGLAAARQ----QS--AKVVGLFCLDPNILQAD-------D------MAPARVAYLIGCLQELQQRYQQAGSQ   70 (471)
T ss_pred             CCCcchHHHHHHHHh----cC--CCEEEEEEEchhhhccc-------c------CCHHHHHHHHHHHHHHHHHHHHCCCC
Confidence            334456677877764    23  47999999876432110       0      00122344455666777777777766


Q ss_pred             EEEEEecCChhhHHHHHHHhcCCCEEEEecC
Q 031713           91 AETMTEMGDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        91 ~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      .  .+..|++.+.|.+.+++.+++.|+....
T Consensus        71 L--~v~~G~p~~vl~~l~~~~~~~~V~~~~~   99 (471)
T TIGR03556        71 L--LILQGDPVQLIPQLAQQLGAKAVYWNLD   99 (471)
T ss_pred             e--EEEECCHHHHHHHHHHHcCCCEEEEecc
Confidence            5  5668999999999999999999998765

This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.

>PRK07313 phosphopantothenoylcysteine decarboxylase; Validated

Probab=92.00  E-value=1.4  Score=29.32  Aligned_cols=35  Identities=11%  Similarity=0.066  Sum_probs=27.8

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEE
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFT   40 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~   40 (154)
                      +++|++++.++..+-++.++.-.+.+. |  .++.++-
T Consensus         1 ~k~Ill~vtGsiaa~~~~~li~~L~~~-g--~~V~vv~   35 (182)
T PRK07313          1 MKNILLAVSGSIAAYKAADLTSQLTKR-G--YQVTVLM   35 (182)
T ss_pred             CCEEEEEEeChHHHHHHHHHHHHHHHC-C--CEEEEEE
Confidence            589999999999999999888877653 5  5766553

>PF02601 Exonuc_VII_L: Exonuclease VII, large subunit; InterPro: IPR020579 Exonuclease VII 3

Probab=91.46  E-value=0.79  Score=33.14  Aligned_cols=54  Identities=17%  Similarity=0.257  Sum_probs=33.2

Q ss_pred             EEecC-ChhhHHHHHHHhc-------CCCEEEEecCCCCCcccc-cccc-hhHHHhhcCCCcEEE
Q 031713           94 MTEMG-DPKNVICEAAEKH-------KIQLLIVGSHSRGPIQRA-FLGS-VSNYCVHNAKCPVLV  148 (154)
Q Consensus        94 ~v~~g-~~~~~i~~~a~~~-------~~dlivlg~~~~~~~~~~-~~gs-~~~~l~~~~~~pvli  148 (154)
                      ..+.| .....|++..+..       .+|+||+++.| +..+.+ .|.+ ..-+-+..+++||+.
T Consensus        49 ~~vQG~~A~~~I~~al~~~~~~~~~~~~Dviii~RGG-Gs~eDL~~FN~e~varai~~~~~Pvis  112 (319)
T PF02601_consen   49 ASVQGEGAAASIVSALRKANEMGQADDFDVIIIIRGG-GSIEDLWAFNDEEVARAIAASPIPVIS  112 (319)
T ss_pred             ccccccchHHHHHHHHHHHHhccccccccEEEEecCC-CChHHhcccChHHHHHHHHhCCCCEEE
Confidence            33446 5677777654432       48999999765 445552 2222 334566788999875

1.11.6 from EC is composed of two nonidentical subunits; one large subunit and 4 small ones []. Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. The large subunit also contains the OB-fold domains (IPR004365 from INTERPRO) that bind to nucleic acids at the N terminus. This entry represents Exonuclease VII, large subunit, C-terminal. ; GO: 0008855 exodeoxyribonuclease VII activity

>PRK14665 mnmA tRNA-specific 2-thiouridylase MnmA; Provisional

Probab=90.97  E-value=5.1  Score=29.72  Aligned_cols=35  Identities=20%  Similarity=0.141  Sum_probs=25.5

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEecc
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARP   43 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~   43 (154)
                      -++|+|++++.-.|..++..+.    ..|  .++..+|+..
T Consensus         5 ~~kVlValSGGVDSsvaa~LL~----~~G--~~V~~v~~~~   39 (360)
T PRK14665          5 NKRVLLGMSGGTDSSVAAMLLL----EAG--YEVTGVTFRF   39 (360)
T ss_pred             CCEEEEEEcCCHHHHHHHHHHH----HcC--CeEEEEEEec
Confidence            4689999999988876665443    335  5888888853

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=90.96  E-value=5.7  Score=30.21  Aligned_cols=96  Identities=19%  Similarity=0.165  Sum_probs=63.9

Q ss_pred             EEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            6 VMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICA   85 (154)
Q Consensus         6 iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   85 (154)
                      .+|.+.++--...+-..|.++-+ .|  .++-++...--.+                            ...+++.....
T Consensus       104 mmvGLQGsGKTTt~~KLA~~lkk-~~--~kvllVaaD~~Rp----------------------------AA~eQL~~La~  152 (451)
T COG0541         104 LMVGLQGSGKTTTAGKLAKYLKK-KG--KKVLLVAADTYRP----------------------------AAIEQLKQLAE  152 (451)
T ss_pred             EEEeccCCChHhHHHHHHHHHHH-cC--CceEEEecccCCh----------------------------HHHHHHHHHHH
Confidence            45667777666667777777777 55  4666665533322                            22456667777


Q ss_pred             hcCCeEEEEEecC-Chh---hHHHHHHHhcCCCEEEEecCCCCCcccccccc
Q 031713           86 KHGVVAETMTEMG-DPK---NVICEAAEKHKIQLLIVGSHSRGPIQRAFLGS  133 (154)
Q Consensus        86 ~~~~~~~~~v~~g-~~~---~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs  133 (154)
                      +.++++-.. ..+ +|.   +.=++.+++..+|++|+.+-||-....-+...
T Consensus       153 q~~v~~f~~-~~~~~Pv~Iak~al~~ak~~~~DvvIvDTAGRl~ide~Lm~E  203 (451)
T COG0541         153 QVGVPFFGS-GTEKDPVEIAKAALEKAKEEGYDVVIVDTAGRLHIDEELMDE  203 (451)
T ss_pred             HcCCceecC-CCCCCHHHHHHHHHHHHHHcCCCEEEEeCCCcccccHHHHHH
Confidence            778887665 333 444   55567889999999999999988777655443

>COG1597 LCB5 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]

Probab=90.09  E-value=3.8  Score=29.52  Aligned_cols=75  Identities=16%  Similarity=0.126  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHHHHHhcCCeEEEEEecCC-hhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           72 AALALLGRAKEICAKHGVVAETMTEMGD-PKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        72 ~~~~~l~~~~~~~~~~~~~~~~~v~~g~-~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      ...+.+.++.+.++++|......+.+.. .+..+++.+...++|.||.+.. .+.     ++.+++-+...-..|+-++|
T Consensus        17 ~~~~~~~~~~~~l~~~g~~~~~~~t~~~g~a~~~a~~a~~~~~D~via~GG-DGT-----v~evingl~~~~~~~LgilP   90 (301)
T COG1597          17 KAKKLLREVEELLEEAGHELSVRVTEEAGDAIEIAREAAVEGYDTVIAAGG-DGT-----VNEVANGLAGTDDPPLGILP   90 (301)
T ss_pred             chhhHHHHHHHHHHhcCCeEEEEEeecCccHHHHHHHHHhcCCCEEEEecC-cch-----HHHHHHHHhcCCCCceEEec
Confidence            4567778888888889999888887765 7777888777779999999853 332     23354544443333377777


Q ss_pred             CC
Q 031713          151 KP  152 (154)
Q Consensus       151 ~~  152 (154)
                      ..
T Consensus        91 ~G   92 (301)
T COG1597          91 GG   92 (301)
T ss_pred             CC
Confidence            54

>cd01985 ETF The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases

Probab=89.54  E-value=4.3  Score=26.66  Aligned_cols=85  Identities=19%  Similarity=0.185  Sum_probs=51.4

Q ss_pred             EEEEEec---------CCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAID---------ESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALA   75 (154)
Q Consensus         5 ~iLv~vd---------~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   75 (154)
                      +|||.++         .++.+..++..|.+++. .+  .++.++.+=+...                             
T Consensus         1 ~ilV~~e~~~~~~~~~l~~~~~e~l~~A~~l~~-~~--~~v~~v~~G~~~~-----------------------------   48 (181)
T cd01985           1 KILVLVEHVPDTAELVLNPLDLEAVEAALRLKE-YG--GEVTALVIGPPAA-----------------------------   48 (181)
T ss_pred             CEEEEEEEEcCCCccccCHhhHHHHHHHHHHhh-cC--CeEEEEEECChHH-----------------------------
Confidence            4666666         56777889999999877 44  5776666532210                             


Q ss_pred             HHHHHHHHHHhcCCeEEEEEec----C-C---hhhHHHHHHHhcCCCEEEEecCCC
Q 031713           76 LLGRAKEICAKHGVVAETMTEM----G-D---PKNVICEAAEKHKIQLLIVGSHSR  123 (154)
Q Consensus        76 ~l~~~~~~~~~~~~~~~~~v~~----g-~---~~~~i~~~a~~~~~dlivlg~~~~  123 (154)
                        +.....+..+|..--..+..    + +   ..+.|.+.+++.++|+|++|+...
T Consensus        49 --~~~~~~~~~~Gad~v~~~~~~~~~~~~~~~~a~~l~~~i~~~~p~~Vl~g~t~~  102 (181)
T cd01985          49 --EVALREALAMGADKVLLVEDPALAGYDPEATAKALAALIKKEKPDLILAGATSI  102 (181)
T ss_pred             --HHHHHHHHHhCCCEEEEEecCcccCCChHHHHHHHHHHHHHhCCCEEEECCccc
Confidence              01111222356653333321    1 1   257788888888999999998754

ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an alpha and a beta subunit which binds one molecule of FAD per dimer . A similar system also exists in some bacteria. The homologous pair of proteins (FixA/FixB) are essential for nitrogen fixation. The alpha subunit of ETF is structurally related to the bacterial nitrogen fixation protein fixB which could play a role in a redox process and feed electrons to ferredoxin. The beta subunit protein is distantly related to and forms a heterodimer with the alpha subunit.

>PRK05579 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated

Probab=89.28  E-value=4.7  Score=30.36  Aligned_cols=36  Identities=14%  Similarity=0.120  Sum_probs=28.3

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEE
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFT   40 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~   40 (154)
                      ..++|++++.++..+-.+.+..-.+-+ .|  .++.++-
T Consensus         5 ~~k~IllgvTGsiaa~k~~~lv~~L~~-~g--~~V~vv~   40 (399)
T PRK05579          5 AGKRIVLGVSGGIAAYKALELVRRLRK-AG--ADVRVVM   40 (399)
T ss_pred             CCCeEEEEEeCHHHHHHHHHHHHHHHh-CC--CEEEEEE
Confidence            568999999999999999988877755 45  6766553

>PRK08091 ribulose-phosphate 3-epimerase; Validated

Probab=89.20  E-value=5.6  Score=27.50  Aligned_cols=46  Identities=13%  Similarity=0.107  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecC
Q 031713           75 ALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        75 ~~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      +...++.+...+.+.++...+ .|.....-+..+.+.++|.+|+|+.
T Consensus       164 ~KI~~lr~~~~~~~~~~~IeV-DGGI~~~ti~~l~~aGaD~~V~GSa  209 (228)
T PRK08091        164 DRVIQVENRLGNRRVEKLISI-DGSMTLELASYLKQHQIDWVVSGSA  209 (228)
T ss_pred             HHHHHHHHHHHhcCCCceEEE-ECCCCHHHHHHHHHCCCCEEEEChh
Confidence            334455555556677666555 4555555666777789999999964

>COG1646 Predicted phosphate-binding enzymes, TIM-barrel fold [General function prediction only]

Probab=88.58  E-value=5.2  Score=27.69  Aligned_cols=53  Identities=15%  Similarity=0.263  Sum_probs=38.3

Q ss_pred             ChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCCC
Q 031713           99 DPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPV  153 (154)
Q Consensus        99 ~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~~  153 (154)
                      +....|.+.+.+.+.|.|++|-..  ....--.-.+.+.+-.+...||++.|...
T Consensus        28 ~~~~ei~~~~~~~GTDaImIGGS~--gvt~~~~~~~v~~ik~~~~lPvilfP~~~   80 (240)
T COG1646          28 EEADEIAEAAAEAGTDAIMIGGSD--GVTEENVDNVVEAIKERTDLPVILFPGSP   80 (240)
T ss_pred             cccHHHHHHHHHcCCCEEEECCcc--cccHHHHHHHHHHHHhhcCCCEEEecCCh
Confidence            456788899999999999999653  22222233455666668889999998764

>cd01995 ExsB ExsB is a transcription regulator related protein

Probab=88.45  E-value=5  Score=25.96  Aligned_cols=85  Identities=14%  Similarity=0.076  Sum_probs=47.7

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEIC   84 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   84 (154)
                      +++|.+.+...|..++..+.+    .+  .++..+|+.......                   ...    +..+.+.+  
T Consensus         1 kvlv~~SGG~DS~~~~~~~~~----~~--~~v~~~~~~~~~~~~-------------------~~~----~~~~~~~~--   49 (169)
T cd01995           1 KAVVLLSGGLDSTTCLAWAKK----EG--YEVHALSFDYGQRHA-------------------KEE----EAAKLIAE--   49 (169)
T ss_pred             CEEEEecCcHHHHHHHHHHHH----cC--CcEEEEEEECCCCCh-------------------hHH----HHHHHHHH--
Confidence            588999998888877766543    24  478888886532110                   000    11122222  


Q ss_pred             HhcCCeEEEEEecCC-hhhHHHHHHHhcCCCEEEEecCC
Q 031713           85 AKHGVVAETMTEMGD-PKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        85 ~~~~~~~~~~v~~g~-~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                       ..|...... .... ....+..++++.+++.|++|.+.
T Consensus        50 -~~g~~~~~~-~~~~~~~~~l~~~a~~~g~~~i~~G~~~   86 (169)
T cd01995          50 -KLGPSTYVP-ARNLIFLSIAAAYAEALGAEAIIIGVNA   86 (169)
T ss_pred             -HHCCCEEEe-CcCHHHHHHHHHHHHHCCCCEEEEeecc
Confidence             222111111 1111 23456677899999999999875

It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown

>TIGR00959 ffh signal recognition particle protein

Probab=88.38  E-value=9.5  Score=29.08  Aligned_cols=92  Identities=15%  Similarity=0.106  Sum_probs=50.8

Q ss_pred             EEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 031713            7 MVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAK   86 (154)
Q Consensus         7 Lv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   86 (154)
                      ++...++-=+..+...|..+....|  .++.++........                            ..+++......
T Consensus       104 ~vG~~GsGKTTtaakLA~~l~~~~g--~kV~lV~~D~~R~~----------------------------a~~QL~~~a~~  153 (428)
T TIGR00959       104 MVGLQGSGKTTTCGKLAYYLKKKQG--KKVLLVACDLYRPA----------------------------AIEQLKVLGQQ  153 (428)
T ss_pred             EECCCCCcHHHHHHHHHHHHHHhCC--CeEEEEeccccchH----------------------------HHHHHHHHHHh
Confidence            3333444445666777776654444  46777755443211                            12234444455


Q ss_pred             cCCeEEEEEecCChhh---HHHHHHHhcCCCEEEEecCCCCCccc
Q 031713           87 HGVVAETMTEMGDPKN---VICEAAEKHKIQLLIVGSHSRGPIQR  128 (154)
Q Consensus        87 ~~~~~~~~v~~g~~~~---~i~~~a~~~~~dlivlg~~~~~~~~~  128 (154)
                      .++++.......+|.+   ..++.+...++|+||+.+.|+.....
T Consensus       154 ~gvp~~~~~~~~~P~~i~~~al~~~~~~~~DvVIIDTaGr~~~d~  198 (428)
T TIGR00959       154 VGVPVFALGKGQSPVEIARRALEYAKENGFDVVIVDTAGRLQIDE  198 (428)
T ss_pred             cCCceEecCCCCCHHHHHHHHHHHHHhcCCCEEEEeCCCccccCH
Confidence            5776544322224433   33445666789999999998766543

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.

>PRK10674 deoxyribodipyrimidine photolyase; Provisional

Probab=88.35  E-value=8.9  Score=29.55  Aligned_cols=93  Identities=12%  Similarity=0.059  Sum_probs=60.9

Q ss_pred             cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCe
Q 031713           11 DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVV   90 (154)
Q Consensus        11 d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~   90 (154)
                      |..-....+|..|++.+.     .+|..++|.++......             ..........-+-+.++.+.+++.|++
T Consensus        11 DLRl~DN~aL~~A~~~~~-----~~vlpvyv~dp~~~~~~-------------~~~~~r~~Fl~esL~~L~~~L~~~g~~   72 (472)
T PRK10674         11 DLRLHDNLALAAACRDPS-----ARVLALFIATPAQWAAH-------------DMAPRQAAFINAQLNALQIALAEKGIP   72 (472)
T ss_pred             CCCcchHHHHHHHHhCCC-----CCEEEEEEECchhhccC-------------CCCHHHHHHHHHHHHHHHHHHHHcCCc
Confidence            444556778877764332     26899999887432110             011233445556677777888887877


Q ss_pred             EEEEEe--cCChhhHHHHHHHhcCCCEEEEecC
Q 031713           91 AETMTE--MGDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        91 ~~~~v~--~g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      ......  .|++.+.+.+.+++.+++-|+....
T Consensus        73 L~v~~g~~~g~~~~vl~~l~~~~~i~~v~~~~~  105 (472)
T PRK10674         73 LLFHEVDDFAASVEWLKQFCQQHQVTHLFYNYQ  105 (472)
T ss_pred             eEEEecCCcCCHHHHHHHHHHHcCCCEEEEecc
Confidence            644332  3689999999999999999998764

>PF04459 DUF512: Protein of unknown function (DUF512); InterPro: IPR007549 This is a domain of uncharacterised prokaryotic proteins

Probab=88.26  E-value=6.2  Score=26.80  Aligned_cols=82  Identities=20%  Similarity=0.097  Sum_probs=52.4

Q ss_pred             HHHHHHHHHHHHH-hcCCeEEEEEecCC------------hhhHHHHHHHh-cCCCEEEEecCCCCCccc-ccccchhHH
Q 031713           73 ALALLGRAKEICA-KHGVVAETMTEMGD------------PKNVICEAAEK-HKIQLLIVGSHSRGPIQR-AFLGSVSNY  137 (154)
Q Consensus        73 ~~~~l~~~~~~~~-~~~~~~~~~v~~g~------------~~~~i~~~a~~-~~~dlivlg~~~~~~~~~-~~~gs~~~~  137 (154)
                      +...++.+.+.++ ..|.++++..+..+            ..+-|++..+. ..-|.|++...-...-.. ++-+-+.+.
T Consensus       108 a~~~l~~~~~~l~~~~~~~v~V~~V~N~fFG~~ItVaGLLTg~Dii~~L~~~~~~d~lllP~~ml~~~~~~fLDD~t~~e  187 (204)
T PF04459_consen  108 AYPFLKPLVEKLNRIPGLEVEVVPVKNRFFGGTITVAGLLTGQDIIEQLKGKELGDLLLLPDVMLRHGEGVFLDDMTLEE  187 (204)
T ss_pred             HHHHHHHHHHHHhccCCCeEEEEEeecCCCCCCeEEeeCccHHHHHHHhCcCCCCCEEEECHHHhcCCCCccCCCCcHHH
Confidence            4556666666662 23666655544332            35556555554 334899998754433333 344778889


Q ss_pred             HhhcCCCcEEEEcCCCC
Q 031713          138 CVHNAKCPVLVVRKPVE  154 (154)
Q Consensus       138 l~~~~~~pvliv~~~~~  154 (154)
                      +.+..++||.+|+.+.|
T Consensus       188 l~~~lg~~v~vv~~~~~  204 (204)
T PF04459_consen  188 LEERLGVPVIVVRGPGE  204 (204)
T ss_pred             HHHHhCCcEEEeCCCCC
Confidence            99999999999987654

It is often found C-terminal to the radical SAM domain (IPR007197 from INTERPRO).

>COG1184 GCD2 Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]

Probab=88.18  E-value=7.9  Score=27.95  Aligned_cols=65  Identities=12%  Similarity=0.309  Sum_probs=41.9

Q ss_pred             HHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCC---CCCcccccccc-hhHHHhhcCCCcEEEEcC
Q 031713           79 RAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHS---RGPIQRAFLGS-VSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        79 ~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~---~~~~~~~~~gs-~~~~l~~~~~~pvliv~~  151 (154)
                      .+.+.+.+.|+++...+     ..++..+.+  ++|.+++|+..   .+.+-+. .|. ...-..++...|++++-.
T Consensus       161 ~~ak~L~~~gI~~~~I~-----Dsa~~~~~~--~vd~VivGad~I~~nG~lvnk-iGT~~lA~~A~e~~~Pf~v~ae  229 (301)
T COG1184         161 IMAKELRQSGIPVTVIV-----DSAVGAFMS--RVDKVLVGADAILANGALVNK-IGTSPLALAARELRVPFYVVAE  229 (301)
T ss_pred             HHHHHHHHcCCceEEEe-----chHHHHHHH--hCCEEEECccceecCCcEEec-cchHHHHHHHHHhCCCEEEEee
Confidence            44556667887776654     345566677  89999999975   2223222 333 334456888899999843

>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed

Probab=88.14  E-value=2.1  Score=32.46  Aligned_cols=52  Identities=19%  Similarity=0.326  Sum_probs=32.8

Q ss_pred             ecC-ChhhHHHHHHHhcC---CCEEEEecCCCCCcccc-cccc-hhHHHhhcCCCcEEE
Q 031713           96 EMG-DPKNVICEAAEKHK---IQLLIVGSHSRGPIQRA-FLGS-VSNYCVHNAKCPVLV  148 (154)
Q Consensus        96 ~~g-~~~~~i~~~a~~~~---~dlivlg~~~~~~~~~~-~~gs-~~~~l~~~~~~pvli  148 (154)
                      +.| .....|++..+..+   +|+||+++.| +..+.+ .|.. ..-+-+..|++||+.
T Consensus       172 vQG~~A~~~i~~al~~~~~~~~Dviii~RGG-GS~eDL~~Fn~e~v~~ai~~~~~Pvis  229 (438)
T PRK00286        172 VQGEGAAASIVAAIERANARGEDVLIVARGG-GSLEDLWAFNDEAVARAIAASRIPVIS  229 (438)
T ss_pred             CcCccHHHHHHHHHHHhcCCCCCEEEEecCC-CCHHHhhccCcHHHHHHHHcCCCCEEE
Confidence            446 57777777554433   5999999765 445553 2222 334566788999875

>PRK13982 bifunctional SbtC-like/phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Provisional

Probab=88.05  E-value=7.5  Score=30.02  Aligned_cols=35  Identities=14%  Similarity=-0.016  Sum_probs=28.5

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEE
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFT   40 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~   40 (154)
                      -++|++.+.++-.+-++.+..-.+.+ .|  .+++++-
T Consensus        70 ~k~IllgVtGsIAayka~~lvr~L~k-~G--~~V~Vvm  104 (475)
T PRK13982         70 SKRVTLIIGGGIAAYKALDLIRRLKE-RG--AHVRCVL  104 (475)
T ss_pred             CCEEEEEEccHHHHHHHHHHHHHHHh-Cc--CEEEEEE
Confidence            58999999999999999998888765 35  6766654

>TIGR02039 CysD sulfate adenylyltransferase, small subunit

Probab=87.95  E-value=8.2  Score=27.83  Aligned_cols=41  Identities=5%  Similarity=-0.078  Sum_probs=31.0

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCC
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTE   45 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~   45 (154)
                      +.+.++++.+...|..++..+.+.....+  .++.++|+....
T Consensus        19 f~~~vv~~SGGKDS~VlLhLa~kaf~~~~--~p~~vl~IDTG~   59 (294)
T TIGR02039        19 FERPVMLYSIGKDSSVLLHLARKAFYPGP--LPFPLLHVDTGW   59 (294)
T ss_pred             cCCcEEEEecChHHHHHHHHHHHHhcccC--CCeEEEEEecCC
Confidence            45678889999999989988876655433  578999996654

In Escherichia coli, ATP sulfurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulfur-containing amino acids. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules.

>PRK11914 diacylglycerol kinase; Reviewed

Probab=87.86  E-value=5.6  Score=28.56  Aligned_cols=71  Identities=15%  Similarity=0.129  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           75 ALLGRAKEICAKHGVVAETMTEMG-DPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        75 ~~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      +..+++.+.+++.+.++....... .-+..+.+.+.+.++|+||+.- |.+.+.     .+++.+. ..+.|+-++|..
T Consensus        26 ~~~~~~~~~l~~~g~~~~~~~t~~~~~~~~~a~~~~~~~~d~vvv~G-GDGTi~-----evv~~l~-~~~~~lgiiP~G   97 (306)
T PRK11914         26 HAAERAIARLHHRGVDVVEIVGTDAHDARHLVAAALAKGTDALVVVG-GDGVIS-----NALQVLA-GTDIPLGIIPAG   97 (306)
T ss_pred             HHHHHHHHHHHHcCCeEEEEEeCCHHHHHHHHHHHHhcCCCEEEEEC-CchHHH-----HHhHHhc-cCCCcEEEEeCC
Confidence            334455566667787766555443 4566666666667889877653 334333     2344443 456889998864

>KOG1650 consensus Predicted K+/H+-antiporter [Inorganic ion transport and metabolism]

Probab=87.43  E-value=6.3  Score=32.40  Aligned_cols=41  Identities=22%  Similarity=0.098  Sum_probs=33.3

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCch
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFI   47 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~   47 (154)
                      +|-+..-+.+.+..|+.++.+++++..  ..+++++..+....
T Consensus       616 ~v~~lF~GG~DDrEALa~~~rm~~~~~--v~lTVirf~~~~~~  656 (769)
T KOG1650|consen  616 KVVVLFLGGKDDREALALAKRMAENPR--VTLTVIRFFPDESK  656 (769)
T ss_pred             EEEEEecCChhhHHHHHHHHHHhhCCc--eEEEEEEeeccchh
Confidence            566667777778889999999999865  89999999887643

>PLN02948 phosphoribosylaminoimidazole carboxylase

Probab=87.26  E-value=5.5  Score=31.57  Aligned_cols=70  Identities=19%  Similarity=0.231  Sum_probs=49.5

Q ss_pred             HHHHHHHHHHHhcCCeEEEEEecC-ChhhHH---HHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           75 ALLGRAKEICAKHGVVAETMTEMG-DPKNVI---CEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        75 ~~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i---~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      ..++++...+++.|++++..+..- ...+.+   ++.+++.+++.||.++...+.+.        .-+...+.+||+-||
T Consensus       424 ~~~~~~~~~l~~~g~~~~~~v~sahr~~~~~~~~~~~~~~~~~~v~i~~ag~~~~l~--------~~~a~~t~~pvi~vp  495 (577)
T PLN02948        424 PTMKDAAEILDSFGVPYEVTIVSAHRTPERMFSYARSAHSRGLQVIIAGAGGAAHLP--------GMVASMTPLPVIGVP  495 (577)
T ss_pred             HHHHHHHHHHHHcCCCeEEEEECCccCHHHHHHHHHHHHHCCCCEEEEEcCccccch--------HHHhhccCCCEEEcC
Confidence            456777888888999999888774 333333   44556678999888886544443        445667789999988


Q ss_pred             CC
Q 031713          151 KP  152 (154)
Q Consensus       151 ~~  152 (154)
                      .+
T Consensus       496 ~~  497 (577)
T PLN02948        496 VK  497 (577)
T ss_pred             CC
Confidence            64

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=87.05  E-value=12  Score=28.63  Aligned_cols=54  Identities=17%  Similarity=0.186  Sum_probs=31.9

Q ss_pred             HHHHHHHhcCCeEEEEEecCChhh---HHHHHHHhcCCCEEEEecCCCCCccccccc
Q 031713           79 RAKEICAKHGVVAETMTEMGDPKN---VICEAAEKHKIQLLIVGSHSRGPIQRAFLG  132 (154)
Q Consensus        79 ~~~~~~~~~~~~~~~~v~~g~~~~---~i~~~a~~~~~dlivlg~~~~~~~~~~~~g  132 (154)
                      ++....+..++++.......+|..   .-++.++..++|+|++.+.|+......+..
T Consensus       146 QLk~~a~~~~vp~~~~~~~~dp~~i~~~~l~~~~~~~~DvViIDTaGr~~~d~~lm~  202 (429)
T TIGR01425       146 QLKQNATKARIPFYGSYTESDPVKIASEGVEKFKKENFDIIIVDTSGRHKQEDSLFE  202 (429)
T ss_pred             HHHHHhhccCCeEEeecCCCCHHHHHHHHHHHHHhCCCCEEEEECCCCCcchHHHHH
Confidence            333444445666644333335543   234455667899999999988766554443

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.

>COG0655 WrbA Multimeric flavodoxin WrbA [General function prediction only]

Probab=86.93  E-value=7.4  Score=26.26  Aligned_cols=43  Identities=12%  Similarity=-0.004  Sum_probs=33.3

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCC
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTE   45 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~   45 (154)
                      |++-.|++......+....++.+++-++..|  +++.++++.+..
T Consensus         1 mki~~I~gs~r~~G~t~~l~~~~~~g~~~~G--~E~~~i~v~~~~   43 (207)
T COG0655           1 MKILGINGSPRSNGNTAKLAEAVLEGAEEAG--AEVEIIRLPEKN   43 (207)
T ss_pred             CeeeEEEecCCCCCcHHHHHHHHHHHHHHcC--CEEEEEEecCCC
Confidence            4555566666556778888999999999877  899999998764

>cd01714 ETF_beta The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases

Probab=86.91  E-value=7.4  Score=26.25  Aligned_cols=83  Identities=16%  Similarity=0.174  Sum_probs=49.5

Q ss_pred             EEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 031713            8 VAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKH   87 (154)
Q Consensus         8 v~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   87 (154)
                      ++.-.++++..++..+..+++..+  .++.++.+-....                               +.....+..+
T Consensus        29 ~~~vi~e~~~~~l~ea~~la~~~g--~~v~av~~G~~~~-------------------------------~~~~~~l~~~   75 (202)
T cd01714          29 VPLIINPYDEYAVEEALRLKEKYG--GEVTVVSMGPPQA-------------------------------EEALREALAM   75 (202)
T ss_pred             CCccCChHhHHHHHHHHHhhhhcC--CEEEEEEECCHHH-------------------------------HHHHHHHHHc
Confidence            344456778888999999988765  6777766532200                               1111112345


Q ss_pred             CCeEEEEEecC--------ChhhHHHHHHHhcCCCEEEEecCCC
Q 031713           88 GVVAETMTEMG--------DPKNVICEAAEKHKIQLLIVGSHSR  123 (154)
Q Consensus        88 ~~~~~~~v~~g--------~~~~~i~~~a~~~~~dlivlg~~~~  123 (154)
                      |..--+.+...        ...+.|.+.+++.++|+|++|+...
T Consensus        76 G~d~V~~~~~~~~~~~~~e~~a~al~~~i~~~~p~lVL~~~t~~  119 (202)
T cd01714          76 GADRAILVSDRAFAGADTLATAKALAAAIKKIGVDLILTGKQSI  119 (202)
T ss_pred             CCCEEEEEecccccCCChHHHHHHHHHHHHHhCCCEEEEcCCcc
Confidence            66422322211        1245677778888899999998754

ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an alpha and a beta subunit which binds one molecule of FAD per dimer . A similar system also exists in some bacteria. The homologous pair of proteins (FixA/FixB) are essential for nitrogen fixation. The beta subunit protein is distantly related to and forms a heterodimer with the alpha subunit.

>TIGR02113 coaC_strep phosphopantothenoylcysteine decarboxylase, streptococcal

Probab=86.85  E-value=5.1  Score=26.50  Aligned_cols=33  Identities=18%  Similarity=0.138  Sum_probs=25.1

Q ss_pred             cEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEE
Q 031713            4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIF   39 (154)
Q Consensus         4 ~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l   39 (154)
                      ++|+|++.++..+..+.+..-.+-+ .|  .+++++
T Consensus         1 k~I~lgvtGs~~a~~~~~ll~~L~~-~g--~~V~vi   33 (177)
T TIGR02113         1 KKILLAVTGSIAAYKAADLTSQLTK-LG--YDVTVL   33 (177)
T ss_pred             CEEEEEEcCHHHHHHHHHHHHHHHH-CC--CEEEEE
Confidence            6899999999999988876666654 35  576654

In most bacteria, a single bifunctional protein catalyses phosphopantothenoylcysteine decarboxylase and phosphopantothenate--cysteine ligase activities, sequential steps in coenzyme A biosynthesis (see TIGR00521). These activities reside in separate proteins encoded by tandem genes in some bacterial lineages. This model describes proteins from the genera Streptococcus and Enterococcus homologous to the N-terminal region of TIGR00521, corresponding to phosphopantothenoylcysteine decarboxylase activity.

>cd01994 Alpha_ANH_like_IV This is a subfamily of Adenine nucleotide alpha hydrolases superfamily

Probab=86.74  E-value=6.7  Score=26.33  Aligned_cols=115  Identities=17%  Similarity=0.096  Sum_probs=58.7

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEIC   84 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   84 (154)
                      +++|++.+...|.-++..+.+    .|  -++..+++..+.....                  . . .....++.+...+
T Consensus         1 kv~v~~SGGkDS~~al~~a~~----~G--~~v~~l~~~~~~~~~~------------------~-~-~h~~~~e~~~~~A   54 (194)
T cd01994           1 KVVALISGGKDSCYALYRALE----EG--HEVVALLNLTPEEGSS------------------M-M-YHTVNHELLELQA   54 (194)
T ss_pred             CEEEEecCCHHHHHHHHHHHH----cC--CEEEEEEEEecCCCCc------------------c-c-ccccCHHHHHHHH
Confidence            478899998888877766665    34  4666666654322110                  0 0 0001233445555


Q ss_pred             HhcCCeEEEEEecC---ChhhHHH----HHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEE
Q 031713           85 AKHGVVAETMTEMG---DPKNVIC----EAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVL  147 (154)
Q Consensus        85 ~~~~~~~~~~v~~g---~~~~~i~----~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvl  147 (154)
                      +..|++....-..+   +..+.+.    +..++ +++.++-|.-- ....+.+..++++++=-.+-.|+|
T Consensus        55 ~~lgipl~~i~~~~~~e~~~~~l~~~l~~~~~~-g~~~vv~G~i~-sd~~~~~~e~~~~~~gl~~~~PLW  122 (194)
T cd01994          55 EAMGIPLIRIEISGEEEDEVEDLKELLRKLKEE-GVDAVVFGAIL-SEYQRTRVERVCERLGLEPLAPLW  122 (194)
T ss_pred             HHcCCcEEEEeCCCCchHHHHHHHHHHHHHHHc-CCCEEEECccc-cHHHHHHHHHHHHHcCCEEEeccc
Confidence            66788765443222   2233333    33333 69999999863 223333333344433333335554

Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily of proteins is predicted to bind ATP. This domainhas a strongly conserved motif SGGKD at the N terminus.

>PRK08745 ribulose-phosphate 3-epimerase; Provisional

Probab=86.72  E-value=8.3  Score=26.58  Aligned_cols=45  Identities=16%  Similarity=0.039  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecC
Q 031713           76 LLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        76 ~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      .+.++++...+.+.++...+ .|.....-+..+.+.++|.+|+|+.
T Consensus       157 KI~~l~~~~~~~~~~~~IeV-DGGI~~eti~~l~~aGaDi~V~GSa  201 (223)
T PRK08745        157 KLRAIRKKIDALGKPIRLEI-DGGVKADNIGAIAAAGADTFVAGSA  201 (223)
T ss_pred             HHHHHHHHHHhcCCCeeEEE-ECCCCHHHHHHHHHcCCCEEEEChh
Confidence            34455555555566665555 4555555666677779999999964

>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination

Probab=86.43  E-value=3.9  Score=25.76  Aligned_cols=61  Identities=16%  Similarity=0.126  Sum_probs=42.0

Q ss_pred             EEEEEec--CChhhHHHHHHHhcCCCEEEEecCCCC----CcccccccchhHHHhhcC-CCcEEEEcC
Q 031713           91 AETMTEM--GDPKNVICEAAEKHKIQLLIVGSHSRG----PIQRAFLGSVSNYCVHNA-KCPVLVVRK  151 (154)
Q Consensus        91 ~~~~v~~--g~~~~~i~~~a~~~~~dlivlg~~~~~----~~~~~~~gs~~~~l~~~~-~~pvliv~~  151 (154)
                      ..+....  +...+.|.+.+++.+++.||+|-.-..    .-.....-.+++.|-... ++||..+-+
T Consensus        28 l~~i~~~~~~~~~~~l~~li~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~~~L~~~~~~ipV~~~DE   95 (135)
T PF03652_consen   28 LETIPRRNREKDIEELKKLIEEYQIDGIVVGLPLNMDGSESEQARRVRKFAEELKKRFPGIPVILVDE   95 (135)
T ss_dssp             EEEEEECCCCCCHHHHHHHHHHCCECEEEEEEEBBCTSSC-CCHHHHHHHHHHHHHHH-TSEEEEEEC
T ss_pred             eEEEECCCCchHHHHHHHHHHHhCCCEEEEeCCcccCCCccHHHHHHHHHHHHHHHhcCCCcEEEECC
Confidence            3444444  368999999999999999999985321    112223445667777776 799988854

The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.

>PRK00109 Holliday junction resolvase-like protein; Reviewed

Probab=86.37  E-value=2  Score=27.15  Aligned_cols=52  Identities=13%  Similarity=0.052  Sum_probs=35.7

Q ss_pred             hhhHHHHHHHhcCCCEEEEecCCC----CCcccccccchhHHHhhcCCCcEEEEcC
Q 031713          100 PKNVICEAAEKHKIQLLIVGSHSR----GPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus       100 ~~~~i~~~a~~~~~dlivlg~~~~----~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      ..+.|.+++++.+++.||+|-.-.    ..........+++.|-...++||..+-+
T Consensus        42 ~~~~l~~~i~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~~~L~~~~~~~v~~~DE   97 (138)
T PRK00109         42 DWDRLEKLIKEWQPDGLVVGLPLNMDGTEGPRTERARKFANRLEGRFGLPVVLVDE   97 (138)
T ss_pred             HHHHHHHHHHHhCCCEEEEeccCCCCCCcCHHHHHHHHHHHHHHHHhCCCEEEEcC
Confidence            478899999999999999995422    1111123345667777777899888754

>cd01990 Alpha_ANH_like_I This is a subfamily of Adenine nucleotide alpha hydrolases superfamily

Probab=86.33  E-value=7.8  Score=25.90  Aligned_cols=86  Identities=20%  Similarity=0.200  Sum_probs=51.9

Q ss_pred             EEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            6 VMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICA   85 (154)
Q Consensus         6 iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   85 (154)
                      |+|++.+...|..++..+.+.   .+  .++..+|+......                          ....+.+...++
T Consensus         1 vvva~SGG~DS~~ll~ll~~~---~~--~~v~~v~vd~g~~~--------------------------~~~~~~~~~~a~   49 (202)
T cd01990           1 VAVAFSGGVDSTLLLKAAVDA---LG--DRVLAVTATSPLFP--------------------------RRELEEAKRLAK   49 (202)
T ss_pred             CEEEccCCHHHHHHHHHHHHH---hC--CcEEEEEeCCCCCC--------------------------HHHHHHHHHHHH
Confidence            578898888888777655443   22  37888888655311                          122334445555


Q ss_pred             hcCCeEEEEEec-----------------C--ChhhHHHHHHHhcCCCEEEEecCC
Q 031713           86 KHGVVAETMTEM-----------------G--DPKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        86 ~~~~~~~~~v~~-----------------g--~~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      ..|++....-..                 .  -....+.+++++.+++.|+.|++.
T Consensus        50 ~lgi~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~l~~~a~~~g~~~I~~G~~~  105 (202)
T cd01990          50 EIGIRHEVIETDELDDPEFAKNPPDRCYLCKKALYEALKEIAEELGLDVVLDGTNA  105 (202)
T ss_pred             HcCCcEEEEeCCccccHHHhcCCCCccchhHHHHHHHHHHHHHHCCCCEEEEcCcc
Confidence            566664432221                 0  122355578899999999999864

Adenine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily of proteins probably binds ATP. This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N terminus.

>cd05565 PTS_IIB_lactose PTS_IIB_lactose: subunit IIB of enzyme II (EII) of the lactose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) found in Firmicutes as well as Actinobacteria

Probab=86.09  E-value=2.6  Score=25.03  Aligned_cols=65  Identities=9%  Similarity=0.039  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           76 LLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        76 ~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      ..+++++.+++.|++++....   ....+.....  ++|++++|..-+..+.      ...........||.+++.
T Consensus        16 la~km~~~a~~~gi~~~i~a~---~~~e~~~~~~--~~Dvill~PQv~~~~~------~i~~~~~~~~ipv~~I~~   80 (99)
T cd05565          16 LANALNKGAKERGVPLEAAAG---AYGSHYDMIP--DYDLVILAPQMASYYD------ELKKDTDRLGIKLVTTTG   80 (99)
T ss_pred             HHHHHHHHHHHCCCcEEEEEe---eHHHHHHhcc--CCCEEEEcChHHHHHH------HHHHHhhhcCCCEEEeCH
Confidence            345667777788988765432   3334555566  8899999976332222      235566667789988863

In this system, EII is a lactose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIC and IIB domains are expressed as a single protein from the lac operon. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include lactose, chitobiose/lichenan, ascorbate, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.

>PRK14057 epimerase; Provisional

Probab=85.99  E-value=9.9  Score=26.79  Aligned_cols=46  Identities=9%  Similarity=-0.022  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecC
Q 031713           75 ALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        75 ~~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      +.+.++.+...+.+..+...+ .|.....-+..+.+.++|.+|+|+.
T Consensus       178 ~KI~~lr~~~~~~~~~~~IeV-DGGI~~~ti~~l~~aGad~~V~GSa  223 (254)
T PRK14057        178 ERVAQLLCLLGDKREGKIIVI-DGSLTQDQLPSLIAQGIDRVVSGSA  223 (254)
T ss_pred             HHHHHHHHHHHhcCCCceEEE-ECCCCHHHHHHHHHCCCCEEEEChH
Confidence            344455555556676666655 5555555666667779999999964

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=85.89  E-value=13  Score=28.22  Aligned_cols=56  Identities=4%  Similarity=0.120  Sum_probs=31.1

Q ss_pred             HHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccch
Q 031713           79 RAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSV  134 (154)
Q Consensus        79 ~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~  134 (154)
                      ++....+..|+++.......+..+.|..+.+..++|+|++.+.|++......+...
T Consensus       287 QLk~yae~lgipv~v~~d~~~L~~aL~~lk~~~~~DvVLIDTaGRs~kd~~lm~EL  342 (436)
T PRK11889        287 QLQDYVKTIGFEVIAVRDEAAMTRALTYFKEEARVDYILIDTAGKNYRASETVEEM  342 (436)
T ss_pred             HHHHHhhhcCCcEEecCCHHHHHHHHHHHHhccCCCEEEEeCccccCcCHHHHHHH
Confidence            34444445576654332222344444444444579999999998876554444444

>TIGR00237 xseA exodeoxyribonuclease VII, large subunit

Probab=85.72  E-value=4.2  Score=30.93  Aligned_cols=53  Identities=23%  Similarity=0.374  Sum_probs=32.2

Q ss_pred             ecC-ChhhHHHHHHH----hcCCCEEEEecCCCCCcccc-cccc-hhHHHhhcCCCcEEEE
Q 031713           96 EMG-DPKNVICEAAE----KHKIQLLIVGSHSRGPIQRA-FLGS-VSNYCVHNAKCPVLVV  149 (154)
Q Consensus        96 ~~g-~~~~~i~~~a~----~~~~dlivlg~~~~~~~~~~-~~gs-~~~~l~~~~~~pvliv  149 (154)
                      +.| .....|+...+    ..++|+||+++.| +..+.+ .|.. ..-+-+..|++||+.-
T Consensus       166 vQG~~a~~~i~~al~~~~~~~~~dviii~RGG-Gs~eDL~~Fn~e~~~rai~~~~~Pvis~  225 (432)
T TIGR00237       166 VQGEGAVQSIVESIELANTKNECDVLIVGRGG-GSLEDLWSFNDEKVARAIFLSKIPIISA  225 (432)
T ss_pred             ccCccHHHHHHHHHHHhhcCCCCCEEEEecCC-CCHHHhhhcCcHHHHHHHHcCCCCEEEe
Confidence            446 56677766543    2347999999765 445552 2322 3335567889998753

This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.

>PRK09722 allulose-6-phosphate 3-epimerase; Provisional

Probab=85.66  E-value=9.7  Score=26.38  Aligned_cols=47  Identities=17%  Similarity=0.207  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecC
Q 031713           74 LALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        74 ~~~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      -+...++++...+.+.++...+ .|.....-+..+.+.++|.+|+|+.
T Consensus       153 l~KI~~lr~~~~~~~~~~~IeV-DGGI~~~~i~~~~~aGad~~V~Gss  199 (229)
T PRK09722        153 LDKIAELKALRERNGLEYLIEV-DGSCNQKTYEKLMEAGADVFIVGTS  199 (229)
T ss_pred             HHHHHHHHHHHHhcCCCeEEEE-ECCCCHHHHHHHHHcCCCEEEEChH
Confidence            3444555566666677766666 4444455555666679999999964

>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed

Probab=85.54  E-value=11  Score=26.99  Aligned_cols=83  Identities=10%  Similarity=0.260  Sum_probs=51.0

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKE   82 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~   82 (154)
                      .+||.|.+.++.++..++-.+..- ...+  +++.++-....                                  .+..
T Consensus        89 ~~ri~vl~Sg~gsnl~al~~~~~~-~~~~--~~i~~visn~~----------------------------------~~~~  131 (286)
T PRK06027         89 RKRVVILVSKEDHCLGDLLWRWRS-GELP--VEIAAVISNHD----------------------------------DLRS  131 (286)
T ss_pred             CcEEEEEEcCCCCCHHHHHHHHHc-CCCC--cEEEEEEEcCh----------------------------------hHHH
Confidence            457888888887777777655432 2222  56555544221                                  1122


Q ss_pred             HHHhcCCeEEEEEec----CChhhHHHHHHHhcCCCEEEEecCC
Q 031713           83 ICAKHGVVAETMTEM----GDPKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        83 ~~~~~~~~~~~~v~~----g~~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      .+++.|+++...-..    .+....+.+..++.++|++|+....
T Consensus       132 lA~~~gIp~~~~~~~~~~~~~~~~~~~~~l~~~~~Dlivlagy~  175 (286)
T PRK06027        132 LVERFGIPFHHVPVTKETKAEAEARLLELIDEYQPDLVVLARYM  175 (286)
T ss_pred             HHHHhCCCEEEeccCccccchhHHHHHHHHHHhCCCEEEEecch
Confidence            256678886552211    2356678888999999999998753

>PLN00200 argininosuccinate synthase; Provisional

Probab=85.25  E-value=14  Score=27.94  Aligned_cols=37  Identities=24%  Similarity=0.298  Sum_probs=28.7

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccC
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPT   44 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~   44 (154)
                      +++|+|++.+.-.|..++.++.+   ..|  .+++.+|+...
T Consensus         5 ~~kVvva~SGGlDSsvla~~L~e---~~G--~eViav~id~G   41 (404)
T PLN00200          5 LNKVVLAYSGGLDTSVILKWLRE---NYG--CEVVCFTADVG   41 (404)
T ss_pred             CCeEEEEEeCCHHHHHHHHHHHH---hhC--CeEEEEEEECC
Confidence            57999999999888877776654   235  68999998655

>cd01713 PAPS_reductase This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase

Probab=84.98  E-value=7.7  Score=24.66  Aligned_cols=38  Identities=16%  Similarity=0.156  Sum_probs=27.5

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCC
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTE   45 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~   45 (154)
                      +|+|++.+...|..++..+.+.....   .++.++|+....
T Consensus         1 ~i~v~~SGGkDS~~ll~l~~~~~~~~---~~~~~v~~dtg~   38 (173)
T cd01713           1 NVVVSFSGGKDSTVLLHLALKALPEL---KPVPVIFLDTGY   38 (173)
T ss_pred             CeEEEecCChHHHHHHHHHHHhcccc---cCceEEEeCCCC
Confidence            57899999999988887776654431   268888886543

PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly modified version of the P loop, the fingerprint peptide of mononucleotide-binding proteins, is present in the active site of the protein, which appears to be a positively charged cleft containing a number of conserved arginine and lysine residues. Although PAPS reductase has no ATPase activity, it shows a striking similarity to the structure of the ATP pyrophosphatase (ATP PPase) domain of GMP synthetase, indicating that both enzyme families have evolved from a common ancestral nucleotide-binding fold. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) . It is also found in NodP nodulation protein P from Rhizobium meliloti which has ATP sulphurylase acti

>cd01986 Alpha_ANH_like Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases and ATP sulphurylases

Probab=84.75  E-value=6.1  Score=23.27  Aligned_cols=34  Identities=18%  Similarity=0.020  Sum_probs=24.9

Q ss_pred             EEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCC
Q 031713            6 VMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTE   45 (154)
Q Consensus         6 iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~   45 (154)
                      |+|++.+...|..++..+.++    +  .++.++|+....
T Consensus         1 v~v~~SGG~DS~~ll~~l~~~----~--~~~~~~~~~~~~   34 (103)
T cd01986           1 VLVAFSGGKDSSVAAALLKKL----G--YQVIAVTVDHGI   34 (103)
T ss_pred             CEEEEeCcHHHHHHHHHHHHh----C--CCEEEEEEcCCC
Confidence            578999988888777666543    3  378889887664

The domain forms a apha/beta/apha fold which binds to Adenosine group..

>PF02844 GARS_N: Phosphoribosylglycinamide synthetase, N domain; InterPro: IPR020562 Phosphoribosylglycinamide synthetase (6

Probab=84.48  E-value=1.1  Score=26.72  Aligned_cols=24  Identities=25%  Similarity=0.427  Sum_probs=20.7

Q ss_pred             CChhhHHHHHHHhcCCCEEEEecC
Q 031713           98 GDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        98 g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      -.-.+.|.+++++.++|++|+|..
T Consensus        48 ~~d~~~l~~~a~~~~idlvvvGPE   71 (100)
T PF02844_consen   48 ITDPEELADFAKENKIDLVVVGPE   71 (100)
T ss_dssp             TT-HHHHHHHHHHTTESEEEESSH
T ss_pred             CCCHHHHHHHHHHcCCCEEEECCh
Confidence            367889999999999999999975

3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) [] catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide: ATP + 5-phosphoribosylamine + glycine = ADP + Pi + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART. This entry represents the N-domain, which is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (IPR005481 from INTERPRO).; GO: 0004637 phosphoribosylamine-glycine ligase activity, 0009113 purine base biosynthetic process; PDB: 3MJF_A 2XD4_A 2XCL_A 2IP4_A 2YW2_B 2YYA_A 3LP8_A 1VKZ_A 2YS6_A 2YRX_A ....

>PF05582 Peptidase_U57: YabG peptidase U57; InterPro: IPR008764 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families

Probab=84.32  E-value=11  Score=27.01  Aligned_cols=48  Identities=15%  Similarity=0.240  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEEec-CChhhHHHHHHHhcCCCEEEEecC
Q 031713           74 LALLGRAKEICAKHGVVAETMTEM-GDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        74 ~~~l~~~~~~~~~~~~~~~~~v~~-g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      ...|+...+.+++.|+++...... ..-.+.|.++.++.++|.+|+.-|
T Consensus       115 ~~YL~~Cl~~Ykql~i~a~G~~~~E~eqp~~i~~Ll~~~~PDIlViTGH  163 (287)
T PF05582_consen  115 EEYLNKCLKVYKQLGIPAVGIHVPEKEQPEKIYRLLEEYRPDILVITGH  163 (287)
T ss_pred             HHHHHHHHHHHHHcCCceEEEEechHHhhHHHHHHHHHcCCCEEEEeCc
Confidence            456788888999999997766655 478899999999999999999755

Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This is a group of peptidases belong to MEROPS peptidase family U57 (clan U-). The type example is the YabG protein of Bacillus subtilis. This is a protease involved in the synthesis and maturation of the spore coat proteins SpoIVA and YrbA of B. subtilis [].

>cd08550 GlyDH-like Glycerol_dehydrogenase-like

Probab=84.23  E-value=13  Score=27.36  Aligned_cols=68  Identities=18%  Similarity=0.167  Sum_probs=40.9

Q ss_pred             HHHHHHHHHhcCCeEEEEEecCCh----hhHHHHHHHhcCCCEEE-EecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           77 LGRAKEICAKHGVVAETMTEMGDP----KNVICEAAEKHKIQLLI-VGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        77 l~~~~~~~~~~~~~~~~~v~~g~~----~~~i~~~a~~~~~dliv-lg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      .+++.+.++..++.+.+.+..|++    ...+.+.+++.++|.|| +|-.  +.      ..++..+......|++.||-
T Consensus        38 ~~~v~~~l~~~~i~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~IIavGGG--s~------~D~aK~ia~~~~~p~i~VPT  109 (349)
T cd08550          38 RPRFEAALAKSIIVVDVIVFGGECSTEEVVKALCGAEEQEADVIIGVGGG--KT------LDTAKAVADRLDKPIVIVPT  109 (349)
T ss_pred             HHHHHHHHHhcCCeeEEEEcCCCCCHHHHHHHHHHHHhcCCCEEEEecCc--HH------HHHHHHHHHHcCCCEEEeCC
Confidence            466667777778776665555542    34456677888999877 5532  11      12333333334689999885


Q ss_pred             C
Q 031713          152 P  152 (154)
Q Consensus       152 ~  152 (154)
                      .
T Consensus       110 t  110 (349)
T cd08550         110 I  110 (349)
T ss_pred             c
Confidence            3

Families of proteins related to glycerol dehydrogenases. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site. Some subfamilies have not been characterized till now.

>TIGR02855 spore_yabG sporulation peptidase YabG

Probab=84.13  E-value=11  Score=26.81  Aligned_cols=49  Identities=14%  Similarity=0.217  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEEec-CChhhHHHHHHHhcCCCEEEEecCC
Q 031713           74 LALLGRAKEICAKHGVVAETMTEM-GDPKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        74 ~~~l~~~~~~~~~~~~~~~~~v~~-g~~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      ...|+...+.+++.++++...... ..-.+.|.++.++.++|++|+.-|.
T Consensus       114 ~~YL~~Cl~~Ykql~i~a~G~~~~E~eqp~~i~~Ll~~~~PDIlViTGHD  163 (283)
T TIGR02855       114 PEYLRKCLKLYKKIGVPVVGIHCKEKEMPEKVLDLIEEVRPDILVITGHD  163 (283)
T ss_pred             HHHHHHHHHHHHHhCCceEEEEecchhchHHHHHHHHHhCCCEEEEeCch
Confidence            355778888888899997665555 5788999999999999999997653

Members of this family are the protein YabG, demonstrated for Bacillus subtilis to be an endopeptidase able to release N-terminal peptides from a number of sporulation proteins, including CotT, CotF, and SpoIVA. It appears to be expressed under control of sigma-K.

>TIGR00655 PurU formyltetrahydrofolate deformylase

Probab=84.05  E-value=13  Score=26.57  Aligned_cols=82  Identities=10%  Similarity=0.246  Sum_probs=51.8

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKE   82 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~   82 (154)
                      .+||.|.+.++.++..++-.+..- ..  .++++.++-...+                                  .+..
T Consensus        84 ~~ki~vl~Sg~g~nl~~l~~~~~~-g~--l~~~i~~visn~~----------------------------------~~~~  126 (280)
T TIGR00655        84 LKRVAILVSKEDHCLGDLLWRWYS-GE--LDAEIALVISNHE----------------------------------DLRS  126 (280)
T ss_pred             CcEEEEEEcCCChhHHHHHHHHHc-CC--CCcEEEEEEEcCh----------------------------------hHHH
Confidence            468999999999988888776532 22  2255555533222                                  1111


Q ss_pred             HHHhcCCeEEEEEec----CChhhHHHHHHHhcCCCEEEEecC
Q 031713           83 ICAKHGVVAETMTEM----GDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        83 ~~~~~~~~~~~~v~~----g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      .+++.|+++...-..    ......+.+..++.++|++|+...
T Consensus       127 ~A~~~gIp~~~~~~~~~~~~~~e~~~~~~l~~~~~Dlivlagy  169 (280)
T TIGR00655       127 LVERFGIPFHYIPATKDNRVEHEKRQLELLKQYQVDLVVLAKY  169 (280)
T ss_pred             HHHHhCCCEEEcCCCCcchhhhHHHHHHHHHHhCCCEEEEeCc
Confidence            255678886543321    123567888899999999999865

This model describes formyltetrahydrofolate deformylases. The enzyme is a homohexamer. Sequences from a related enzyme formyl tetrahydrofolate-specific enzyme, phosphoribosylglycinamide formyltransferase, serve as an outgroup for phylogenetic analysis. Putative members of this family, scoring below the trusted cutoff, include a sequence from Rhodobacter capsulatus that lacks an otherwise conserved C-terminal region.

>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed

Probab=83.90  E-value=14  Score=26.64  Aligned_cols=83  Identities=10%  Similarity=0.132  Sum_probs=52.3

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKE   82 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~   82 (154)
                      .+||.|.+.++.++..++-.+.+-- ..+  +++.++  +....                                .+.+
T Consensus        93 ~~kiavl~Sg~g~nl~al~~~~~~~-~l~--~~i~~v--isn~~--------------------------------~~~~  135 (289)
T PRK13010         93 RPKVVIMVSKFDHCLNDLLYRWRMG-ELD--MDIVGI--ISNHP--------------------------------DLQP  135 (289)
T ss_pred             CeEEEEEEeCCCccHHHHHHHHHCC-CCC--cEEEEE--EECCh--------------------------------hHHH
Confidence            3578888888888888887775322 222  455544  33310                                1124


Q ss_pred             HHHhcCCeEEEEEec----CChhhHHHHHHHhcCCCEEEEecCC
Q 031713           83 ICAKHGVVAETMTEM----GDPKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        83 ~~~~~~~~~~~~v~~----g~~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      .+++.|+++...-..    ......+.+..++.++|++|+....
T Consensus       136 ~A~~~gIp~~~~~~~~~~~~~~~~~~~~~l~~~~~Dlivlagym  179 (289)
T PRK13010        136 LAVQHDIPFHHLPVTPDTKAQQEAQILDLIETSGAELVVLARYM  179 (289)
T ss_pred             HHHHcCCCEEEeCCCcccccchHHHHHHHHHHhCCCEEEEehhh
Confidence            556778886542211    2345678899999999999998653

>TIGR00853 pts-lac PTS system, lactose/cellobiose family IIB component

Probab=83.65  E-value=3.4  Score=24.24  Aligned_cols=66  Identities=11%  Similarity=0.125  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           76 LLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        76 ~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      +.+++.+.+++.|++++.....  . ..+.....  ++|+|+++..=+..+      ..........++||.++++.
T Consensus        19 l~~k~~~~~~~~gi~~~v~a~~--~-~~~~~~~~--~~Dvill~pqi~~~~------~~i~~~~~~~~ipv~~I~~~   84 (95)
T TIGR00853        19 LVNKMNKAAEEYGVPVKIAAGS--Y-GAAGEKLD--DADVVLLAPQVAYML------PDLKKETDKKGIPVEVINGA   84 (95)
T ss_pred             HHHHHHHHHHHCCCcEEEEEec--H-HHHHhhcC--CCCEEEECchHHHHH------HHHHHHhhhcCCCEEEeChh
Confidence            3456667777788876554322  2 22334444  789999997532211      12355677778999998753

Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Lac family includes several sequenced lactose (b-galactoside) permeases of Gram-positive bacteria as well as those in E. coli. While the Lac family usually consists of two polypeptide components IIA and IICB, the Chb permease of E. coli consists of three IIA, IIB and IIC. This family is specific for the IIB subunit of the Lac PTS family.

>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function

Probab=83.26  E-value=7  Score=22.85  Aligned_cols=71  Identities=20%  Similarity=0.096  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHhcCCeEEEEEecC-Chhh--HHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           75 ALLGRAKEICAKHGVVAETMTEMG-DPKN--VICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        75 ~~l~~~~~~~~~~~~~~~~~v~~g-~~~~--~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      .....+.+.+++.|.....+-+.+ ....  .|-....  ++|+||+-+.--   +.- .-..+.+..++..+|++.++.
T Consensus        10 ~~~~~~~~~~~~~G~~~~~hg~~~~~~~~~~~l~~~i~--~aD~VIv~t~~v---sH~-~~~~vk~~akk~~ip~~~~~~   83 (97)
T PF10087_consen   10 DRERRYKRILEKYGGKLIHHGRDGGDEKKASRLPSKIK--KADLVIVFTDYV---SHN-AMWKVKKAAKKYGIPIIYSRS   83 (97)
T ss_pred             ccHHHHHHHHHHcCCEEEEEecCCCCccchhHHHHhcC--CCCEEEEEeCCc---ChH-HHHHHHHHHHHcCCcEEEECC
Confidence            345667777778898876662222 2333  3666677  999999987532   211 112456677888899999874

>PRK08185 hypothetical protein; Provisional

Probab=82.58  E-value=7  Score=28.01  Aligned_cols=66  Identities=9%  Similarity=0.028  Sum_probs=45.7

Q ss_pred             HHhcCCeEEEEEecC-ChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEE
Q 031713           84 CAKHGVVAETMTEMG-DPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVV  149 (154)
Q Consensus        84 ~~~~~~~~~~~v~~g-~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv  149 (154)
                      .++.+.-+----... ...+++++.|++.+..+|+..+.+.-......+......+.+++.+||.+-
T Consensus         8 A~~~~yaV~AfN~~n~e~~~avi~AAee~~sPvIl~~~~~~~~~~~~~~~~~~~~~a~~~~vPV~lH   74 (283)
T PRK08185          8 AKEHQFAVGAFNVADSCFLRAVVEEAEANNAPAIIAIHPNELDFLGDNFFAYVRERAKRSPVPFVIH   74 (283)
T ss_pred             HHHcCceEEEEEeCCHHHHHHHHHHHHHhCCCEEEEeCcchhhhccHHHHHHHHHHHHHCCCCEEEE
Confidence            333443333333334 789999999999999999998876433333336677788889999998764

>PF01261 AP_endonuc_2: Xylose isomerase-like TIM barrel; InterPro: IPR012307 This TIM alpha/beta barrel structure is found in xylose isomerase (P19148 from SWISSPROT) and in endonuclease IV (P12638 from SWISSPROT, 3

Probab=82.40  E-value=12  Score=24.74  Aligned_cols=79  Identities=15%  Similarity=0.003  Sum_probs=54.6

Q ss_pred             HHHHHHHHHHcccCCCCCeEEEEEec---cCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCeEEE
Q 031713           17 HYALQWALENLGDAISKSDLIIFTAR---PTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAET   93 (154)
Q Consensus        17 ~~~l~~a~~la~~~~~~~~l~~l~v~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~   93 (154)
                      ..-+..++++|+..|  ++...+|.-   .......                 +...+...+.++++.+.+++.|+.+..
T Consensus        70 ~~~~~~~i~~a~~lg--~~~i~~~~g~~~~~~~~~~-----------------~~~~~~~~~~l~~l~~~a~~~gv~i~l  130 (213)
T PF01261_consen   70 LEYLKKAIDLAKRLG--AKYIVVHSGRYPSGPEDDT-----------------EENWERLAENLRELAEIAEEYGVRIAL  130 (213)
T ss_dssp             HHHHHHHHHHHHHHT--BSEEEEECTTESSSTTSSH-----------------HHHHHHHHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHHHHhC--CCceeecCcccccccCCCH-----------------HHHHHHHHHHHHHHHhhhhhhcceEEE
Confidence            567788899999988  898888865   1111111                 245666677888888888888988777


Q ss_pred             EEecCCh---h---hHHHHHHHhcCCC
Q 031713           94 MTEMGDP---K---NVICEAAEKHKIQ  114 (154)
Q Consensus        94 ~v~~g~~---~---~~i~~~a~~~~~d  114 (154)
                      +...+..   .   +.+.++.++.+.+
T Consensus       131 E~~~~~~~~~~~~~~~~~~~l~~~~~~  157 (213)
T PF01261_consen  131 ENHPGPFSETPFSVEEIYRLLEEVDSP  157 (213)
T ss_dssp             E-SSSSSSSEESSHHHHHHHHHHHTTT
T ss_pred             ecccCccccchhhHHHHHHHHhhcCCC
Confidence            6655433   2   7888888876654

1.21.2 from EC). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae []. ; PDB: 3KWS_B 3DX5_A 3CQH_B 3CQI_A 3CQK_A 3CQJ_B 2G0W_B 1DXI_A 2ZDS_D 3TVA_B ....

>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]

Probab=82.20  E-value=7.1  Score=29.72  Aligned_cols=52  Identities=21%  Similarity=0.433  Sum_probs=32.1

Q ss_pred             ecC-ChhhHHHHHH---Hhc-CCCEEEEecCCCCCccccc-cc-chhHHHhhcCCCcEEE
Q 031713           96 EMG-DPKNVICEAA---EKH-KIQLLIVGSHSRGPIQRAF-LG-SVSNYCVHNAKCPVLV  148 (154)
Q Consensus        96 ~~g-~~~~~i~~~a---~~~-~~dlivlg~~~~~~~~~~~-~g-s~~~~l~~~~~~pvli  148 (154)
                      +.| +....|++.+   ++. .+|+||+|+.| +.++.++ |+ -..-+-+..|++||+-
T Consensus       172 VQG~~A~~eIv~aI~~an~~~~~DvlIVaRGG-GSiEDLW~FNdE~vaRAi~~s~iPvIS  230 (440)
T COG1570         172 VQGEGAAEEIVEAIERANQRGDVDVLIVARGG-GSIEDLWAFNDEIVARAIAASRIPVIS  230 (440)
T ss_pred             ccCCCcHHHHHHHHHHhhccCCCCEEEEecCc-chHHHHhccChHHHHHHHHhCCCCeEe
Confidence            346 5777777653   333 49999999654 5566632 22 2333556778899864

>TIGR00521 coaBC_dfp phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase, prokaryotic

Probab=82.17  E-value=19  Score=27.10  Aligned_cols=36  Identities=8%  Similarity=0.175  Sum_probs=28.5

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEE
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFT   40 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~   40 (154)
                      .-++|++++.++..+..+++..-.+.+ .|  .++.++-
T Consensus         2 ~~k~IllgiTGSiaa~~~~~ll~~L~~-~g--~~V~vv~   37 (390)
T TIGR00521         2 ENKKILLGVTGGIAAYKTVELVRELVR-QG--AEVKVIM   37 (390)
T ss_pred             CCCEEEEEEeCHHHHHHHHHHHHHHHh-CC--CEEEEEE
Confidence            468999999999999999988877755 35  6766553

This model represents a bifunctional enzyme that catalyzes the second and third steps (cysteine ligation, EC 6.3.2.5, and decarboxylation, EC 4.1.1.36) in the biosynthesis of coenzyme A (CoA) from pantothenate in bacteria. In early descriptions of this flavoprotein, a ts mutation in one region of the protein appeared to cause a defect in DNA metaobolism rather than an increased need for the pantothenate precursor beta-alanine. This protein was then called dfp, for DNA/pantothenate metabolism flavoprotein. The authors responsible for detecting phosphopantothenate--cysteine ligase activity suggest renaming this bifunctional protein coaBC for its role in CoA biosynthesis. This enzyme contains the FMN cofactor, but no FAD or pyruvoyl group. The amino-terminal region contains the phosphopantothenoylcysteine decarboxylase activity.

>PRK13337 putative lipid kinase; Reviewed

Probab=82.06  E-value=16  Score=26.21  Aligned_cols=71  Identities=14%  Similarity=0.148  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHhcCCeEEEEEec-CChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhc-CCCcEEEEcCC
Q 031713           76 LLGRAKEICAKHGVVAETMTEM-GDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHN-AKCPVLVVRKP  152 (154)
Q Consensus        76 ~l~~~~~~~~~~~~~~~~~v~~-g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~-~~~pvliv~~~  152 (154)
                      ...++...+.+.+.+++..... ...+..+.+.+.+.++|+||+.- |.+.+.     .+++.++.. ...|+-++|..
T Consensus        20 ~~~~~~~~l~~~~~~~~~~~t~~~~~a~~~a~~~~~~~~d~vvv~G-GDGTl~-----~vv~gl~~~~~~~~lgiiP~G   92 (304)
T PRK13337         20 NLPDVLQKLEQAGYETSAHATTGPGDATLAAERAVERKFDLVIAAG-GDGTLN-----EVVNGIAEKENRPKLGIIPVG   92 (304)
T ss_pred             HHHHHHHHHHHcCCEEEEEEecCCCCHHHHHHHHHhcCCCEEEEEc-CCCHHH-----HHHHHHhhCCCCCcEEEECCc
Confidence            3445666677788887665554 34555556555566788777653 344333     344444432 34688888864

>PRK13054 lipid kinase; Reviewed

Probab=82.04  E-value=16  Score=26.17  Aligned_cols=70  Identities=16%  Similarity=0.131  Sum_probs=41.7

Q ss_pred             HHHHHHHHHhcCCeEEEEEec-CChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhc---CCCcEEEEcCC
Q 031713           77 LGRAKEICAKHGVVAETMTEM-GDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHN---AKCPVLVVRKP  152 (154)
Q Consensus        77 l~~~~~~~~~~~~~~~~~v~~-g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~---~~~pvliv~~~  152 (154)
                      ..++...+.+.+.+++..... ..-+..+.+.+...++|.||+.- |.+.+.     .+++.++..   ..+|+-++|-.
T Consensus        20 ~~~~~~~l~~~g~~~~v~~t~~~~~a~~~a~~~~~~~~d~vvv~G-GDGTl~-----evv~~l~~~~~~~~~~lgiiP~G   93 (300)
T PRK13054         20 LREAVGLLREEGHTLHVRVTWEKGDAARYVEEALALGVATVIAGG-GDGTIN-----EVATALAQLEGDARPALGILPLG   93 (300)
T ss_pred             HHHHHHHHHHcCCEEEEEEecCCCcHHHHHHHHHHcCCCEEEEEC-CccHHH-----HHHHHHHhhccCCCCcEEEEeCC
Confidence            334455567778877664443 23456666665556788877663 344333     355656543   34789999864

>PF04244 DPRP: Deoxyribodipyrimidine photo-lyase-related protein; InterPro: IPR007357 This family appears to be related to DNA photolyases

Probab=81.70  E-value=6  Score=27.27  Aligned_cols=76  Identities=12%  Similarity=0.111  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHHHHHhcCCeEEEEEec-----CChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcE
Q 031713           72 AALALLGRAKEICAKHGVVAETMTEM-----GDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPV  146 (154)
Q Consensus        72 ~~~~~l~~~~~~~~~~~~~~~~~v~~-----g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pv  146 (154)
                      .....+..+.+.+++.|.++...-..     ++..+.|.+..++++++-|.+-..+.-.+.+     ....+.....+|+
T Consensus        46 l~~saMRhfa~~L~~~G~~V~Y~~~~~~~~~~s~~~~L~~~~~~~~~~~~~~~~P~d~~l~~-----~l~~~~~~~~i~~  120 (224)
T PF04244_consen   46 LFFSAMRHFADELRAKGFRVHYIELDDPENTQSFEDALARALKQHGIDRLHVMEPGDYRLEQ-----RLESLAQQLGIPL  120 (224)
T ss_dssp             HHHHHHHHHHHHHHHTT--EEEE-TT-TT--SSHHHHHHHHHHHH----EEEE--S-HHHHH-----HHHH----SSS-E
T ss_pred             HHHHHHHHHHHHHHhCCCEEEEEeCCCccccccHHHHHHHHHHHcCCCEEEEECCCCHHHHH-----HHHhhhcccCCce
Confidence            34556677778888889998876655     2567899999999999999998765433333     3466777788999


Q ss_pred             EEEcCC
Q 031713          147 LVVRKP  152 (154)
Q Consensus       147 liv~~~  152 (154)
                      -+++.+
T Consensus       121 ~~~~~~  126 (224)
T PF04244_consen  121 EVLEDP  126 (224)
T ss_dssp             EEE--T
T ss_pred             EEeCCC
Confidence            888754

; PDB: 3ZXS_A.

>TIGR00032 argG argininosuccinate synthase

Probab=81.30  E-value=21  Score=26.96  Aligned_cols=34  Identities=26%  Similarity=0.331  Sum_probs=26.3

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccC
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPT   44 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~   44 (154)
                      +|+|++.+.-.|..++.++.+.    |  .+++.+|+...
T Consensus         1 kVvla~SGGlDSsvll~~l~e~----g--~~V~av~id~G   34 (394)
T TIGR00032         1 KVVLAYSGGLDTSVCLKWLREK----G--YEVIAYTADVG   34 (394)
T ss_pred             CEEEEEcCCHHHHHHHHHHHHc----C--CEEEEEEEecC
Confidence            5889999988888777766542    5  68999999654

argG in bacteria, ARG1 in Saccharomyces cerevisiae. There is a very unusual clustering in the alignment, with a deep split between one cohort of E. coli, H. influenzae, and Streptomyces, and the other cohort of eukaryotes, archaea, and the rest of the eubacteria.

>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF

Probab=81.29  E-value=4  Score=25.53  Aligned_cols=53  Identities=13%  Similarity=0.010  Sum_probs=36.4

Q ss_pred             ChhhHHHHHHHhcCCCEEEEecCCC----CCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           99 DPKNVICEAAEKHKIQLLIVGSHSR----GPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        99 ~~~~~i~~~a~~~~~dlivlg~~~~----~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      ...+.|.+.+++.+++.||+|-.-.    ..-.....-.+++.|-...+.||..+-+
T Consensus        35 ~~~~~l~~~i~~~~~~~iVvGlP~~~dG~~~~~a~~v~~f~~~L~~~~~~~v~~~DE   91 (130)
T TIGR00250        35 PDWSRIEELLKEWTPDKIVVGLPLNMDGTEGPLTERAQKFANRLEGRFGVPVVLWDE   91 (130)
T ss_pred             HHHHHHHHHHHHcCCCEEEEeccCCCCcCcCHHHHHHHHHHHHHHHHhCCCEEEEcC
Confidence            4578899999999999999995321    1111123335667777777899988754

This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.

>PF00834 Ribul_P_3_epim: Ribulose-phosphate 3 epimerase family; InterPro: IPR000056 Ribulose-phosphate 3-epimerase (5

Probab=81.23  E-value=4.7  Score=27.29  Aligned_cols=47  Identities=13%  Similarity=0.191  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEec
Q 031713           73 ALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGS  120 (154)
Q Consensus        73 ~~~~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~  120 (154)
                      .-+.++++.+...+.|..+...+ .|.....-+..+.+.++|.+|.|+
T Consensus       149 ~~~KI~~l~~~~~~~~~~~~I~v-DGGI~~~~~~~~~~aGad~~V~Gs  195 (201)
T PF00834_consen  149 VLEKIRELRKLIPENGLDFEIEV-DGGINEENIKQLVEAGADIFVAGS  195 (201)
T ss_dssp             HHHHHHHHHHHHHHHTCGSEEEE-ESSESTTTHHHHHHHT--EEEESH
T ss_pred             HHHHHHHHHHHHHhcCCceEEEE-ECCCCHHHHHHHHHcCCCEEEECH
Confidence            34445666777777777777766 454555555556667999999996

1.3.1 from EC) (also known as pentose-5-phosphate 3-epimerase or PPE) is the enzyme that converts D-ribulose 5-phosphate into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle. In Ralstonia eutropha (Alcaligenes eutrophus) two copies of the gene coding for PPE are known [], one is chromosomally encoded P40117 from SWISSPROT, the other one is on a plasmid Q04539 from SWISSPROT. PPE has been found in a wide range of bacteria, archaebacteria, fungi and plants. All the proteins have from 209 to 241 amino acid residues. The enzyme has a TIM barrel structure.; GO: 0004750 ribulose-phosphate 3-epimerase activity, 0005975 carbohydrate metabolic process; PDB: 3CTL_A 3CT7_D 3CU2_A 1RPX_A 3OVR_A 3OVP_A 3OVQ_B 3QC3_B 3INP_A 1TQJ_D ....

>TIGR02699 archaeo_AfpA archaeoflavoprotein AfpA

Probab=80.87  E-value=8.4  Score=25.47  Aligned_cols=33  Identities=9%  Similarity=0.029  Sum_probs=23.9

Q ss_pred             EEEEEecCC-chHHHHHHHHHHHcccCCCCCeEEEE
Q 031713            5 KVMVAIDES-ECRHYALQWALENLGDAISKSDLIIF   39 (154)
Q Consensus         5 ~iLv~vd~~-~~~~~~l~~a~~la~~~~~~~~l~~l   39 (154)
                      ||++++-++ ......++....++++.|  .+++++
T Consensus         1 ~i~~gitGsg~~l~e~v~~l~~L~~~~g--~eV~vv   34 (174)
T TIGR02699         1 RIAWGITGSGDKLPETYSIMKDVKNRYG--DEIDVF   34 (174)
T ss_pred             CEEEEEEccHHHHHHHHHHHHHHHHhcC--CEEEEE
Confidence            588999998 444557788888887666  676655

The prototypical member of this archaeal protein family is AF1518 from Archaeoglobus fulgidus. This homodimer with two non-covalently bound FMN cofactors can receive electrons from ferredoxin, but not from a number of other electron donors such as NADH or rubredoxin. It can then donate electrons to various reductases.

>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]

Probab=80.84  E-value=24  Score=27.28  Aligned_cols=89  Identities=18%  Similarity=0.114  Sum_probs=59.7

Q ss_pred             cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCe
Q 031713           11 DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVV   90 (154)
Q Consensus        11 d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~   90 (154)
                      |..-+...+|.+|++-...     -+.++++.++.....               .......-..+-|+.+.+.+.+.|+ 
T Consensus        11 DLR~~DN~aL~~A~~~~~~-----~~~~vfi~~~~~~~~---------------~~~~~~~Fl~~sL~~L~~~L~~~gi-   69 (461)
T COG0415          11 DLRLTDNAALAAACQSGQP-----VIIAVFILDPEQLGH---------------ASPRHAAFLLQSLQALQQSLAELGI-   69 (461)
T ss_pred             ccccCChHHHHHHHhcCCC-----ceEEEEEechhhccc---------------cCHHHHHHHHHHHHHHHHHHHHcCC-
Confidence            4455677788888875553     235666666543311               1123344455667777777777774 


Q ss_pred             EEEEEecCChhhHHHHHHHhcCCCEEEEecC
Q 031713           91 AETMTEMGDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        91 ~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                       ...+..|++.+.+.+++++.+++-|+-...
T Consensus        70 -~L~v~~~~~~~~l~~~~~~~~~~~v~~n~~   99 (461)
T COG0415          70 -PLLVREGDPEQVLPELAKQLAATTVFWNRD   99 (461)
T ss_pred             -ceEEEeCCHHHHHHHHHHHhCcceEEeeee
Confidence             456778999999999999999888887765

>COG1927 Mtd Coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin dehydrogenase [Energy production and conversion]

Probab=80.82  E-value=9.5  Score=26.07  Aligned_cols=48  Identities=10%  Similarity=0.158  Sum_probs=36.4

Q ss_pred             hhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713          101 KNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus       101 ~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .....+..++.++|++|+++......    -.+-+..++..+..|.+|+-+.
T Consensus        49 eaav~~~~e~~~pDfvi~isPNpaaP----GP~kARE~l~~s~~PaiiigDa   96 (277)
T COG1927          49 EAAVTEMLEEFNPDFVIYISPNPAAP----GPKKAREILSDSDVPAIIIGDA   96 (277)
T ss_pred             HHHHHHHHHhcCCCEEEEeCCCCCCC----CchHHHHHHhhcCCCEEEecCC
Confidence            34555678999999999998654322    2456789999999999999654

>cd02067 B12-binding B12 binding domain (B12-BD)

Probab=80.68  E-value=10  Score=22.93  Aligned_cols=43  Identities=14%  Similarity=0.064  Sum_probs=30.7

Q ss_pred             HHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCC
Q 031713           79 RAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        79 ~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      -+...++..|.++. ......+.+.+.+.+.+.++|+|.++...
T Consensus        18 ~~~~~l~~~G~~V~-~lg~~~~~~~l~~~~~~~~pdvV~iS~~~   60 (119)
T cd02067          18 IVARALRDAGFEVI-DLGVDVPPEEIVEAAKEEDADAIGLSGLL   60 (119)
T ss_pred             HHHHHHHHCCCEEE-ECCCCCCHHHHHHHHHHcCCCEEEEeccc
Confidence            34455666786661 12233578899999999999999998763

This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.

>PRK13059 putative lipid kinase; Reviewed

Probab=80.56  E-value=18  Score=25.85  Aligned_cols=71  Identities=10%  Similarity=0.071  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhc-CCCcEEEEcCC
Q 031713           76 LLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHN-AKCPVLVVRKP  152 (154)
Q Consensus        76 ~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~-~~~pvliv~~~  152 (154)
                      ..+++...+.+.|.++...........+....+.+.++|.||+. .|.+.+.     .+++.++.. .++|+-++|-.
T Consensus        20 ~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~d~vi~~-GGDGTv~-----evv~gl~~~~~~~~lgviP~G   91 (295)
T PRK13059         20 ELDKVIRIHQEKGYLVVPYRISLEYDLKNAFKDIDESYKYILIA-GGDGTVD-----NVVNAMKKLNIDLPIGILPVG   91 (295)
T ss_pred             HHHHHHHHHHHCCcEEEEEEccCcchHHHHHHHhhcCCCEEEEE-CCccHHH-----HHHHHHHhcCCCCcEEEECCC
Confidence            34556667777787755433332112233334445577877665 3444333     355666543 45899999854

>PRK11070 ssDNA exonuclease RecJ; Provisional

Probab=80.52  E-value=24  Score=28.13  Aligned_cols=36  Identities=17%  Similarity=0.160  Sum_probs=29.5

Q ss_pred             cCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCC
Q 031713           87 HGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        87 ~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      .|.+.-..+--|.....-++++++.++|+||+.+|.
T Consensus       126 ~~~~LiItvD~Gi~~~e~i~~a~~~gidvIVtDHH~  161 (575)
T PRK11070        126 RGAQLIVTVDNGISSHAGVAHAHALGIPVLVTDHHL  161 (575)
T ss_pred             cCCCEEEEEcCCcCCHHHHHHHHHCCCCEEEECCCC
Confidence            466666666668888888899999999999999884

>PRK12857 fructose-1,6-bisphosphate aldolase; Reviewed

Probab=80.42  E-value=12  Score=26.90  Aligned_cols=70  Identities=17%  Similarity=0.191  Sum_probs=46.0

Q ss_pred             HHHHHHhcCCeEEEEEecC-ChhhHHHHHHHhcCCCEEEEecCCCCCccc-ccccchhHHHhhcCCCcEEEE
Q 031713           80 AKEICAKHGVVAETMTEMG-DPKNVICEAAEKHKIQLLIVGSHSRGPIQR-AFLGSVSNYCVHNAKCPVLVV  149 (154)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~~~~~dlivlg~~~~~~~~~-~~~gs~~~~l~~~~~~pvliv  149 (154)
                      +.+.+++.+.-+----..+ ...+++++.|++.+..+|+..+.+.-...+ -.+......+.+++++||.+-
T Consensus         9 iL~~A~~~~yaV~AfNv~n~e~~~avi~AAee~~sPvIlq~~~~~~~~~g~~~~~~~~~~~A~~~~VPValH   80 (284)
T PRK12857          9 LLKKAEKGGYAVGAFNCNNMEIVQAIVAAAEAEKSPVIIQASQGAIKYAGIEYISAMVRTAAEKASVPVALH   80 (284)
T ss_pred             HHHHHHHcCCeEEEEEeCCHHHHHHHHHHHHHhCCCEEEEechhHhhhCCHHHHHHHHHHHHHHCCCCEEEE
Confidence            3333444443333333334 789999999999999999988765332222 235566777888999998764

>COG0036 Rpe Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]

Probab=80.20  E-value=14  Score=25.45  Aligned_cols=63  Identities=16%  Similarity=0.191  Sum_probs=48.5

Q ss_pred             HHHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHh
Q 031713           75 ALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCV  139 (154)
Q Consensus        75 ~~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~  139 (154)
                      ....+..+..++.|++.-..+..+.|.+.+..+..  ..|+|.+=+-..++..+.|..++.++|-
T Consensus        96 ~~~~r~i~~Ik~~G~kaGv~lnP~Tp~~~i~~~l~--~vD~VllMsVnPGfgGQ~Fi~~~l~Ki~  158 (220)
T COG0036          96 EHIHRTIQLIKELGVKAGLVLNPATPLEALEPVLD--DVDLVLLMSVNPGFGGQKFIPEVLEKIR  158 (220)
T ss_pred             cCHHHHHHHHHHcCCeEEEEECCCCCHHHHHHHHh--hCCEEEEEeECCCCcccccCHHHHHHHH
Confidence            34556667777789888887777899999999999  8898888777677777777777666553

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	154
2gm3_A	175	Crystal Structure Of An Universal Stress Protein Fa		4e-13
3tnj_A	150	Crystal Structure Of Universal Stress Protein From		4e-06
2pfs_A	150	Crystal Structure Of Universal Stress Protein From		5e-06
1wjg_A	137	Crystal Structure Of A Probable Atp Binding Protein		8e-06
3idf_A	138	The Crystal Structure Of A Usp-Like Protein From Wo		2e-04
1mjh_A	162	Structure-Based Assignment Of The Biochemical Funct		3e-04
3s3t_A	146	Universal Stress Protein Uspa From Lactobacillus Pl		8e-04

>pdb|2GM3|A Chain A, Crystal Structure Of An Universal Stress Protein Family Protein From Arabidopsis Thaliana At3g01520 With Amp Bound Length = 175

Iteration: 1
 Score = 70.5 bits (171), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 47/159 (29%), Positives = 77/159 (48%), Gaps = 14/159 (8%)
Query: 5   KVMVAIDESECRHY---------ALQWALENLGDAISKSD---LIIFTARPTEFIYVQAS 52
           KV VA++ S  + Y         A +W LE +  + + SD   L++      E  +    
Sbjct: 7   KVXVAVNASTIKDYPNPSISCKRAFEWTLEKIVRS-NTSDFKILLLHVQVVDEDGFDDVD 65
Query: 53  MFGAAPPDLLMSIQENQKKXXXXXXGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHK 112
              A+P D     Q N+ K          + C + GV  E   + GDPK+VIC+  ++ +
Sbjct: 66  SIYASPEDFRDXRQSNKAKGLHLLEFFVNK-CHEIGVGCEAWIKTGDPKDVICQEVKRVR 124
Query: 113 IQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK 151
              L+VGS   G  Q+ F+G+VS +CV +A+CPV  +++
Sbjct: 125 PDFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVXTIKR 163

>pdb|3TNJ|A Chain A, Crystal Structure Of Universal Stress Protein From Nitrosomonas Europaea With Amp Bound Length = 150

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/53 (43%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 98  GDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
           G+P+  I   AE+  + L++VGSH R  +    LGS +N  +H AKC VL VR
Sbjct: 95  GEPREEIIRIAEQENVDLIVVGSHGRHGLA-LLLGSTANSVLHYAKCDVLAVR 146

>pdb|2PFS|A Chain A, Crystal Structure Of Universal Stress Protein From Nitrosomonas Europaea Length = 150

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/53 (43%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 98  GDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
           G+P+  I   AE+  + L++VGSH R  +    LGS +N  +H AKC VL VR
Sbjct: 95  GEPREEIIRIAEQENVDLIVVGSHGRHGLA-LLLGSTANSVLHYAKCDVLAVR 146

>pdb|1WJG|A Chain A, Crystal Structure Of A Probable Atp Binding Protein From Thermus Themophilus Hb8 Length = 137

Iteration: 1
 Score = 46.2 bits (108), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 32/95 (33%), Positives = 44/95 (46%), Gaps = 3/95 (3%)
Query: 59  PDLLMS--IQENQKKXXXXXXGRAKEICAKHGVVAETMTEM-GDPKNVICEAAEKHKIQL 115
           PD L     +E  ++      G  +E  A  GV  E    + G P   I +AA   K  L
Sbjct: 43  PDYLGEPFFEEALRRRLERAEGVLEEARALTGVPKEDALLLEGVPAEAILQAARAEKADL 102
Query: 116 LIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
           +++G+   G +   FLGS S   V  A CPVL+VR
Sbjct: 103 IVMGTRGLGALGSLFLGSQSQRVVAEAPCPVLLVR 137

>pdb|3IDF|A Chain A, The Crystal Structure Of A Usp-Like Protein From Wolinella Succinogenes To 2.0a Length = 138

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 35/147 (23%), Positives = 68/147 (46%), Gaps = 10/147 (6%)
Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
           KK++ AID++E    A Q+ L+  G   +   L +   +P   +Y +A +  AA  ++ M
Sbjct: 2   KKLLFAIDDTEACERAAQYILDMFGKD-ADCTLTLIHVKPEFMLYGEAVL--AAYDEIEM 58
Query: 64  SIQENQKKXXXXXXGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSR 123
             +E  K        +      + G+    + + G+P  ++ E A+ +   LLI+GS   
Sbjct: 59  KEEEKAK----LLTQKFSTFFTEKGINPFVVIKEGEPVEMVLEEAKDY--NLLIIGSSEN 112
Query: 124 GPIQRAFLGSVSNYCVHNAKCPVLVVR 150
             + + F     ++ +  A  PVL+V+
Sbjct: 113 SFLNKIFASHQDDF-IQKAPIPVLIVK 138

>pdb|1MJH|A Chain A, Structure-Based Assignment Of The Biochemical Function Of Hypothetical Protein Mj0577: A Test Case Of Structural Genomics Length = 162

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/55 (32%), Positives = 32/55 (58%)
Query: 97  MGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK 151
           +G P   I + AE   + ++I+GSH +  ++   LGSV+   +  +  PVLVV++
Sbjct: 105 VGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKR 159

>pdb|3S3T|A Chain A, Universal Stress Protein Uspa From Lactobacillus Plantarum Length = 146

Iteration: 1
 Score = 39.3 bits (90), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 92  ETMTEMGDPKNVICEAAEKH-KIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
           +T    G PK+ I + A++H +I L+++G+       R  +GS ++Y V +A C V+V+R
Sbjct: 87  KTEISYGIPKHTIEDYAKQHPEIDLIVLGATGTNSPHRVAVGSTTSYVVDHAPCNVIVIR 146

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	154
2gm3_A	175	Unknown protein; AT3G01520, putative ethylene-resp	4e-51
3idf_A	138	USP-like protein; universal, stress, PSI, MCSG, st	4e-43
1tq8_A	163	Hypothetical protein RV1636; MTCY01B2.28, structur	4e-36
1mjh_A	162	Protein (ATP-binding domain of protein MJ0577); hy	3e-34
3s3t_A	146	Nucleotide-binding protein, universal stress PROT	6e-32
2z08_A	137	Universal stress protein family; uncharacterized c	2e-31
3hgm_A	147	Universal stress protein TEAD; rossman fold, signa	5e-31
3fg9_A	156	Protein of universal stress protein USPA family; A	6e-31
3tnj_A	150	Universal stress protein (USP); structural genomic	3e-30
2dum_A	170	Hypothetical protein PH0823; conserved hypothetica	1e-29
3fdx_A	143	Putative filament protein / universal stress PROT;	6e-28
1jmv_A	141	USPA, universal stress protein A; chaperone; 1.85A	2e-26
3loq_A	294	Universal stress protein; structural genomics, PSI	1e-25
3loq_A	294	Universal stress protein; structural genomics, PSI	1e-22
3dlo_A	155	Universal stress protein; unknown function, struct	2e-25
3olq_A	319	Universal stress protein E; structural genomics, P	2e-21
3olq_A	319	Universal stress protein E; structural genomics, P	8e-16
3cis_A	309	Uncharacterized protein; alpha/beta hydrolase, ATP	4e-20
3cis_A	309	Uncharacterized protein; alpha/beta hydrolase, ATP	3e-17
3ab8_A	268	Putative uncharacterized protein TTHA0350; tandem-	7e-19
3ab8_A	268	Putative uncharacterized protein TTHA0350; tandem-	4e-16
3mt0_A	290	Uncharacterized protein PA1789; structural genomic	1e-16
3mt0_A	290	Uncharacterized protein PA1789; structural genomic	4e-13
1q77_A	138	Hypothetical protein AQ_178; structural genomics,	8e-10

>2gm3_A Unknown protein; AT3G01520, putative ethylene-responsive protein, USP domain, nucleotide binding domain, AMP; HET: MSE AMP; 2.46A {Arabidopsis thaliana} SCOP: c.26.2.4 Length = 175

 Score =  159 bits (405), Expect = 4e-51
 Identities = 45/163 (27%), Positives = 81/163 (49%), Gaps = 10/163 (6%)

Query: 2   DKKKVMVAIDESECRHY---------ALQWALENLGDA-ISKSDLIIFTARPTEFIYVQA 51
           +  KVMVA++ S  + Y         A +W LE +  +  S   +++   +  +      
Sbjct: 4   EPTKVMVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQVVDEDGFDD 63

Query: 52  SMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKH 111
                A P+    ++++ K   L LL      C + GV  E   + GDPK+VIC+  ++ 
Sbjct: 64  VDSIYASPEDFRDMRQSNKAKGLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRV 123

Query: 112 KIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE 154
           +   L+VGS   G  Q+ F+G+VS +CV +A+CPV+ +++  +
Sbjct: 124 RPDFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVMTIKRNAD 166

>3idf_A USP-like protein; universal, stress, PSI, MCSG, structural genomics, midwest center for structural genomics structure initiative; 2.00A {Wolinella succinogenes} Length = 138

 Score =  138 bits (349), Expect = 4e-43
 Identities = 34/147 (23%), Positives = 64/147 (43%), Gaps = 10/147 (6%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
           KK++ AID++E    A Q+ L+  G   +   L +   +P   +Y      G A      
Sbjct: 2   KKLLFAIDDTEACERAAQYILDMFGKD-ADCTLTLIHVKPEFMLY------GEAVLAAYD 54

Query: 64  SIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSR 123
            I+  +++ A  L  +      + G+    + + G+P  ++ E A+     LLI+GS   
Sbjct: 55  EIEMKEEEKAKLLTQKFSTFFTEKGINPFVVIKEGEPVEMVLEEAK--DYNLLIIGSSEN 112

Query: 124 GPIQRAFLGSVSNYCVHNAKCPVLVVR 150
             + +    S  +  +  A  PVL+V+
Sbjct: 113 SFLNK-IFASHQDDFIQKAPIPVLIVK 138

>1tq8_A Hypothetical protein RV1636; MTCY01B2.28, structural target, NYSGXRC, PSI, protein structure initiative; 2.40A {Mycobacterium tuberculosis} SCOP: c.26.2.4 Length = 163

 Score =  121 bits (305), Expect = 4e-36
 Identities = 40/150 (26%), Positives = 57/150 (38%), Gaps = 9/150 (6%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
           K V+V  D S+    A+  A +    A + + LII +A        Q     AA      
Sbjct: 18  KTVVVGTDGSDSSMRAVDRAAQ---IAGADAKLIIASA-----YLPQHEDARAADILKDE 69

Query: 64  SIQENQKKAALALLGRAKEICAKHGVV-AETMTEMGDPKNVICEAAEKHKIQLLIVGSHS 122
           S +         +L  AKE     G    E    +G P + +   A++ K  LL+VG+  
Sbjct: 70  SYKVTGTAPIYEILHDAKERAHNAGAKNVEERPIVGAPVDALVNLADEEKADLLVVGNVG 129

Query: 123 RGPIQRAFLGSVSNYCVHNAKCPVLVVRKP 152
              I    LGSV       AK  VL+V   
Sbjct: 130 LSTIAGRLLGSVPANVSRRAKVDVLIVHTT 159

>1mjh_A Protein (ATP-binding domain of protein MJ0577); hypothetical protein, structural genomics, functional assignment; HET: ATP; 1.70A {Methanocaldococcus jannaschii} SCOP: c.26.2.4 Length = 162

 Score =  116 bits (293), Expect = 3e-34
 Identities = 31/155 (20%), Positives = 61/155 (39%), Gaps = 6/155 (3%)

Query: 4   KKVMVAIDESECRHYALQWALE--NLGDA----ISKSDLIIFTARPTEFIYVQASMFGAA 57
           KK++   D SE    AL+       L       +   D      R    + +  +    +
Sbjct: 6   KKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNKS 65

Query: 58  PPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLI 117
             +    ++    + A   +   K+     G   + +  +G P   I + AE   + ++I
Sbjct: 66  VEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIII 125

Query: 118 VGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP 152
           +GSH +  ++   LGSV+   +  +  PVLVV++ 
Sbjct: 126 MGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRK 160

>3s3t_A Nucleotide-binding protein, universal stress PROT family; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; HET: ATP; 1.90A {Lactobacillus plantarum} Length = 146

 Score =  110 bits (277), Expect = 6e-32
 Identities = 31/151 (20%), Positives = 66/151 (43%), Gaps = 14/151 (9%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYV--QASMFGAAPPDL 61
             ++V +D S+    A   A+  +     +++L          +YV   ++    A   +
Sbjct: 6   TNILVPVDSSDAAQAAFTEAVN-IAQR-HQANLTA--------LYVVDDSAYHTPALDPV 55

Query: 62  LMSIQENQKKAALALLGRAKEICAKHGVV-AETMTEMGDPKNVICE-AAEKHKIQLLIVG 119
           L  + + +   A   + + ++  A       +T    G PK+ I + A +  +I L+++G
Sbjct: 56  LSELLDAEAAHAKDAMRQRQQFVATTSAPNLKTEISYGIPKHTIEDYAKQHPEIDLIVLG 115

Query: 120 SHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
           +       R  +GS ++Y V +A C V+V+R
Sbjct: 116 ATGTNSPHRVAVGSTTSYVVDHAPCNVIVIR 146

>2z08_A Universal stress protein family; uncharacterized conserved protein, structural genomics, unknown function, NPPSFA; HET: ATP; 1.55A {Thermus thermophilus} SCOP: c.26.2.4 PDB: 1wjg_A* 2z09_A* 2z3v_A Length = 137

 Score =  108 bits (272), Expect = 2e-31
 Identities = 38/148 (25%), Positives = 61/148 (41%), Gaps = 14/148 (9%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
           K +++A D SE    A + A     +A   + LI+        ++    +          
Sbjct: 3   KTILLAYDGSEHARRAAEVAKA-EAEA-HGARLIV--------VHAYEPVPDYLGEPFFE 52

Query: 64  SIQENQKKAALALLGRAKEICAKHGVVA-ETMTEMGDPKNVICEAAEKHKIQLLIVGSHS 122
                + + A  +L   +E  A  GV   + +   G P   I +AA   K  L+++G+  
Sbjct: 53  EALRRRLERAEGVL---EEARALTGVPKEDALLLEGVPAEAILQAARAEKADLIVMGTRG 109

Query: 123 RGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
            G +   FLGS S   V  A CPVL+VR
Sbjct: 110 LGALGSLFLGSQSQRVVAEAPCPVLLVR 137

>3hgm_A Universal stress protein TEAD; rossman fold, signaling protein; HET: ATP; 1.90A {Halomonas elongata} Length = 147

 Score =  108 bits (271), Expect = 5e-31
 Identities = 37/149 (24%), Positives = 62/149 (41%), Gaps = 7/149 (4%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
            ++MV +D S+    AL+  +  L    + ++L I        +    +    A P+ L 
Sbjct: 3   NRIMVPVDGSKGAVKALEKGVG-LQQL-TGAELYILCVFKHHSLL--EASLSMARPEQLD 58

Query: 64  SIQENQKKAALALLGRAKEICAKHGVVA---ETMTEMGDPKNVICEAAEKHKIQLLIVGS 120
              +  K  A  +  +AK    + GV A       + G P   I   A K +  L+++G+
Sbjct: 59  IPDDALKDYATEIAVQAKTRATELGVPADKVRAFVKGGRPSRTIVRFARKRECDLVVIGA 118

Query: 121 HSRGPIQRAFLGSVSNYCVHNAKCPVLVV 149
                 +   LGSV+     +A CPVLVV
Sbjct: 119 QGTNGDKSLLLGSVAQRVAGSAHCPVLVV 147

>3fg9_A Protein of universal stress protein USPA family; APC60691, nucleotide- binding, lactobacillus plantarum WCFS1, structural genomics PSI-2; 1.47A {Lactobacillus plantarum} Length = 156

 Score =  108 bits (271), Expect = 6e-31
 Identities = 29/152 (19%), Positives = 64/152 (42%), Gaps = 16/152 (10%)

Query: 4   KKVMVAID--ESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDL 61
           +++++ +D  ++     A ++A     D      L I +   +E      ++F +  P  
Sbjct: 16  RRILLTVDEDDNTSSERAFRYATTLAHD--YDVPLGICSVLESE----DINIFDSLTPSK 69

Query: 62  LMSIQENQKKAALALLGRAKEICAKHGV--VAETMTEMGDPKNVIC-EAAEKHKIQLLIV 118
           +    + ++K    ++    ++  + GV  V   + E GD  +VI  +   + K  LL+ 
Sbjct: 70  I----QAKRKHVEDVVAEYVQLAEQRGVNQVEPLVYEGGDVDDVILEQVIPEFKPDLLVT 125

Query: 119 GSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
           G+ +  P  +   G++       A   V+VVR
Sbjct: 126 GADTEFPHSK-IAGAIGPRLARKAPISVIVVR 156

>3tnj_A Universal stress protein (USP); structural genomics, PSI-biology, midwest center for structu genomics, MCSG, chaperone; HET: AMP; 2.00A {Nitrosomonas europaea} PDB: 2pfs_A* Length = 150

 Score =  105 bits (265), Expect = 3e-30
 Identities = 37/152 (24%), Positives = 61/152 (40%), Gaps = 9/152 (5%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
             +++A+D S      +Q     L      + L +        I +  + +G A P    
Sbjct: 7   HHILLAVDFSSEDSQVVQKVRN-LASQ-IGARLSLIHVLDN--IPMPDTPYGTAIPLDTE 62

Query: 64  SIQENQKKAALALLGRAKEICAKHGV-VAETMTEMGDPKNVICEAAEKHKIQLLIVGSHS 122
           +  +         L    +I    G+  A      G+P+  I   AE+  + L++VGSH 
Sbjct: 63  TTYDAMLDVEKQKL---SQIGNTLGIDPAHRWLVWGEPREEIIRIAEQENVDLIVVGSHG 119

Query: 123 RGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE 154
           R  +    LGS +N  +H AKC VL VR   +
Sbjct: 120 RHGL-ALLLGSTANSVLHYAKCDVLAVRLRDD 150

>2dum_A Hypothetical protein PH0823; conserved hypothetical protein, putative universal protein A structural genomics, NPPSFA; 2.75A {Pyrococcus horikoshii} Length = 170

 Score =  105 bits (263), Expect = 1e-29
 Identities = 35/158 (22%), Positives = 63/158 (39%), Gaps = 11/158 (6%)

Query: 4   KKVMVAIDESECRHYALQWALE--NLGDAISKSDLIIFTA---RPTEFIYVQASMFGAAP 58
           +KV+   D SE  + A++   +   +       ++I+         E +    S F    
Sbjct: 6   RKVLFPTDFSEGAYRAVEVFEKRNKMEVG----EVILLHVIDEGTLEELMDGYSFFYDNA 61

Query: 59  PDLLMSIQENQKKAALALLGRAKEICAK--HGVVAETMTEMGDPKNVICEAAEKHKIQLL 116
              L  I+E  K+ A   L    E   +        T+   G P + I + AE+  + L+
Sbjct: 62  EIELKDIKEKLKEEASRKLQEKAEEVKRAFRAKNVRTIIRFGIPWDEIVKVAEEENVSLI 121

Query: 117 IVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE 154
           I+ S  +  +   FLGS     +   K PVL++++  E
Sbjct: 122 ILPSRGKLSLSHEFLGSTVMRVLRKTKKPVLIIKEVDE 159

>3fdx_A Putative filament protein / universal stress PROT; structural genomics, APC60640.1, universal protein F, PSI-2; HET: MSE ATP; 1.58A {Klebsiella pneumoniae subsp} PDB: 3fh0_A* Length = 143

 Score =   99 bits (250), Expect = 6e-28
 Identities = 32/149 (21%), Positives = 53/149 (35%), Gaps = 9/149 (6%)

Query: 4   KKVMVAIDESECRH--YALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDL 61
             ++V ID S+       +             +++   T  P+   Y    M   A    
Sbjct: 2   NAILVPIDISDKEFTERIISHVES-EARI-DDAEVHFLTVIPSLPYYASLGMAYTAELPG 59

Query: 62  LMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSH 121
           +  ++E     +   L    +  +            G PK+ I   A+     L+I+ SH
Sbjct: 60  MDELRE----GSETQLKEIAKKFSIPEDRMHFHVAEGSPKDKILALAKSLPADLVIIASH 115

Query: 122 SRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
               I    LGS +   V +A+C VLVVR
Sbjct: 116 RPD-ITTYLLGSNAAAVVRHAECSVLVVR 143

>1jmv_A USPA, universal stress protein A; chaperone; 1.85A {Haemophilus influenzae} SCOP: c.26.2.4 Length = 141

 Score = 95.8 bits (239), Expect = 2e-26
 Identities = 29/148 (19%), Positives = 61/148 (41%), Gaps = 14/148 (9%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
           K ++VA+D SE     L+ A+  +      + L I        I+V  +        + +
Sbjct: 3   KHILVAVDLSEESPILLKKAVG-IAKR-HDAKLSI--------IHVDVNFSDLYTGLIDV 52

Query: 64  SIQENQKKAALALLGRAKEICAKHGV-VAETMTEMGDPKNVICEAAEKHKIQLLIVGSHS 122
           ++   Q + +        ++       ++E ++  GD   V+ +A E++ + LL+ G H 
Sbjct: 53  NMSSMQDRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHHQ 112

Query: 123 RGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
                 + L S +   ++  K  +LVV 
Sbjct: 113 DF---WSKLMSSTRQVMNTIKIDMLVVP 137

>3loq_A Universal stress protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: AMP; 2.32A {Archaeoglobus fulgidus} Length = 294

 Score = 97.4 bits (243), Expect = 1e-25
 Identities = 29/151 (19%), Positives = 51/151 (33%), Gaps = 28/151 (18%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
            +V+VA D S+    AL++A                               G     ++ 
Sbjct: 171 DRVLVAYDFSKWADRALEYAKF------------------------VVKKTGG-ELHIIH 205

Query: 64  SIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSR 123
             ++  K A L +    +E+    G+      E G P   I    E+     + +GS   
Sbjct: 206 VSEDGDKTADLRV---MEEVIGAEGIEVHVHIESGTPHKAILAKREEINATTIFMGSRGA 262

Query: 124 GPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE 154
           G +    LGS S   +  +  PV V ++  +
Sbjct: 263 GSVMTMILGSTSESVIRRSPVPVFVCKRGDD 293

>3loq_A Universal stress protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: AMP; 2.32A {Archaeoglobus fulgidus} Length = 294

 Score = 89.7 bits (223), Expect = 1e-22
 Identities = 27/155 (17%), Positives = 58/155 (37%), Gaps = 16/155 (10%)

Query: 4   KKVMVAIDESECRHYALQWALE--NLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDL 61
             +++  D SE     L++  +   +G      ++ +              +   +    
Sbjct: 23  NAMLLPTDLSENSFKVLEYLGDFKKVGVE----EIGVLFVINL------TKLSTVSGGID 72

Query: 62  LMSIQENQKKAALALLGRAKEICAKHGVVAETMTEM--GDPKNVICEAAEKHKIQLLIVG 119
           +    +   + A  +L    +     G+ AE +     GDP   I +A+E      + +G
Sbjct: 73  IDHYIDEMSEKAEEVLPEVAQKIEAAGIKAEVIKPFPAGDPVVEIIKASEN--YSFIAMG 130

Query: 120 SHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE 154
           S      ++  LGSVS   +H++K PV + +  + 
Sbjct: 131 SRGASKFKKILLGSVSEGVLHDSKVPVYIFKHDMV 165

>3dlo_A Universal stress protein; unknown function, structural genomics, PSI-2, protein struct initiative, midwest center for structural genomics; HET: MSE; 1.97A {Archaeoglobus fulgidus} PDB: 3qtb_A* Length = 155

 Score = 93.6 bits (233), Expect = 2e-25
 Identities = 29/154 (18%), Positives = 55/154 (35%), Gaps = 30/154 (19%)

Query: 4   KKVMVAID-ESECRHYALQWALENLGDAISKSDLIIFTARPTE----FIYVQASMFGAAP 58
             ++VA+D +S+     L++A E               AR        ++          
Sbjct: 25  MPIVVAVDKKSDRAERVLRFAAE--------------EARLRGVPVYVVHSLPGGGRTKD 70

Query: 59  PDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEM--GDPKNVICEAAEKHKIQLL 116
            D++          A   L  A  I  K G   E    +   +P + I + A++     +
Sbjct: 71  EDII---------EAKETLSWAVSIIRKEGAEGEEHLLVRGKEPPDDIVDFADEVDAIAI 121

Query: 117 IVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
           ++G   R P  +   GSV+   +  A  PV+ ++
Sbjct: 122 VIGIRKRSPTGKLIFGSVARDVILKANKPVICIK 155

>3olq_A Universal stress protein E; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: UNL; 1.82A {Proteus mirabilis} Length = 319

 Score = 86.9 bits (215), Expect = 2e-21
 Identities = 28/151 (18%), Positives = 53/151 (35%), Gaps = 1/151 (0%)

Query: 1   MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPD 60
            +   ++VA + S    Y     L+ +      S  I              +    A   
Sbjct: 154 PEYGTIVVAANLSNEESYHDALNLKLIELTNDLSHRIQKDPDVHLLSAYPVAPINIAIEL 213

Query: 61  LLMSIQENQKKAALALLGRAKEICAKHGVVAE-TMTEMGDPKNVICEAAEKHKIQLLIVG 119
                           L   KE+  K  +  E T  + G P+ VI +  E+    ++++G
Sbjct: 214 PDFDPNLYNNALRGQHLIAMKELRQKFSIPEEKTHVKEGLPEQVIPQVCEELNAGIVVLG 273

Query: 120 SHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
              R  +  AFLG+ +   + + KC +L ++
Sbjct: 274 ILGRTGLSAAFLGNTAEQLIDHIKCDLLAIK 304

>3olq_A Universal stress protein E; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: UNL; 1.82A {Proteus mirabilis} Length = 319

 Score = 71.5 bits (175), Expect = 8e-16
 Identities = 23/148 (15%), Positives = 49/148 (33%), Gaps = 7/148 (4%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
           + ++V ID ++    AL+ A+  +    +   +  F         +   M     PD   
Sbjct: 8   QNLLVVIDPNQDDQPALRRAVY-IVQR-NGGRIKAFLPVYD----LSYDMTTLLSPDERN 61

Query: 64  SIQENQKKAALALLGRAKEICAKHGVVAETMTEM-GDPKNVICEAAEKHKIQLLIVGSHS 122
           ++++       A + +      + G+  +        P   I E     K  LLI  +H 
Sbjct: 62  AMRKGVINQKTAWIKQQARYYLEAGIQIDIKVIWHNRPYEAIIEEVITDKHDLLIKMAHQ 121

Query: 123 RGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
              +       +    +     PV +V+
Sbjct: 122 HDKLGSLIFTPLDWQLLRKCPAPVWMVK 149

>3cis_A Uncharacterized protein; alpha/beta hydrolase, ATP, universal stress protein, unknown function; HET: ATP; 2.90A {Mycobacterium tuberculosis} PDB: 2jax_A* Length = 309

 Score = 83.6 bits (207), Expect = 4e-20
 Identities = 30/150 (20%), Positives = 52/150 (34%), Gaps = 15/150 (10%)

Query: 5   KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMS 64
            V+V +D S     A   A +              + R  + + + A           + 
Sbjct: 173 PVLVGVDGSSASELATAIAFD------------EASRRNVDLVALHAWSDVDVSEWPGID 220

Query: 65  IQENQKKAALALLGRAKEICAKH-GVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSR 123
               Q  A   L  R      ++  V    +     P   + + +E+   QL++VGS  R
Sbjct: 221 WPATQSMAEQVLAERLAGWQERYPNVAITRVVVRDQPARQLVQRSEE--AQLVVVGSRGR 278

Query: 124 GPIQRAFLGSVSNYCVHNAKCPVLVVRKPV 153
           G      +GSV       A+ PV+V R+ +
Sbjct: 279 GGYAGMLVGSVGETVAQLARTPVIVARESL 308

>3cis_A Uncharacterized protein; alpha/beta hydrolase, ATP, universal stress protein, unknown function; HET: ATP; 2.90A {Mycobacterium tuberculosis} PDB: 2jax_A* Length = 309

 Score = 75.5 bits (186), Expect = 3e-17
 Identities = 29/150 (19%), Positives = 51/150 (34%), Gaps = 8/150 (5%)

Query: 6   VMVAIDESECRHYALQWALENLGDAIS-KSDLIIFTARPTEFIYVQASMFGAAPPDLLMS 64
           ++V ID+S     A++WA     DA   K  L +  A   E                   
Sbjct: 22  IIVGIDDSPAAQVAVRWAAR---DAELRKIPLTLVHAVSPEVATWLEVPLPPGVLRWQQD 78

Query: 65  IQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRG 124
              +    AL ++ +A            +          + + +      L++VG    G
Sbjct: 79  HGRHLIDDALKVVEQASLRA--GPPTVHSEIVPAAAVPTLVDMS--KDAVLMVVGCLGSG 134

Query: 125 PIQRAFLGSVSNYCVHNAKCPVLVVRKPVE 154
                 LGSVS+  + +A CPV+++     
Sbjct: 135 RWPGRLLGSVSSGLLRHAHCPVVIIHDEDS 164

>3ab8_A Putative uncharacterized protein TTHA0350; tandem-type universal stress protein, unknown function; HET: ATP; 1.70A {Thermus thermophilus} PDB: 3ab7_A* Length = 268

 Score = 79.4 bits (196), Expect = 7e-19
 Identities = 30/156 (19%), Positives = 53/156 (33%), Gaps = 13/156 (8%)

Query: 5   KVMVAIDESECRHYALQWALE--NLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLL 62
           ++++A D S     A   A        A     L +     T    +   +   A    +
Sbjct: 2   RILLATDGSPQARGAEALAEWLAYKLSA----PLTVLFVVDTRLARIPELLDFGALTVPV 57

Query: 63  MSIQENQKKAAL----ALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIV 118
             ++   ++A      A+L R ++     GV  E + E G P   I   A      LL++
Sbjct: 58  PVLRTELERALALRGEAVLERVRQSALAAGVAVEAVLEEGVPHEAILRRARAA--DLLVL 115

Query: 119 GSHSR-GPIQRAFLGSVSNYCVHNAKCPVLVVRKPV 153
           G            LGS ++  +  +  PVL+     
Sbjct: 116 GRSGEAHGDGFGGLGSTADRVLRASPVPVLLAPGEP 151

>3ab8_A Putative uncharacterized protein TTHA0350; tandem-type universal stress protein, unknown function; HET: ATP; 1.70A {Thermus thermophilus} PDB: 3ab7_A* Length = 268

 Score = 72.1 bits (177), Expect = 4e-16
 Identities = 29/150 (19%), Positives = 47/150 (31%), Gaps = 33/150 (22%)

Query: 1   MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPD 60
           ++ +  ++  D SE    AL                              A   G     
Sbjct: 152 VELEGALLGYDASESAVRALHALAP------------------------LARALGL-GVR 186

Query: 61  LLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGS 120
           ++   ++     A A    A+     HGV A  +   GD  + +          LL +G+
Sbjct: 187 VVSVHEDPA--RAEAWALEAEAYLRDHGVEASALVLGGDAADHLLRLQ--GPGDLLALGA 242

Query: 121 HSRGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
             R    R   GS +   + NA+ PVL  R
Sbjct: 243 PVR----RLVFGSTAERVIRNAQGPVLTAR 268

>3mt0_A Uncharacterized protein PA1789; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: MSE; 1.58A {Pseudomonas aeruginosa} Length = 290

 Score = 73.9 bits (181), Expect = 1e-16
 Identities = 17/98 (17%), Positives = 39/98 (39%), Gaps = 4/98 (4%)

Query: 56  AAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMT-EMGDPKNVICEAAEKHKIQ 114
            +  D    + E  +          +   A++G   E +  E G    +I   A+K    
Sbjct: 183 LSSADPTFQLSETIEARYREAC---RTFQAEYGFSDEQLHIEEGPADVLIPRTAQKLDAV 239

Query: 115 LLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP 152
           + ++G+ +R  +  A +G+ +   +   +  VLV++  
Sbjct: 240 VTVIGTVARTGLSGALIGNTAEVVLDTLESDVLVLKPD 277

>3mt0_A Uncharacterized protein PA1789; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: MSE; 1.58A {Pseudomonas aeruginosa} Length = 290

 Score = 63.8 bits (155), Expect = 4e-13
 Identities = 27/153 (17%), Positives = 49/153 (32%), Gaps = 28/153 (18%)

Query: 1   MDK-KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPP 59
           M   + ++V I+  +    AL+ A                           A +  +   
Sbjct: 4   MQAIRSILVVIEPDQLEGLALKRAQL------------------------IAGVTQS-HL 38

Query: 60  DLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVG 119
            LL+  +     AAL  L  A+E+  +   V+            I    +     L+I  
Sbjct: 39  HLLVCEKRRDHSAALNDL--AQELREEGYSVSTNQAWKDSLHQTIIAEQQAEGCGLIIKQ 96

Query: 120 SHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP 152
                P+++A L       +  A CPVL+ +  
Sbjct: 97  HFPDNPLKKAILTPDDWKLLRFAPCPVLMTKTA 129

>1q77_A Hypothetical protein AQ_178; structural genomics, universal stress protein, PSI, protein structure initiative; 2.70A {Aquifex aeolicus} SCOP: c.26.2.4 Length = 138

 Score = 52.8 bits (126), Expect = 8e-10
 Identities = 19/129 (14%), Positives = 39/129 (30%), Gaps = 4/129 (3%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
           K ++V  D       A+ +A+    +    ++L I      E +Y               
Sbjct: 5   KVLLVLTDAYSDCEKAITYAVN-FSEK-LGAELDILAV--LEDVYNLERANVTFGLPFPP 60

Query: 64  SIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSR 123
            I+E  KK     L    E       +      +G     + +  E    +L++   +  
Sbjct: 61  EIKEESKKRIERRLREVWEKLTGSTEIPGVEYRIGPLSEEVKKFVEGKGYELVVWACYPS 120

Query: 124 GPIQRAFLG 132
             + +   G
Sbjct: 121 AYLCKVIDG 129

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	154
3s3t_A	146	Nucleotide-binding protein, universal stress PROT	100.0
1mjh_A	162	Protein (ATP-binding domain of protein MJ0577); hy	99.98
2dum_A	170	Hypothetical protein PH0823; conserved hypothetica	99.97
3hgm_A	147	Universal stress protein TEAD; rossman fold, signa	99.97
3fg9_A	156	Protein of universal stress protein USPA family; A	99.97
3idf_A	138	USP-like protein; universal, stress, PSI, MCSG, st	99.97
3dlo_A	155	Universal stress protein; unknown function, struct	99.97
3tnj_A	150	Universal stress protein (USP); structural genomic	99.97
1tq8_A	163	Hypothetical protein RV1636; MTCY01B2.28, structur	99.97
2gm3_A	175	Unknown protein; AT3G01520, putative ethylene-resp	99.97
2z08_A	137	Universal stress protein family; uncharacterized c	99.97
3olq_A	319	Universal stress protein E; structural genomics, P	99.95
3fdx_A	143	Putative filament protein / universal stress PROT;	99.95
1jmv_A	141	USPA, universal stress protein A; chaperone; 1.85A	99.95
3loq_A	294	Universal stress protein; structural genomics, PSI	99.94
3cis_A	309	Uncharacterized protein; alpha/beta hydrolase, ATP	99.93
3ab8_A	268	Putative uncharacterized protein TTHA0350; tandem-	99.93
1q77_A	138	Hypothetical protein AQ_178; structural genomics,	99.93
3mt0_A	290	Uncharacterized protein PA1789; structural genomic	99.93
3mt0_A	290	Uncharacterized protein PA1789; structural genomic	99.93
3loq_A	294	Universal stress protein; structural genomics, PSI	99.92
3cis_A	309	Uncharacterized protein; alpha/beta hydrolase, ATP	99.91
3olq_A	319	Universal stress protein E; structural genomics, P	99.91
3ab8_A	268	Putative uncharacterized protein TTHA0350; tandem-	99.87
2iel_A	138	Hypothetical protein TT0030; TT0030,thermus thermo	97.86
1wy5_A	317	TILS, hypothetical UPF0072 protein AQ_1887; N-type	96.71
3a2k_A	464	TRNA(Ile)-lysidine synthase; ligase, pseudo-knot,	96.71
3g40_A	294	Na-K-CL cotransporter; alpha/beta fold 10-stranded	96.45
2xry_A	482	Deoxyribodipyrimidine photolyase; DNA damage, DNA	95.79
4b4k_A	181	N5-carboxyaminoimidazole ribonucleotide mutase; is	95.79
3g40_A	294	Na-K-CL cotransporter; alpha/beta fold 10-stranded	95.53
3umv_A	506	Deoxyribodipyrimidine photo-lyase; CPD cyclobutane	95.28
2ywx_A	157	Phosphoribosylaminoimidazole carboxylase catalyti;	95.26
4grd_A	173	N5-CAIR mutase, phosphoribosylaminoimidazole carbo	95.24
3oow_A	166	Phosphoribosylaminoimidazole carboxylase,catalyic;	95.07
1xmp_A	170	PURE, phosphoribosylaminoimidazole carboxylase; pu	95.0
3trh_A	169	Phosphoribosylaminoimidazole carboxylase carboxylt	94.98
3kuu_A	174	Phosphoribosylaminoimidazole carboxylase catalyti	94.87
3rg8_A	159	Phosphoribosylaminoimidazole carboxylase, PURE PR;	94.57
3ors_A	163	N5-carboxyaminoimidazole ribonucleotide mutase; is	94.51
1zun_A	325	Sulfate adenylyltransferase subunit 2; beta barrel	94.43
1o4v_A	183	Phosphoribosylaminoimidazole mutase PURE; structur	94.39
1u11_A	182	PURE (N5-carboxyaminoimidazole ribonucleotide MUT;	94.34
3lp6_A	174	Phosphoribosylaminoimidazole carboxylase catalyti;	94.29
1o97_C	264	Electron transferring flavoprotein beta-subunit; F	93.95
2wq7_A	543	RE11660P; lyase-DNA complex, DNA repair, DNA lesio	93.89
1ni5_A	433	Putative cell cycle protein MESJ; structural genom	93.77
3ih5_A	217	Electron transfer flavoprotein alpha-subunit; alph	93.62
1efv_B	255	Electron transfer flavoprotein; electron transport	92.25
1efp_B	252	ETF, protein (electron transfer flavoprotein); ele	91.95
3bl5_A	219	Queuosine biosynthesis protein QUEC; PREQ1 biosynt	91.37
1np7_A	489	DNA photolyase; protein with FAD cofactor; HET: DN	91.36
2nz2_A	413	Argininosuccinate synthase; amino-acid biosynthesi	91.0
3k32_A	203	Uncharacterized protein MJ0690; predicted subunit	90.77
3tvs_A	538	Cryptochrome-1; circadian clock light entrainment,	90.49
3p9x_A	211	Phosphoribosylglycinamide formyltransferase; struc	90.48
1iv0_A	98	Hypothetical protein; rnaseh-like, YQGF, structura	90.41
3da8_A	215	Probable 5'-phosphoribosylglycinamide formyltransf	90.18
2hma_A	376	Probable tRNA (5-methylaminomethyl-2-thiouridylat	89.68
4ds3_A	209	Phosphoribosylglycinamide formyltransferase; struc	89.64
3kcq_A	215	Phosphoribosylglycinamide formyltransferase; struc	88.34
3fy4_A	537	6-4 photolyase; DNA repair, clock cryptochrome; HE	88.21
2e0i_A	440	432AA long hypothetical deoxyribodipyrimidine PHO;	87.58
1owl_A	484	Photolyase, deoxyribodipyrimidine photolyase; DNA	87.36
1k92_A	455	Argininosuccinate synthase, argininosuccinate SY;	86.25
2h31_A	425	Multifunctional protein ADE2; alpha-beta-alpha, li	85.92
1dnp_A	471	DNA photolyase; DNA repair, electron transfer, exc	85.27
1sur_A	215	PAPS reductase; assimilatory sulfate reduction, 3-	85.14
2j07_A	420	Deoxyribodipyrimidine photo-lyase; flavoprotein, n	84.74
3s40_A	304	Diacylglycerol kinase; structural genomics, the ce	84.29
2ywb_A	503	GMP synthase [glutamine-hydrolyzing]; GMP syntheta	84.16
3fni_A	159	Putative diflavin flavoprotein A 3; alpha-beta pro	83.92
2j4d_A	525	Cryptochrome 3, cryptochrome DASH; DNA-binding pro	83.8
2qv7_A	337	Diacylglycerol kinase DGKB; alpha-beta domain 1, b	83.79
1kor_A	400	Argininosuccinate synthetase; ligase, riken struct	83.43
3hly_A	161	Flavodoxin-like domain; Q5MZP6_SYNP6, flavoprotein	83.09
1nu0_A	138	Hypothetical protein YQGF; structural genomics, st	83.0
3rjz_A	237	N-type ATP pyrophosphatase superfamily; structural	82.03
2l69_A	134	Rossmann 2X3 fold protein; structural genomics, no	81.14

>3s3t_A Nucleotide-binding protein, universal stress PROT family; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; HET: ATP; 1.90A {Lactobacillus plantarum} SCOP: c.26.2.0

Probab=100.00  E-value=4.8e-32  Score=172.13  Aligned_cols=142  Identities=20%  Similarity=0.313  Sum_probs=125.8

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      |+|++||||+|+++.+..++++|+.+|+..+  ++|+++||.+......      ...........+..++..++.++++
T Consensus         3 ~~~~~ILv~~D~s~~s~~al~~A~~la~~~~--a~l~ll~v~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~l~~~   74 (146)
T 3s3t_A            3 ARYTNILVPVDSSDAAQAAFTEAVNIAQRHQ--ANLTALYVVDDSAYHT------PALDPVLSELLDAEAAHAKDAMRQR   74 (146)
T ss_dssp             CCCCEEEEECCSSHHHHHHHHHHHHHHHHHT--CEEEEEEEEECCCCCC------GGGHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CccceEEEEcCCCHHHHHHHHHHHHHHHhcC--CEEEEEEEecCccccc------cccccccHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999999999999999977  9999999988754321      0111144556677778888999999


Q ss_pred             HHHHHhcCC-eEEEEEecCChhhHHHH-HHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           81 KEICAKHGV-VAETMTEMGDPKNVICE-AAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        81 ~~~~~~~~~-~~~~~v~~g~~~~~i~~-~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      .+.+...|+ ++++.+..|++.+.|++ ++++.++||||||+++++.+.++++||++++++++++||||+||
T Consensus        75 ~~~~~~~g~~~~~~~~~~g~~~~~I~~~~a~~~~~dliV~G~~~~~~~~~~~~Gs~~~~vl~~~~~pVlvV~  146 (146)
T 3s3t_A           75 QQFVATTSAPNLKTEISYGIPKHTIEDYAKQHPEIDLIVLGATGTNSPHRVAVGSTTSYVVDHAPCNVIVIR  146 (146)
T ss_dssp             HHHHTTSSCCCCEEEEEEECHHHHHHHHHHHSTTCCEEEEESCCSSCTTTCSSCHHHHHHHHHCSSEEEEEC
T ss_pred             HHHHHhcCCcceEEEEecCChHHHHHHHHHhhcCCCEEEECCCCCCCcceEEEcchHHHHhccCCCCEEEeC
Confidence            999998899 89999999999999999 99999999999999999999999999999999999999999997

>1mjh_A Protein (ATP-binding domain of protein MJ0577); hypothetical protein, structural genomics, functional assignment; HET: ATP; 1.70A {Methanocaldococcus jannaschii} SCOP: c.26.2.4

Probab=99.98  E-value=1.3e-30  Score=168.29  Aligned_cols=150  Identities=20%  Similarity=0.296  Sum_probs=122.7

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCC-----chhhcc-cC--CCCCchHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTE-----FIYVQA-SM--FGAAPPDLLMSIQENQKKAA   73 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~-----~~~~~~-~~--~~~~~~~~~~~~~~~~~~~~   73 (154)
                      ++++||||+|+++.+..++++|+.+|+..+  ++|+++||.+..     .....+ ..  +........+...+..++..
T Consensus         4 ~~~~ILv~vD~s~~s~~al~~a~~la~~~~--a~l~ll~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (162)
T 1mjh_A            4 MYKKILYPTDFSETAEIALKHVKAFKTLKA--EEVILLHVIDEREIKKRDIFSLLLGVAGLNKSVEEFENELKNKLTEEA   81 (162)
T ss_dssp             CCCEEEEECCSCHHHHHHHHHHHHTCCSSC--CEEEEEEEEEGGGTC-----------------CHHHHHHHHHHHHHHH
T ss_pred             ccceEEEEeCCCHHHHHHHHHHHHHHhhcC--CeEEEEEEecCccccccccccccccccccccchhhhHHHHHHHHHHHH
Confidence            589999999999999999999999999987  999999998754     110000 00  00000011234556667778


Q ss_pred             HHHHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCCC
Q 031713           74 LALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPV  153 (154)
Q Consensus        74 ~~~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~~  153 (154)
                      ++.++++.+.+...|+++++.+..|++.++|++++++.++||||||+++++.+.++++||++++++++++|||++||++.
T Consensus        82 ~~~l~~~~~~~~~~g~~~~~~v~~G~~~~~I~~~a~~~~~dlIV~G~~g~~~~~~~~~GSv~~~vl~~~~~pVlvv~~~~  161 (162)
T 1mjh_A           82 KNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKN  161 (162)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEEEEECHHHHHHHHHHHTTCSEEEEESCCSSCCTTCSSCHHHHHHHHHCCSCEEEECCCC
T ss_pred             HHHHHHHHHHHHHcCCceEEEEcCCCHHHHHHHHHHHcCCCEEEEcCCCCCCccceEecchHHHHHHhCCCCEEEEeCCC
Confidence            88899998888888999999999999999999999999999999999999999999999999999999999999998764

>2dum_A Hypothetical protein PH0823; conserved hypothetical protein, putative universal protein A structural genomics, NPPSFA; 2.75A {Pyrococcus horikoshii}

Probab=99.97  E-value=2.5e-30  Score=168.18  Aligned_cols=150  Identities=20%  Similarity=0.207  Sum_probs=118.2

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCC--CCc-hHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFG--AAP-PDLLMSIQENQKKAALALLG   78 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~--~~~-~~~~~~~~~~~~~~~~~~l~   78 (154)
                      ++++||||+|+++.+..++++|+.+|+..+  ++|+++||.+..........+.  ... ....+...+..++..++.++
T Consensus         4 m~~~ILv~vD~s~~s~~al~~A~~la~~~~--a~l~ll~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~   81 (170)
T 2dum_A            4 MFRKVLFPTDFSEGAYRAVEVFEKRNKMEV--GEVILLHVIDEGTLEELMDGYSFFYDNAEIELKDIKEKLKEEASRKLQ   81 (170)
T ss_dssp             CCSEEEEECCSSHHHHHHHHHHHHHCCSCC--SEEEEEEEEETTGGGCCC------------CCTTSHHHHHHHHHHHHH
T ss_pred             ccceEEEEecCCHHHHHHHHHHHHHHHhcC--CEEEEEEEecCccccccccccccccccccccHHHHHHHHHHHHHHHHH
Confidence            789999999999999999999999999987  9999999987653321100010  000 00001223445566777888


Q ss_pred             HHHHHHHhcCCeEEE--EEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCCC
Q 031713           79 RAKEICAKHGVVAET--MTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPV  153 (154)
Q Consensus        79 ~~~~~~~~~~~~~~~--~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~~  153 (154)
                      ++.+.+...|+++++  .+..|++.+.|++++++.++||||||+++++.+.++++||++++|+++++||||+||+..
T Consensus        82 ~~~~~~~~~g~~~~~~~~~~~g~~~~~I~~~a~~~~~DlIV~G~~g~~~~~~~~~Gsv~~~vl~~~~~PVlvv~~~~  158 (170)
T 2dum_A           82 EKAEEVKRAFRAKNVRTIIRFGIPWDEIVKVAEEENVSLIILPSRGKLSLSHEFLGSTVMRVLRKTKKPVLIIKEVD  158 (170)
T ss_dssp             HHHHHHHHHTTCSEEEEEEEEECHHHHHHHHHHHTTCSEEEEESCCCCC--TTCCCHHHHHHHHHCSSCEEEECCCC
T ss_pred             HHHHHHHHcCCceeeeeEEecCChHHHHHHHHHHcCCCEEEECCCCCCccccceechHHHHHHHhCCCCEEEEccCC
Confidence            888888778999888  888999999999999999999999999999999999999999999999999999998764

>3hgm_A Universal stress protein TEAD; rossman fold, signaling protein; HET: ATP; 1.90A {Halomonas elongata} SCOP: c.26.2.0

Probab=99.97  E-value=5.3e-31  Score=167.41  Aligned_cols=144  Identities=25%  Similarity=0.298  Sum_probs=119.9

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      ||++||||+|+|+.+..++++|+.+|+..+  ++|+++||.+..........  .......+...+..++..++.++++.
T Consensus         1 M~~~ILv~vD~s~~s~~al~~A~~la~~~~--a~l~ll~v~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~~   76 (147)
T 3hgm_A            1 MFNRIMVPVDGSKGAVKALEKGVGLQQLTG--AELYILCVFKHHSLLEASLS--MARPEQLDIPDDALKDYATEIAVQAK   76 (147)
T ss_dssp             CCSEEEEECCSBHHHHHHHHHHHHHHHHHC--CEEEEEEEECCHHHHHHTBS--SCCCGGGCCCTTHHHHHHHHHHHHHH
T ss_pred             CCceEEEEeCCCHHHHHHHHHHHHHHHhcC--CEEEEEEEecCccccccccc--ccChhhhhhHHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999987  99999999987652211001  11111112223445567778888888


Q ss_pred             HHHHhcCCeE---EEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEE
Q 031713           82 EICAKHGVVA---ETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVV  149 (154)
Q Consensus        82 ~~~~~~~~~~---~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv  149 (154)
                      +.+...|+++   ++.+..|++.++|++++++.++||||||+++++.+.++++||++++++++++|||++|
T Consensus        77 ~~~~~~g~~~~~~~~~~~~g~~~~~I~~~a~~~~~dliV~G~~~~~~~~~~~~Gs~~~~vl~~~~~pVlvV  147 (147)
T 3hgm_A           77 TRATELGVPADKVRAFVKGGRPSRTIVRFARKRECDLVVIGAQGTNGDKSLLLGSVAQRVAGSAHCPVLVV  147 (147)
T ss_dssp             HHHHHTTCCGGGEEEEEEESCHHHHHHHHHHHTTCSEEEECSSCTTCCSCCCCCHHHHHHHHHCSSCEEEC
T ss_pred             HHHHhcCCCccceEEEEecCCHHHHHHHHHHHhCCCEEEEeCCCCccccceeeccHHHHHHhhCCCCEEEC
Confidence            8888889888   9999999999999999999999999999999999999999999999999999999986

>3fg9_A Protein of universal stress protein USPA family; APC60691, nucleotide- binding, lactobacillus plantarum WCFS1, structural genomics PSI-2; 1.47A {Lactobacillus plantarum}

Probab=99.97  E-value=2.3e-30  Score=166.14  Aligned_cols=139  Identities=22%  Similarity=0.319  Sum_probs=119.7

Q ss_pred             CCCcEEEEEec--CCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAID--ESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLG   78 (154)
Q Consensus         1 m~~~~iLv~vd--~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~   78 (154)
                      |+|++||||+|  +++.+..++++|..+|+..+  ++|+++||.+......    +..    ......+..++..++.++
T Consensus        13 ~~~~~ILv~vD~~~s~~s~~al~~a~~la~~~~--a~l~ll~v~~~~~~~~----~~~----~~~~~~~~~~~~~~~~l~   82 (156)
T 3fg9_A           13 LVYRRILLTVDEDDNTSSERAFRYATTLAHDYD--VPLGICSVLESEDINI----FDS----LTPSKIQAKRKHVEDVVA   82 (156)
T ss_dssp             CCCC-EEEECCSCCCHHHHHHHHHHHHHHHHHT--CCEEEEEEECCCCTTC----CCS----SHHHHHHHHHHHHHHHHH
T ss_pred             ccCceEEEEECCCCCHHHHHHHHHHHHHHHhcC--CEEEEEEEEeCCCccc----ccc----CCHHHHHHHHHHHHHHHH
Confidence            58999999999  99999999999999999977  9999999998764321    111    123455666777888899


Q ss_pred             HHHHHHHhcCC-eEEEEEec-CChhhHHHHH-HHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           79 RAKEICAKHGV-VAETMTEM-GDPKNVICEA-AEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        79 ~~~~~~~~~~~-~~~~~v~~-g~~~~~i~~~-a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      ++.+.+...|+ .+++.+.. |++.++|+++ +++.++||||||+++++.+. .++||++++++++++|||++||
T Consensus        83 ~~~~~~~~~g~~~~~~~v~~~g~~~~~I~~~~a~~~~~DlIV~G~~g~~~~~-~~~Gs~~~~vl~~a~~PVlvV~  156 (156)
T 3fg9_A           83 EYVQLAEQRGVNQVEPLVYEGGDVDDVILEQVIPEFKPDLLVTGADTEFPHS-KIAGAIGPRLARKAPISVIVVR  156 (156)
T ss_dssp             HHHHHHHHHTCSSEEEEEEECSCHHHHHHHTHHHHHCCSEEEEETTCCCTTS-SSCSCHHHHHHHHCSSEEEEEC
T ss_pred             HHHHHHHHcCCCceEEEEEeCCCHHHHHHHHHHHhcCCCEEEECCCCCCccc-eeecchHHHHHHhCCCCEEEeC
Confidence            99888888899 49999999 9999999999 99999999999999999887 5899999999999999999996

>3idf_A USP-like protein; universal, stress, PSI, MCSG, structural genomics, midwest center for structural genomics structure initiative; 2.00A {Wolinella succinogenes}

Probab=99.97  E-value=6e-30  Score=161.01  Aligned_cols=136  Identities=25%  Similarity=0.379  Sum_probs=118.4

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHc-ccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHH-HHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENL-GDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQK-KAALALLGRA   80 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la-~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~~   80 (154)
                      |++||||+|+++.+..++++|+.+| +..+  ++|+++||.+......       ..........+..+ +..++.++++
T Consensus         1 ~~~ILv~~D~s~~s~~al~~a~~la~~~~~--a~l~ll~v~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~l~~~   71 (138)
T 3idf_A            1 MKKLLFAIDDTEACERAAQYILDMFGKDAD--CTLTLIHVKPEFMLYG-------EAVLAAYDEIEMKEEEKAKLLTQKF   71 (138)
T ss_dssp             CEEEEEECCSSHHHHHHHHHHHHHHTTCTT--EEEEEEEEECCCCCCH-------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEeCCCHHHHHHHHHHHHHhccCCC--CEEEEEEEecCCCccc-------ccccCcHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999 8877  9999999998764321       01112233445555 7888899999


Q ss_pred             HHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           81 KEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        81 ~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      .+.+...|+++++.+..|++.++|.++++  ++||||||+++++.+.+++ ||++++++++++||||+||
T Consensus        72 ~~~~~~~g~~~~~~v~~g~~~~~I~~~a~--~~dliV~G~~~~~~~~~~~-Gs~~~~vl~~~~~pVlvv~  138 (138)
T 3idf_A           72 STFFTEKGINPFVVIKEGEPVEMVLEEAK--DYNLLIIGSSENSFLNKIF-ASHQDDFIQKAPIPVLIVK  138 (138)
T ss_dssp             HHHHHTTTCCCEEEEEESCHHHHHHHHHT--TCSEEEEECCTTSTTSSCC-CCTTCHHHHHCSSCEEEEC
T ss_pred             HHHHHHCCCCeEEEEecCChHHHHHHHHh--cCCEEEEeCCCcchHHHHh-CcHHHHHHhcCCCCEEEeC
Confidence            99999899999999999999999999999  9999999999999999999 9999999999999999997

>3dlo_A Universal stress protein; unknown function, structural genomics, PSI-2, protein struct initiative, midwest center for structural genomics; HET: MSE; 1.97A {Archaeoglobus fulgidus} PDB: 3qtb_A*

Probab=99.97  E-value=4.3e-30  Score=164.92  Aligned_cols=131  Identities=21%  Similarity=0.270  Sum_probs=115.0

Q ss_pred             CCCcEEEEEecC-CchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDE-SECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGR   79 (154)
Q Consensus         1 m~~~~iLv~vd~-~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~   79 (154)
                      |+|++||||+|+ ++.+..++++|+.+|+..+  ++|+++||.+......                 +...+..++.+++
T Consensus        22 mm~~~ILv~vD~~s~~s~~al~~A~~la~~~~--a~l~llhV~~~~~~~~-----------------~~~~~~~~~~l~~   82 (155)
T 3dlo_A           22 MIYMPIVVAVDKKSDRAERVLRFAAEEARLRG--VPVYVVHSLPGGGRTK-----------------DEDIIEAKETLSW   82 (155)
T ss_dssp             CCCCCEEEECCSSSHHHHHHHHHHHHHHHHHT--CCEEEEEEECCSTTSC-----------------HHHHHHHHHHHHH
T ss_pred             cccCeEEEEECCCCHHHHHHHHHHHHHHHhcC--CEEEEEEEEcCCCccc-----------------HHHHHHHHHHHHH
Confidence            899999999999 9999999999999999977  8999999988643211                 2344567778888


Q ss_pred             HHHHHHhcCCeEEEE--EecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           80 AKEICAKHGVVAETM--TEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        80 ~~~~~~~~~~~~~~~--v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      +.+.+.+.|+++++.  +..|++.++|++++++.++||||||+++++.+.++++||++++++++++||||+|+
T Consensus        83 ~~~~~~~~g~~~~~~~~v~~G~~~~~I~~~a~~~~~DLIV~G~~g~~~~~~~~lGSv~~~vl~~a~~PVLvVr  155 (155)
T 3dlo_A           83 AVSIIRKEGAEGEEHLLVRGKEPPDDIVDFADEVDAIAIVIGIRKRSPTGKLIFGSVARDVILKANKPVICIK  155 (155)
T ss_dssp             HHHHHHHTTCCEEEEEEESSSCHHHHHHHHHHHTTCSEEEEECCEECTTSCEECCHHHHHHHHHCSSCEEEEC
T ss_pred             HHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHcCCCEEEECCCCCCCCCCEEeccHHHHHHHhCCCCEEEeC
Confidence            888888888876654  55699999999999999999999999999999999999999999999999999986

>3tnj_A Universal stress protein (USP); structural genomics, PSI-biology, midwest center for structu genomics, MCSG, chaperone; HET: AMP; 2.00A {Nitrosomonas europaea} PDB: 2pfs_A*

Probab=99.97  E-value=8.2e-30  Score=162.50  Aligned_cols=146  Identities=22%  Similarity=0.232  Sum_probs=102.9

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      |++++||||+|+++.+..++++|+.+|+..+  ++|+++||.+.........+...  ....+...+...+..++.++++
T Consensus         4 ~~~~~ILv~vD~s~~s~~al~~a~~la~~~~--a~l~ll~v~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~   79 (150)
T 3tnj_A            4 SVYHHILLAVDFSSEDSQVVQKVRNLASQIG--ARLSLIHVLDNIPMPDTPYGTAI--PLDTETTYDAMLDVEKQKLSQI   79 (150)
T ss_dssp             CCCSEEEEECCCSTTHHHHHHHHHHHHHHHT--CEEEEEEEEC--------CTTCC--CSSSCCCHHHHHHHHHHHHHHH
T ss_pred             CccceEEEEeCCCHHHHHHHHHHHHHHhhcC--CEEEEEEEEcCcccccccccccc--CcCHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999977  99999999887543210001000  0000112233344455555555


Q ss_pred             HHHHHhcCCe-EEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCCCC
Q 031713           81 KEICAKHGVV-AETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE  154 (154)
Q Consensus        81 ~~~~~~~~~~-~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~~~  154 (154)
                      .+.+   |++ +++.+..|++.++|++++++.++||||||+++++.+. +++||++++++++++|||++||++.+
T Consensus        80 ~~~~---~~~~~~~~~~~g~~~~~I~~~a~~~~~dliV~G~~~~~~~~-~~~Gs~~~~vl~~~~~pVlvv~~~~d  150 (150)
T 3tnj_A           80 GNTL---GIDPAHRWLVWGEPREEIIRIAEQENVDLIVVGSHGRHGLA-LLLGSTANSVLHYAKCDVLAVRLRDD  150 (150)
T ss_dssp             HHHH---TCCGGGEEEEESCHHHHHHHHHHHTTCSEEEEEEC---------CCCHHHHHHHHCSSEEEEEECCC-
T ss_pred             HHHc---CCCcceEEEecCCHHHHHHHHHHHcCCCEEEEecCCCCCcC-eEecchHHHHHHhCCCCEEEEeCCCC
Confidence            4433   666 5788889999999999999999999999999999999 99999999999999999999998764

>1tq8_A Hypothetical protein RV1636; MTCY01B2.28, structural target, NYSGXRC, PSI, protein structure initiative; 2.40A {Mycobacterium tuberculosis} SCOP: c.26.2.4

Probab=99.97  E-value=5.3e-30  Score=165.73  Aligned_cols=143  Identities=27%  Similarity=0.251  Sum_probs=113.7

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEE--EeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIF--TARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLG   78 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l--~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~   78 (154)
                      +++++||||+|+|+.+..++++|+.+|+ .+  ++|+++  ||.+......   +....    .+.+.+..++..++.++
T Consensus        15 ~~~~~ILv~vD~s~~s~~al~~A~~lA~-~~--a~l~ll~a~v~~~~~~~~---~~~~~----~~~~~~~~~~~~~~~l~   84 (163)
T 1tq8_A           15 SAYKTVVVGTDGSDSSMRAVDRAAQIAG-AD--AKLIIASAYLPQHEDARA---ADILK----DESYKVTGTAPIYEILH   84 (163)
T ss_dssp             CCCCEEEEECCSSHHHHHHHHHHHHHHT-TT--SEEEEEEECCC---------------------------CCTHHHHHH
T ss_pred             ccCCEEEEEcCCCHHHHHHHHHHHHHhC-CC--CEEEEEEeeeccCccccc---ccccc----cHHHHHHHHHHHHHHHH
Confidence            3689999999999999999999999999 88  999999  8876543201   00000    11223334556778888


Q ss_pred             HHHHHHHhcCCe-EEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCCC
Q 031713           79 RAKEICAKHGVV-AETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPV  153 (154)
Q Consensus        79 ~~~~~~~~~~~~-~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~~  153 (154)
                      ++.+.+...|++ +++.+..|++.++|++++++.++||||||+++++.+.++++||++++|+++++|||++||++.
T Consensus        85 ~~~~~~~~~gv~~v~~~v~~G~~~~~I~~~a~~~~~DLIV~G~~g~~~~~~~~lGSva~~vl~~a~~PVlvV~~~~  160 (163)
T 1tq8_A           85 DAKERAHNAGAKNVEERPIVGAPVDALVNLADEEKADLLVVGNVGLSTIAGRLLGSVPANVSRRAKVDVLIVHTTE  160 (163)
T ss_dssp             HHHHHHHTTTCCEEEEEEECSSHHHHHHHHHHHTTCSEEEEECCCCCSHHHHHTBBHHHHHHHHTTCEEEEECCC-
T ss_pred             HHHHHHHHcCCCeEEEEEecCCHHHHHHHHHHhcCCCEEEECCCCCCcccceeeccHHHHHHHhCCCCEEEEeCCC
Confidence            888888888998 999999999999999999999999999999999999999999999999999999999998764

>2gm3_A Unknown protein; AT3G01520, putative ethylene-responsive protein, USP domain, nucleotide binding domain, AMP; HET: MSE AMP; 2.46A {Arabidopsis thaliana} SCOP: c.26.2.4

Probab=99.97  E-value=3.1e-29  Score=163.71  Aligned_cols=149  Identities=29%  Similarity=0.532  Sum_probs=108.9

Q ss_pred             CCcEEEEEecCCc---------hHHHHHHHHHHHccc---CCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESE---------CRHYALQWALENLGD---AISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQ   69 (154)
Q Consensus         2 ~~~~iLv~vd~~~---------~~~~~l~~a~~la~~---~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~   69 (154)
                      .+++||||+|+++         .+..++++|+.++..   .+  ++|+++||.+...................+.+.+..
T Consensus         4 ~~~~ILv~vD~s~~~~~~~~~~~s~~al~~a~~la~~~~~~~--a~l~ll~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (175)
T 2gm3_A            4 EPTKVMVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSD--FKILLLHVQVVDEDGFDDVDSIYASPEDFRDMRQSN   81 (175)
T ss_dssp             -CEEEEEECCBCSSSCTTCBCHHHHHHHHHHHHHTTTTCTTS--EEEEEEEEEC----------CCCCSHHHHHHHTTSH
T ss_pred             CccEEEEEECCCcccccccccHHHHHHHHHHHHHhhcccCCC--CEEEEEEEeecccccccccccccCCHHHHHHHHHHH
Confidence            5899999999999         999999999998743   45  899999998654321100000011222233333444


Q ss_pred             HHHHHHHHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEE
Q 031713           70 KKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVV  149 (154)
Q Consensus        70 ~~~~~~~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv  149 (154)
                      .+..++.++++.+.+...|+++++.+..|++.+.|++++++.++||||||+++++.+.++++||++++|+++++||||+|
T Consensus        82 ~~~~~~~l~~~~~~~~~~g~~~~~~v~~G~~~~~I~~~a~~~~~DLIVmG~~g~~~~~~~~~Gsva~~vl~~a~~pVlvv  161 (175)
T 2gm3_A           82 KAKGLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVMTI  161 (175)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCEEEEEEEESCHHHHHHHHHHHHCCSEEEEEECCCC--------CHHHHHHHHCSSCEEEE
T ss_pred             HHHHHHHHHHHHHHHHHCCCceEEEEecCCHHHHHHHHHHHhCCCEEEEeCCCCChhhhhhcCchHHHHHhCCCCCEEEE
Confidence            55667788888888888899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 031713          150 RKP  152 (154)
Q Consensus       150 ~~~  152 (154)
                      |+.
T Consensus       162 ~~~  164 (175)
T 2gm3_A          162 KRN  164 (175)
T ss_dssp             ECC
T ss_pred             cCC
Confidence            865

>2z08_A Universal stress protein family; uncharacterized conserved protein, structural genomics, unknown function, NPPSFA; HET: ATP; 1.55A {Thermus thermophilus} SCOP: c.26.2.4 PDB: 1wjg_A* 2z09_A* 2z3v_A

Probab=99.97  E-value=1.4e-29  Score=159.27  Aligned_cols=136  Identities=29%  Similarity=0.391  Sum_probs=108.0

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      ||++||||+|+++.+..++++|..+|+..+  ++++++||.++.....     ...   ..+...+..++..++.++++.
T Consensus         1 m~~~ILv~~D~s~~s~~al~~a~~la~~~~--a~l~ll~v~~~~~~~~-----~~~---~~~~~~~~~~~~~~~~l~~~~   70 (137)
T 2z08_A            1 MFKTILLAYDGSEHARRAAEVAKAEAEAHG--ARLIVVHAYEPVPDYL-----GEP---FFEEALRRRLERAEGVLEEAR   70 (137)
T ss_dssp             CCSEEEEECCSSHHHHHHHHHHHHHHHHHT--CEEEEEEEECC----------------------CHHHHHHHHHHHHHH
T ss_pred             CcceEEEEeCCCHHHHHHHHHHHHHHhhcC--CEEEEEEEecCCCccc-----ccc---chHHHHHHHHHHHHHHHHHHH
Confidence            589999999999999999999999999977  8999999987532111     000   011222333445555666554


Q ss_pred             HHHHhcCC-eEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           82 EICAKHGV-VAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        82 ~~~~~~~~-~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      +.   .|+ ++++.+..|++.++|++++++.++||||||+++++.+.++++||++++++++++|||++||
T Consensus        71 ~~---~g~~~~~~~~~~g~~~~~I~~~a~~~~~dliV~G~~~~~~~~~~~~Gs~~~~vl~~~~~pVlvv~  137 (137)
T 2z08_A           71 AL---TGVPKEDALLLEGVPAEAILQAARAEKADLIVMGTRGLGALGSLFLGSQSQRVVAEAPCPVLLVR  137 (137)
T ss_dssp             HH---HCCCGGGEEEEESSHHHHHHHHHHHTTCSEEEEESSCTTCCSCSSSCHHHHHHHHHCSSCEEEEC
T ss_pred             HH---cCCCccEEEEEecCHHHHHHHHHHHcCCCEEEECCCCCchhhhhhhccHHHHHHhcCCCCEEEeC
Confidence            43   578 7888888999999999999999999999999999999999999999999999999999997

>3olq_A Universal stress protein E; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: UNL; 1.82A {Proteus mirabilis}

Probab=99.95  E-value=2.9e-27  Score=167.39  Aligned_cols=146  Identities=15%  Similarity=0.143  Sum_probs=123.8

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      |+|++||||+|+|+.+..++++|+.+|+..+  ++|+++||.+......    .........+...+...+.+++.++++
T Consensus         5 ~~~k~ILv~~D~s~~s~~al~~A~~lA~~~~--a~l~ll~v~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~l~~~   78 (319)
T 3olq_A            5 EKYQNLLVVIDPNQDDQPALRRAVYIVQRNG--GRIKAFLPVYDLSYDM----TTLLSPDERNAMRKGVINQKTAWIKQQ   78 (319)
T ss_dssp             CCSCEEEEECCTTCSCCHHHHHHHHHHHHHC--CEEEEEEEECCGGGGC----TTTSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccceEEEEECCCcccHHHHHHHHHHHHHcC--CeEEEEEEecccchhh----ccccChhhHHHHHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999988  9999999987643221    111233444555566667778888888


Q ss_pred             HHHHHhcCCeEEEEEe-cCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           81 KEICAKHGVVAETMTE-MGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        81 ~~~~~~~~~~~~~~v~-~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .+.+...|+++++.+. .|++.+.|.+++++.++||||||+++++.+.++++|+++++++++++||||+||+.
T Consensus        79 ~~~~~~~~v~~~~~~~~~g~~~~~i~~~a~~~~~DLiV~G~~g~~~~~~~~~Gs~~~~vl~~~~~PVlvv~~~  151 (319)
T 3olq_A           79 ARYYLEAGIQIDIKVIWHNRPYEAIIEEVITDKHDLLIKMAHQHDKLGSLIFTPLDWQLLRKCPAPVWMVKDK  151 (319)
T ss_dssp             HHHHHHTTCCEEEEEEECSCHHHHHHHHHHHHTCSEEEEEEBCC--CCSCBCCHHHHHHHHHCSSCEEEEESS
T ss_pred             HHHHhhcCCeEEEEEEecCChHHHHHHHHHhcCCCEEEEecCcCchhhcccccccHHHHHhcCCCCEEEecCc
Confidence            8888888999999999 79999999999999999999999999999999999999999999999999999865

>3fdx_A Putative filament protein / universal stress PROT; structural genomics, APC60640.1, universal protein F, PSI-2; HET: MSE ATP; 1.58A {Klebsiella pneumoniae subsp} PDB: 3fh0_A*

Probab=99.95  E-value=3.1e-28  Score=153.96  Aligned_cols=138  Identities=25%  Similarity=0.284  Sum_probs=105.6

Q ss_pred             CcEEEEEecCCch--HHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESEC--RHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         3 ~~~iLv~vd~~~~--~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      .++||||+|+++.  +..++++|+.+|+..+  ++|+++||.+......   .........    .+..++..++.++.+
T Consensus         1 ~k~ILv~vD~s~~~~s~~al~~a~~la~~~~--a~l~ll~v~~~~~~~~---~~~~~~~~~----~~~~~~~~~~~~~~l   71 (143)
T 3fdx_A            1 SNAILVPIDISDKEFTERIISHVESEARIDD--AEVHFLTVIPSLPYYA---SLGMAYTAE----LPGMDELREGSETQL   71 (143)
T ss_dssp             CCEEEEECCTTCSSCCTTHHHHHHHHHHHHT--CEEEEEEEECC-----------------------CHHHHHHHHHHHH
T ss_pred             CCEEEEEecCChHhhHHHHHHHHHHHHHhcC--CeEEEEEEecCCcccc---cccccccch----hhhHHHHHHHHHHHH
Confidence            3799999999999  9999999999999977  9999999998754321   111000000    112233344555556


Q ss_pred             HHHHHhcCC---eEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           81 KEICAKHGV---VAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        81 ~~~~~~~~~---~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      .+.+++.++   .+++.+..|++.++|.+++++.++||||||+++ +.+.++++||++++++++++||||+||
T Consensus        72 ~~~~~~~~~~~~~v~~~~~~g~~~~~I~~~a~~~~~dliV~G~~~-~~~~~~~~Gs~~~~v~~~~~~pVlvv~  143 (143)
T 3fdx_A           72 KEIAKKFSIPEDRMHFHVAEGSPKDKILALAKSLPADLVIIASHR-PDITTYLLGSNAAAVVRHAECSVLVVR  143 (143)
T ss_dssp             HHHHTTSCCCGGGEEEEEEESCHHHHHHHHHHHTTCSEEEEESSC-TTCCSCSSCHHHHHHHHHCSSEEEEEC
T ss_pred             HHHHHHcCCCCCceEEEEEecChHHHHHHHHHHhCCCEEEEeCCC-CCCeeeeeccHHHHHHHhCCCCEEEeC
Confidence            666666554   478889999999999999999999999999995 889999999999999999999999997

>1jmv_A USPA, universal stress protein A; chaperone; 1.85A {Haemophilus influenzae} SCOP: c.26.2.4

Probab=99.95  E-value=2.3e-27  Score=149.66  Aligned_cols=140  Identities=21%  Similarity=0.155  Sum_probs=105.2

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      ||++||||+|+++.+..++++|..+|+..+  ++|+++||.+......     ........+...+...+..++.++++.
T Consensus         1 m~~~ILv~~D~s~~s~~al~~a~~la~~~~--a~l~ll~v~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~l~~~~   73 (141)
T 1jmv_A            1 MYKHILVAVDLSEESPILLKKAVGIAKRHD--AKLSIIHVDVNFSDLY-----TGLIDVNMSSMQDRISTETQKALLDLA   73 (141)
T ss_dssp             CCSEEEEEECCSTTHHHHHHHHHHHHHHHT--CEEEEEEEEECCGGGC-----CCCEEHHHHHHTTCCCCHHHHHHHHHH
T ss_pred             CCceEEEEecCchhhHHHHHHHHHHHHhcC--CEEEEEEEecCchhhh-----ccccccchHHHHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999977  8999999985422111     001111111122222233444444443


Q ss_pred             HHHHhcCCeE-EEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCCCC
Q 031713           82 EICAKHGVVA-ETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE  154 (154)
Q Consensus        82 ~~~~~~~~~~-~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~~~  154 (154)
                         +..|+++ ++.+..|++.+.|++++++.++||||||++ ++.+.+  +||++++++++++|||++||++.+
T Consensus        74 ---~~~~~~~~~~~~~~g~~~~~I~~~a~~~~~dliV~G~~-~~~~~~--lgs~~~~vl~~~~~pVlvv~~~~~  141 (141)
T 1jmv_A           74 ---ESVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHH-QDFWSK--LMSSTRQVMNTIKIDMLVVPLRDE  141 (141)
T ss_dssp             ---HHSSSCCCCEEEEEECHHHHHHHHHHHTTCCEEEEEEC-CCCHHH--HHHHHHHHHTTCCSEEEEEECCC-
T ss_pred             ---HHcCCCceEEEEecCCHHHHHHHHHHhcCCCEEEEeCC-Cchhhh--hcchHHHHHhcCCCCEEEeeCCCC
Confidence               3457775 677888999999999999999999999999 888777  489999999999999999998753

>3loq_A Universal stress protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: AMP; 2.32A {Archaeoglobus fulgidus}

Probab=99.94  E-value=2.3e-27  Score=166.28  Aligned_cols=143  Identities=17%  Similarity=0.229  Sum_probs=120.0

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      |||++||||+|+++.+..++++|+.+|+..+  ++|+++||.+......   . .  .....+...+..++..++.++++
T Consensus        20 ~m~~~ILv~vD~s~~s~~al~~A~~lA~~~~--a~l~ll~v~~~~~~~~---~-~--~~~~~~~~~~~~~~~~~~~l~~~   91 (294)
T 3loq_A           20 FQSNAMLLPTDLSENSFKVLEYLGDFKKVGV--EEIGVLFVINLTKLST---V-S--GGIDIDHYIDEMSEKAEEVLPEV   91 (294)
T ss_dssp             STTCEEEEECCSCTGGGGGGGGHHHHHHTTC--CEEEEECCEECTTC-----------CCCTTHHHHHHHHHHHHHHHHH
T ss_pred             HhhccEEEecCCCHHHHHHHHHHHHHHhhcC--CEEEEEEEecCccccc---c-c--ccccHHHHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999987  9999999988754321   0 0  01112233445566778888889


Q ss_pred             HHHHHhcCCeEEE-EEe-cCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCCC
Q 031713           81 KEICAKHGVVAET-MTE-MGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPV  153 (154)
Q Consensus        81 ~~~~~~~~~~~~~-~v~-~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~~  153 (154)
                      .+.+...|+++++ .+. .|++.++|  ++++.++|+||||+++++.+.++++|+++++++++++|||++||+..
T Consensus        92 ~~~~~~~g~~~~~~~v~~~g~~~~~I--~a~~~~~DliV~G~~g~~~~~~~~~Gs~~~~vl~~~~~PVlvv~~~~  164 (294)
T 3loq_A           92 AQKIEAAGIKAEVIKPFPAGDPVVEI--IKASENYSFIAMGSRGASKFKKILLGSVSEGVLHDSKVPVYIFKHDM  164 (294)
T ss_dssp             HHHHHHTTCEEEECSSCCEECHHHHH--HHHHTTSSEEEEECCCCCHHHHHHHCCHHHHHHHHCSSCEEEECCCT
T ss_pred             HHHHHHcCCCcceeEeeccCChhHhe--eeccCCCCEEEEcCCCCccccceeeccHHHHHHhcCCCCEEEecCcc
Confidence            8888888999998 777 89999999  99999999999999999999999999999999999999999999763

>3cis_A Uncharacterized protein; alpha/beta hydrolase, ATP, universal stress protein, unknown function; HET: ATP; 2.90A {Mycobacterium tuberculosis} PDB: 2jax_A*

Probab=99.93  E-value=1.1e-25  Score=158.74  Aligned_cols=141  Identities=20%  Similarity=0.300  Sum_probs=115.8

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      +++++||||+|+++.+..++++|+.+|+..+  ++|+++||.++.....   .......    ...+...+..++.++++
T Consensus        17 ~~~~~ILv~~D~s~~s~~al~~A~~lA~~~~--a~l~ll~v~~~~~~~~---~~~~~~~----~~~~~~~~~~~~~l~~~   87 (309)
T 3cis_A           17 NSSLGIIVGIDDSPAAQVAVRWAARDAELRK--IPLTLVHAVSPEVATW---LEVPLPP----GVLRWQQDHGRHLIDDA   87 (309)
T ss_dssp             -CTTEEEEECCSSHHHHHHHHHHHHHHHHHT--CCEEEEEECCCCCCCT---TCCCCCH----HHHHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCHHHHHHHHHHHHHHHhcC--CcEEEEEEecCccccc---ccCCCCc----hhhHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999987  8999999987432111   0011111    23334455667777777


Q ss_pred             HHHHHhc-----CCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           81 KEICAKH-----GVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        81 ~~~~~~~-----~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .+.+.+.     |+++++.+..|++.+.|+++++  ++||||||+++++.+.++++||++++++++++|||++||..
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~I~~~a~--~~DliV~G~~g~~~~~~~~~Gs~~~~vl~~~~~PVlvv~~~  162 (309)
T 3cis_A           88 LKVVEQASLRAGPPTVHSEIVPAAAVPTLVDMSK--DAVLMVVGCLGSGRWPGRLLGSVSSGLLRHAHCPVVIIHDE  162 (309)
T ss_dssp             HHHHHHHCSSSCCSCEEEEEESSCHHHHHHHHGG--GEEEEEEESSCTTCCTTCCSCHHHHHHHHHCSSCEEEECTT
T ss_pred             HHHHHHhcccCCCceEEEEEecCCHHHHHHHHhc--CCCEEEECCCCCccccccccCcHHHHHHHhCCCCEEEEcCC
Confidence            7777765     8999999999999999999997  99999999999999999999999999999999999999865

>3ab8_A Putative uncharacterized protein TTHA0350; tandem-type universal stress protein, unknown function; HET: ATP; 1.70A {Thermus thermophilus} PDB: 3ab7_A*

Probab=99.93  E-value=7.6e-26  Score=156.62  Aligned_cols=146  Identities=21%  Similarity=0.221  Sum_probs=116.7

Q ss_pred             cEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcc-cCCCCCc---hHHHHHHHHHHHHHHHHHHHH
Q 031713            4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQA-SMFGAAP---PDLLMSIQENQKKAALALLGR   79 (154)
Q Consensus         4 ~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~-~~~~~~~---~~~~~~~~~~~~~~~~~~l~~   79 (154)
                      ++||||+|+|+.+..++++|..+|+..+  ++++++||.+.......+ .+.....   .+..+...+...+..++.+++
T Consensus         1 k~ILv~vD~s~~s~~al~~A~~lA~~~~--a~l~ll~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~   78 (268)
T 3ab8_A            1 MRILLATDGSPQARGAEALAEWLAYKLS--APLTVLFVVDTRLARIPELLDFGALTVPVPVLRTELERALALRGEAVLER   78 (268)
T ss_dssp             CCEEEECCSCGGGHHHHHHHHHHHHHHT--CCEEEEEEEEHHHHTHHHHC-------CHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEcCCCHHHHHHHHHHHHHHHHhC--CcEEEEEEeccCCcccccccCchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999987  899999998754321100 0111000   011112244556677888888


Q ss_pred             HHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCC-CcccccccchhHHHhhcCCCcEEEEcCCC
Q 031713           80 AKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRG-PIQRAFLGSVSNYCVHNAKCPVLVVRKPV  153 (154)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~-~~~~~~~gs~~~~l~~~~~~pvliv~~~~  153 (154)
                      +.+.+...|+++++.+..|++.+.|.++  +.++||||||+++++ .+.++++||++++++++++|||++||+..
T Consensus        79 ~~~~~~~~g~~~~~~~~~g~~~~~I~~~--~~~~dliV~G~~g~~~~~~~~~~Gs~~~~v~~~a~~PVlvv~~~~  151 (268)
T 3ab8_A           79 VRQSALAAGVAVEAVLEEGVPHEAILRR--ARAADLLVLGRSGEAHGDGFGGLGSTADRVLRASPVPVLLAPGEP  151 (268)
T ss_dssp             HHHHHHHTTCCEEEEEEEECHHHHHHHH--HTTCSEEEEESSCTTSCTTCCSCCHHHHHHHHHCSSCEEEECSSC
T ss_pred             HHHHHHhCCCCeEEEEecCCHHHHHHhh--ccCCCEEEEeccCCCccccccccchhHHHHHHhCCCCEEEECCCC
Confidence            8888888899999999999999999999  779999999999998 89999999999999999999999999753

>1q77_A Hypothetical protein AQ_178; structural genomics, universal stress protein, PSI, protein structure initiative; 2.70A {Aquifex aeolicus} SCOP: c.26.2.4

Probab=99.93  E-value=2.4e-25  Score=139.92  Aligned_cols=132  Identities=14%  Similarity=0.099  Sum_probs=102.9

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEec-cC-Cchh-hcccCCCCCchHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTAR-PT-EFIY-VQASMFGAAPPDLLMSIQENQKKAALALL   77 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~-~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   77 (154)
                      .+|++||||+|+++.+..++++|..+|+..+  ++|+++||. +. +... ....++.. ..    ...+...+..++.+
T Consensus         2 ~~~~~ILv~~D~s~~s~~al~~a~~la~~~~--a~l~ll~v~~~~~~~~~~~~~~~~~~-~~----~~~~~~~~~~~~~l   74 (138)
T 1q77_A            2 NAMKVLLVLTDAYSDCEKAITYAVNFSEKLG--AELDILAVLEDVYNLERANVTFGLPF-PP----EIKEESKKRIERRL   74 (138)
T ss_dssp             CCCEEEEEEESTTCCCHHHHHHHHHHHTTTC--CEEEEEEECHHHHHHHHHHHHHCCCC-CT----HHHHHHHHHHHHHH
T ss_pred             CcccEEEEEccCCHhHHHHHHHHHHHHHHcC--CeEEEEEEecccccccccccccCCCC-Ch----HHHHHHHHHHHHHH
Confidence            4789999999999999999999999999977  999999998 63 1111 00001111 11    23344455566677


Q ss_pred             HHHHHH--HHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           78 GRAKEI--CAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        78 ~~~~~~--~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      +++ +.  +...| ++++.+..|++.+.|++++++.++||||||++++         |++++++++++|||++||
T Consensus        75 ~~~-~~~~~~~~~-~~~~~~~~g~~~~~I~~~a~~~~~dliV~G~~g~---------sv~~~vl~~a~~PVlvv~  138 (138)
T 1q77_A           75 REV-WEKLTGSTE-IPGVEYRIGPLSEEVKKFVEGKGYELVVWACYPS---------AYLCKVIDGLNLASLIVK  138 (138)
T ss_dssp             HHH-HHHHHSCCC-CCCEEEECSCHHHHHHHHHTTSCCSEEEECSCCG---------GGTHHHHHHSSSEEEECC
T ss_pred             HHH-HHHhhccCC-cceEEEEcCCHHHHHHHHHHhcCCCEEEEeCCCC---------chHHHHHHhCCCceEeeC
Confidence            777 66  34557 7888888999999999999999999999999865         899999999999999986

>3mt0_A Uncharacterized protein PA1789; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: MSE; 1.58A {Pseudomonas aeruginosa}

Probab=99.93  E-value=9.1e-25  Score=152.89  Aligned_cols=137  Identities=18%  Similarity=0.271  Sum_probs=106.9

Q ss_pred             CCcEEEEEecCCch-------HHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESEC-------RHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAAL   74 (154)
Q Consensus         2 ~~~~iLv~vd~~~~-------~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   74 (154)
                      .+++||||+|+++.       +..++++|..+|+..+  ++++++||.+......   .    ....  ...+..++..+
T Consensus       133 ~~~~Ilva~D~s~~~~~~~~~s~~al~~a~~la~~~~--a~l~ll~v~~~~~~~~---~----~~~~--~~~~~~~~~~~  201 (290)
T 3mt0_A          133 TGGKILAAVDVGNNDGEHRSLHAGIISHAYDIAGLAK--ATLHVISAHPSPMLSS---A----DPTF--QLSETIEARYR  201 (290)
T ss_dssp             TTCEEEEEECTTCCSHHHHHHHHHHHHHHHHHHHHTT--CEEEEEEEEC----------------CH--HHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCcchhhhHHHHHHHHHHHHHHHHcC--CeEEEEEEecCccccc---c----Cchh--HHHHHHHHHHH
Confidence            47899999999998       9999999999999987  9999999998754322   0    0110  22233333444


Q ss_pred             HHHHHHHHHHHhcCCe-EEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           75 ALLGRAKEICAKHGVV-AETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        75 ~~l~~~~~~~~~~~~~-~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      +.++++.   ++.|++ ++..+..|++.++|.+++++.++||||||+++++.+.++++||++++++++++||||+||+.
T Consensus       202 ~~l~~~~---~~~g~~~~~~~v~~g~~~~~I~~~a~~~~~dLiVmG~~g~~~~~~~~~Gsv~~~vl~~~~~pVLvv~~~  277 (290)
T 3mt0_A          202 EACRTFQ---AEYGFSDEQLHIEEGPADVLIPRTAQKLDAVVTVIGTVARTGLSGALIGNTAEVVLDTLESDVLVLKPD  277 (290)
T ss_dssp             HHHHHHH---HHHTCCTTTEEEEESCHHHHHHHHHHHHTCSEEEEECCSSCCGGGCCSCHHHHHHHTTCSSEEEEECCH
T ss_pred             HHHHHHH---HHcCCCcceEEEeccCHHHHHHHHHHhcCCCEEEECCCCCcCCcceecchHHHHHHhcCCCCEEEECCC
Confidence            4444443   344774 66778889999999999999999999999999999999999999999999999999999864

>3mt0_A Uncharacterized protein PA1789; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: MSE; 1.58A {Pseudomonas aeruginosa}

Probab=99.93  E-value=7.2e-25  Score=153.40  Aligned_cols=123  Identities=19%  Similarity=0.216  Sum_probs=108.7

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      +|++||||+|+++.+..++++|+.+|+..+  ++|+++|+.++  ..                        .++.++++.
T Consensus         6 ~~~~ILv~~D~s~~s~~al~~A~~la~~~~--a~l~ll~v~~~--~~------------------------~~~~l~~~~   57 (290)
T 3mt0_A            6 AIRSILVVIEPDQLEGLALKRAQLIAGVTQ--SHLHLLVCEKR--RD------------------------HSAALNDLA   57 (290)
T ss_dssp             TCCEEEEECCSSCSCCHHHHHHHHHHHHHC--CEEEEEEECSS--SC------------------------CHHHHHHHH
T ss_pred             hhceEEEEeCCCccchHHHHHHHHHHHhcC--CeEEEEEeeCc--HH------------------------HHHHHHHHH
Confidence            689999999999999999999999999987  89999999873  11                        134455566


Q ss_pred             HHHHhcCCeEEEEEec-CChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           82 EICAKHGVVAETMTEM-GDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        82 ~~~~~~~~~~~~~v~~-g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      +.+...|+++++.+.. |++.+.|.+++++.++||||||+++++.+.++++|+++++++++++||||++|+.
T Consensus        58 ~~~~~~~~~~~~~~~~~g~~~~~i~~~a~~~~~dliV~G~~~~~~~~~~~~gs~~~~vl~~~~~PVlvv~~~  129 (290)
T 3mt0_A           58 QELREEGYSVSTNQAWKDSLHQTIIAEQQAEGCGLIIKQHFPDNPLKKAILTPDDWKLLRFAPCPVLMTKTA  129 (290)
T ss_dssp             HHHHHTTCCEEEEEECSSSHHHHHHHHHHHHTCSEEEEECCCSCTTSTTSCCHHHHHHHHHCSSCEEEECCC
T ss_pred             HHHhhCCCeEEEEEEeCCCHHHHHHHHHHhcCCCEEEEecccCCchhhcccCHHHHHHHhcCCCCEEEecCC
Confidence            6666789999999884 7899999999999999999999999999999999999999999999999999943

>3loq_A Universal stress protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: AMP; 2.32A {Archaeoglobus fulgidus}

Probab=99.92  E-value=3.9e-24  Score=149.87  Aligned_cols=124  Identities=23%  Similarity=0.289  Sum_probs=111.8

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      .+++||||+|+++.+..++++|..+|+..+  ++|+++||.+...                          .++.++++.
T Consensus       169 ~~~~Ilv~~d~s~~s~~al~~a~~la~~~~--~~l~ll~v~~~~~--------------------------~~~~l~~~~  220 (294)
T 3loq_A          169 LFDRVLVAYDFSKWADRALEYAKFVVKKTG--GELHIIHVSEDGD--------------------------KTADLRVME  220 (294)
T ss_dssp             TTSEEEEECCSSHHHHHHHHHHHHHHHHHT--CEEEEEEECSSSC--------------------------CHHHHHHHH
T ss_pred             cCCEEEEEECCCHHHHHHHHHHHHHhhhcC--CEEEEEEEccCch--------------------------HHHHHHHHH
Confidence            478999999999999999999999999877  8999999988742                          134456666


Q ss_pred             HHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCCC
Q 031713           82 EICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPV  153 (154)
Q Consensus        82 ~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~~  153 (154)
                      +.+...|+++++.+..|++.++|.+++++.++||||||+++++.+.++++||++++++++++||||+||++.
T Consensus       221 ~~l~~~~~~~~~~~~~g~~~~~I~~~a~~~~~dLlV~G~~~~~~~~~~~~Gs~~~~vl~~~~~pvLvv~~~~  292 (294)
T 3loq_A          221 EVIGAEGIEVHVHIESGTPHKAILAKREEINATTIFMGSRGAGSVMTMILGSTSESVIRRSPVPVFVCKRGD  292 (294)
T ss_dssp             HHHHHTTCCEEEEEECSCHHHHHHHHHHHTTCSEEEEECCCCSCHHHHHHHCHHHHHHHHCSSCEEEECSCT
T ss_pred             HHHHHcCCcEEEEEecCCHHHHHHHHHHhcCcCEEEEeCCCCCCccceeeCcHHHHHHhcCCCCEEEECCCC
Confidence            677778999999999999999999999999999999999999999999999999999999999999998765

>3cis_A Uncharacterized protein; alpha/beta hydrolase, ATP, universal stress protein, unknown function; HET: ATP; 2.90A {Mycobacterium tuberculosis} PDB: 2jax_A*

Probab=99.91  E-value=1.4e-23  Score=147.97  Aligned_cols=136  Identities=21%  Similarity=0.288  Sum_probs=108.2

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      .+++||||+|+++.+..++++|..+|+..+  ++|+++||.+.....    ......   .+    ...+..++.++++.
T Consensus       170 ~~~~Ilv~~D~s~~s~~al~~a~~la~~~~--a~l~ll~v~~~~~~~----~~~~~~---~~----~~~~~~~~~l~~~~  236 (309)
T 3cis_A          170 QQAPVLVGVDGSSASELATAIAFDEASRRN--VDLVALHAWSDVDVS----EWPGID---WP----ATQSMAEQVLAERL  236 (309)
T ss_dssp             CCCCEEEECCSSHHHHHHHHHHHHHHHHTT--CCEEEEEESCSSCCT----TCSSCC---HH----HHHHHHHHHHHHHH
T ss_pred             CCCeEEEEeCCChHHHHHHHHHHHHHHhcC--CEEEEEEEeeccccc----CCCccc---HH----HHHHHHHHHHHHHH
Confidence            368999999999999999999999999977  899999998764321    001111   11    12233344455554


Q ss_pred             HHHHh--cCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           82 EICAK--HGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        82 ~~~~~--~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      ..+.+  .|+.++..+..|++.++|+++++  ++||||||+++++.+.++++||++++|+++++|||+++|++
T Consensus       237 ~~~~~~~~~~~~~~~~~~g~~~~~I~~~a~--~adliV~G~~~~~~~~~~l~Gsv~~~vl~~~~~pVlvv~~~  307 (309)
T 3cis_A          237 AGWQERYPNVAITRVVVRDQPARQLVQRSE--EAQLVVVGSRGRGGYAGMLVGSVGETVAQLARTPVIVARES  307 (309)
T ss_dssp             TTHHHHCTTSCEEEEEESSCHHHHHHHHHT--TCSEEEEESSCSSCCTTCSSCHHHHHHHHHCSSCEEEECC-
T ss_pred             HHHHhhCCCCcEEEEEEcCCHHHHHHHhhC--CCCEEEECCCCCCCccccccCcHHHHHHhcCCCCEEEeCCC
Confidence            44433  48889998999999999999998  99999999999999999999999999999999999999875

>3olq_A Universal stress protein E; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: UNL; 1.82A {Proteus mirabilis}

Probab=99.91  E-value=1.1e-23  Score=148.92  Aligned_cols=142  Identities=18%  Similarity=0.252  Sum_probs=110.7

Q ss_pred             CCcEEEEEecCCc-------hHHHHHHHHHHHcccC--CCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESE-------CRHYALQWALENLGDA--ISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKA   72 (154)
Q Consensus         2 ~~~~iLv~vd~~~-------~~~~~l~~a~~la~~~--~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   72 (154)
                      .+++||||+|+++       .+..++++|..+|+..  +  ++|+++||.+......   ... ......+...+..++.
T Consensus       155 ~~~~Ilva~D~s~~~~~~~~~s~~al~~a~~la~~~~~~--a~l~ll~v~~~~~~~~---~~~-~~~~~~~~~~~~~~~~  228 (319)
T 3olq_A          155 EYGTIVVAANLSNEESYHDALNLKLIELTNDLSHRIQKD--PDVHLLSAYPVAPINI---AIE-LPDFDPNLYNNALRGQ  228 (319)
T ss_dssp             TTCEEEEECCCSCCSTHHHHHHHHHHHHHHHHHHHHCSS--CCEEEEEEECCCSCSC---CTT-CTTCCHHHHHHHHHHH
T ss_pred             cCCeEEEEECCCCcchhHHHHHHHHHHHHHHHHHhccCC--CeEEEEEeecCcchhh---hcc-CCcccHHHHHHHHHHH
Confidence            4789999999999       5799999999999997  6  8999999998764322   111 0111122333344444


Q ss_pred             HHHHHHHHHHHHHhcCCe-EEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           73 ALALLGRAKEICAKHGVV-AETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        73 ~~~~l~~~~~~~~~~~~~-~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      .++.++.+.   +..|+. ++..+..|++.+.|.+++++.++||||||+++++.+.++++||++++++++++||||+||+
T Consensus       229 ~~~~l~~~~---~~~~~~~~~~~v~~g~~~~~I~~~a~~~~~dLiV~G~~g~~~~~~~~~Gsv~~~vl~~~~~pVLvv~~  305 (319)
T 3olq_A          229 HLIAMKELR---QKFSIPEEKTHVKEGLPEQVIPQVCEELNAGIVVLGILGRTGLSAAFLGNTAEQLIDHIKCDLLAIKP  305 (319)
T ss_dssp             HHHHHHHHH---HHTTCCGGGEEEEESCHHHHHHHHHHHTTEEEEEEECCSCCSTHHHHHHHHHHHHHTTCCSEEEEECC
T ss_pred             HHHHHHHHH---HHhCCCcccEEEecCCcHHHHHHHHHHhCCCEEEEeccCccCCccccccHHHHHHHhhCCCCEEEECC
Confidence            444444443   445653 5677888999999999999999999999999999999999999999999999999999987


Q ss_pred             C
Q 031713          152 P  152 (154)
Q Consensus       152 ~  152 (154)
                      .
T Consensus       306 ~  306 (319)
T 3olq_A          306 D  306 (319)
T ss_dssp             T
T ss_pred             C
Confidence            5

>3ab8_A Putative uncharacterized protein TTHA0350; tandem-type universal stress protein, unknown function; HET: ATP; 1.70A {Thermus thermophilus} PDB: 3ab7_A*

Probab=99.87  E-value=1.7e-21  Score=134.72  Aligned_cols=116  Identities=23%  Similarity=0.277  Sum_probs=101.3

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      .+++||||+|+++.+..++++|..+|...+  ++++++||.+..                         +..++.++++.
T Consensus       153 ~~~~ilv~~d~s~~~~~al~~a~~la~~~~--a~l~ll~v~~~~-------------------------~~~~~~l~~~~  205 (268)
T 3ab8_A          153 ELEGALLGYDASESAVRALHALAPLARALG--LGVRVVSVHEDP-------------------------ARAEAWALEAE  205 (268)
T ss_dssp             CCCEEEEECCSCHHHHHHHHHHHHHHHHHT--CCEEEEEECSSH-------------------------HHHHHHHHHHH
T ss_pred             CCCEEEEEECCCHHHHHHHHHHHHhhhcCC--CEEEEEEEcCcH-------------------------HHHHHHHHHHH
Confidence            368999999999999999999999999877  899999998752                         12234556667


Q ss_pred             HHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           82 EICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        82 ~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      +.+...|+++++.+..|++.++|.+++++.  ||||||+    .+.++++||++++++++++|||+++|
T Consensus       206 ~~l~~~~~~~~~~~~~g~~~~~i~~~a~~~--dliV~G~----~~~~~~~Gs~~~~vl~~~~~pvlvv~  268 (268)
T 3ab8_A          206 AYLRDHGVEASALVLGGDAADHLLRLQGPG--DLLALGA----PVRRLVFGSTAERVIRNAQGPVLTAR  268 (268)
T ss_dssp             HHHHHTTCCEEEEEECSCHHHHHHHHCCTT--EEEEEEC----CCSCCSSCCHHHHHHHHCSSCEEEEC
T ss_pred             HHHHHcCCceEEEEeCCChHHHHHHHHHhC--CEEEECC----cccccEeccHHHHHHhcCCCCEEEeC
Confidence            777778999999888999999999999977  9999998    67889999999999999999999996

>2iel_A Hypothetical protein TT0030; TT0030,thermus thermophilus, structural genomics, PSI, protein structure initiative; 1.60A {Thermus thermophilus} SCOP: c.26.2.4

Probab=97.86  E-value=0.00075  Score=41.14  Aligned_cols=130  Identities=15%  Similarity=0.068  Sum_probs=94.1

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKE   82 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~   82 (154)
                      |+++||.+.-.-.+..+.+....+..... ...+.+|  .|.....    .+..        ..+..+..+++.++.-..
T Consensus         1 m~~vlVlae~tl~~~dl~~vl~~l~~~~~-~~~f~VL--VPa~~~~----a~~~--------e~~~a~~~A~~~l~~sl~   65 (138)
T 2iel_A            1 MARYLVVAHRTAKSPELAAKLKELLAQDP-EARFVLL--VPAVPPP----GWVY--------EENEVRRRAEEEAAAAKR   65 (138)
T ss_dssp             -CEEEEECSTTTTCHHHHHHHHHHHHHCT-TCEEEEE--EEEECCC----CSCC----------CHHHHHHHHHHHHHHH
T ss_pred             CceEEEEecCccCcHhHHHHHHHhhcCCC-ceEEEEE--ecCCCCc----cccc--------ChHHHHHHHHHHHHHHHH
Confidence            47899999887777777766556665421 1344222  2222110    1111        223456667788888888


Q ss_pred             HHHhcCCeEE-EEEecCChhhHHHHHHHhcC--CCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEE
Q 031713           83 ICAKHGVVAE-TMTEMGDPKNVICEAAEKHK--IQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVV  149 (154)
Q Consensus        83 ~~~~~~~~~~-~~v~~g~~~~~i~~~a~~~~--~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv  149 (154)
                      .++..|+.+. ..+..++|..+|.....+.+  +|-||+-+.. ...++||.-..+.+.=+ ...||+=+
T Consensus        66 aL~~~G~~a~~G~v~d~~Pl~AL~~~v~~~~~~~deiIV~T~P-h~vs~~fh~DwasrAr~-~gvPVlhl  133 (138)
T 2iel_A           66 ALEAQGIPVEEAKAGDISPLLAIEEELLAHPGAYQGIVLSTLP-PGLSRWLRLDVHTQAER-FGLPVIHV  133 (138)
T ss_dssp             HHHTTTCCCSEEEEEESSHHHHHHHHHHHSTTSCSEEEEEECC-TTTCHHHHTTHHHHGGG-GSSCEEEE
T ss_pred             HHHHcCCcccccccCCCChHHHHHHHHHhcCCCCceEEEEcCC-chHHHHHhccHHHHHHh-cCCCEEEE
Confidence            8999999988 99999999999999999999  9999999985 45889999999998888 89999865

>1wy5_A TILS, hypothetical UPF0072 protein AQ_1887; N-type ATP-ppase, structural genomics, translation, NPPSFA; 2.42A {Aquifex aeolicus} SCOP: c.26.2.5 d.229.1.1 PDB: 2e21_A* 2e89_A*

Probab=96.71  E-value=0.022  Score=40.01  Aligned_cols=94  Identities=11%  Similarity=-0.046  Sum_probs=63.3

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCe-EEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSD-LIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~-l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      -++++|++.+...|..++..+..+....|  .+ +.++|+.......                        .....+.+.
T Consensus        24 ~~~vlva~SGG~DS~~Ll~ll~~~~~~~g--~~~v~av~vd~g~r~~------------------------s~~~~~~v~   77 (317)
T 1wy5_A           24 ERRVLIAFSGGVDSVVLTDVLLKLKNYFS--LKEVALAHFNHMLRES------------------------AERDEEFCK   77 (317)
T ss_dssp             CCEEEEECCSSHHHHHHHHHHHHSTTTTT--CSEEEEEEEECCSSTH------------------------HHHHHHHHH
T ss_pred             CCEEEEEecchHHHHHHHHHHHHHHHHcC--CCEEEEEEEECCCCcc------------------------cHHHHHHHH
Confidence            46899999999999988888777766555  57 9999997653211                        122344555


Q ss_pred             HHHHhcCCeEEEEEec--------C-Chh--------hHHHHHHHhcCCCEEEEecCC
Q 031713           82 EICAKHGVVAETMTEM--------G-DPK--------NVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        82 ~~~~~~~~~~~~~v~~--------g-~~~--------~~i~~~a~~~~~dlivlg~~~  122 (154)
                      +.++..|+++.+.-..        | ++.        ..+.+.+++.+++.|+.|++.
T Consensus        78 ~~a~~lgi~~~v~~~~~~~~~~~~~~~~e~~ar~~Ry~~l~~~a~~~g~~~i~~Gh~~  135 (317)
T 1wy5_A           78 EFAKERNMKIFVGKEDVRAFAKENRMSLEEAGRFLRYKFLKEILESEGFDCIATAHHL  135 (317)
T ss_dssp             HHHHHHTCCEEEEECCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHTTCSEEECCCCH
T ss_pred             HHHHHcCCcEEEEEEechhhhccCCCCHHHHHHHHHHHHHHHHHHHcCCCEEEEeCch
Confidence            6666678886554421        2 111        244556788899999999863

>3a2k_A TRNA(Ile)-lysidine synthase; ligase, pseudo-knot, ligase/RNA complex; 3.65A {Geobacillus kaustophilus}

Probab=96.71  E-value=0.019  Score=42.55  Aligned_cols=95  Identities=18%  Similarity=0.154  Sum_probs=66.7

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKE   82 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~   82 (154)
                      -++|+|++.+...|..++..+..+....+  .++.++||......                       .......+.+.+
T Consensus        18 ~~~vlVa~SGG~DS~~Ll~ll~~~~~~~~--~~v~avhvdhglrg-----------------------~~s~~~~~~v~~   72 (464)
T 3a2k_A           18 GAAVIVGVSGGPDSLALLHVFLSLRDEWK--LQVIAAHVDHMFRG-----------------------RESEEEMEFVKR   72 (464)
T ss_dssp             SSBEEEECCSSHHHHHHHHHHHHHHHTTT--CBCEEEEEECTTCT-----------------------HHHHHHHHHHHH
T ss_pred             CCEEEEEEcCcHHHHHHHHHHHHHHHHcC--CeEEEEEEECCCCc-----------------------cccHHHHHHHHH
Confidence            46899999999999999988888776666  68999999765320                       112233456677


Q ss_pred             HHHhcCCeEEEEEec--------C-Ch--------hhHHHHHHHhcCCCEEEEecCC
Q 031713           83 ICAKHGVVAETMTEM--------G-DP--------KNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        83 ~~~~~~~~~~~~v~~--------g-~~--------~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      .|+..|+++.+.-..        | ++        ...+.+++++.+++.|+.|++.
T Consensus        73 ~~~~lgi~~~v~~~~~~~~~~~~~~~~e~~aR~~Ry~~l~~~a~~~g~~~IatgH~~  129 (464)
T 3a2k_A           73 FCVERRILCETAQIDVPAFQRSAGLGAQEAARICRYRFFAELMEKHQAGYVAVGHHG  129 (464)
T ss_dssp             HHHHTTCEEEEEECCCHHHHTTTTCCSHHHHHHHHHHHHHHHHHTTTCCEEECCCCH
T ss_pred             HHHHcCCcEEEEEechhhhhhccCCCHHHHHHHHHHHHHHHHHHHcCcCEEEEeCCh
Confidence            777889886654432        1 11        1345567888899999999863

>3g40_A Na-K-CL cotransporter; alpha/beta fold 10-stranded twisted beta sheet, transport protein; 1.90A {Methanosarcina acetivorans}

Probab=96.45  E-value=0.12  Score=35.76  Aligned_cols=121  Identities=8%  Similarity=-0.022  Sum_probs=80.5

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEIC   84 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   84 (154)
                      +|||++.........+++|..+....|   -++++++.+......                   ..   ++ ++.+.+.+
T Consensus        22 ~iLV~sg~p~~~~~li~la~~lt~~~G---~ltv~~i~p~~~~~~-------------------l~---~q-l~~l~~~l   75 (294)
T 3g40_A           22 NLLVPVEDPRELMGTFDFLRDITYPKG---SVKLLGLAGNTDKEN-------------------LL---SQ-LPSISEGF   75 (294)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHHTTTC---EEEEEECC---CTTC-------------------HH---HH-HHHHHHHH
T ss_pred             cEEEecCCchhhhhHHHHHHHhccCce---eEEEEEEccCCCccH-------------------HH---HH-HHHHHHHH
Confidence            699999888889999999999999876   999999987653321                   01   11 36668888


Q ss_pred             HhcCCeEEEEEecC-ChhhHHHHHHHhc-----CCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCCC
Q 031713           85 AKHGVVAETMTEMG-DPKNVICEAAEKH-----KIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPV  153 (154)
Q Consensus        85 ~~~~~~~~~~v~~g-~~~~~i~~~a~~~-----~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~~  153 (154)
                      ++.++..-+.++.- ++...+...++.+     .++.|++|......-. --+..+.. -+++....|++++..+
T Consensus        76 ~~r~v~a~~~vi~a~d~~~G~~~lvq~yglg~l~PNTilLg~~~~~e~~-~~y~~~i~-~~~~~~~nVlil~~~~  148 (294)
T 3g40_A           76 QEEGVFSSWTIIDTAEFEENLVVGMEALTGSFFRPSILFLRLPENRDRD-EEIREIIR-KASMYRMGVLLFSKHP  148 (294)
T ss_dssp             HHTTCEEEEEEC-----CHHHHHHHHHHTTCSSCSCEEEEECCSSGGGH-HHHHHHHH-HHHHTTCEEEEEECCT
T ss_pred             HhCCceeEEEEEecCChhHHHHHHHHHcCCCCCCCCEEEeCCCCChhhh-HHHHHHHH-HHHHhCceEEEEecCC
Confidence            88999988877774 7888888877654     5788999986433222 12333333 2345578888887543

>2xry_A Deoxyribodipyrimidine photolyase; DNA damage, DNA repair; HET: FAD; 1.50A {Methanosarcina mazei} PDB: 2xrz_A*

Probab=95.79  E-value=0.14  Score=38.08  Aligned_cols=114  Identities=14%  Similarity=0.129  Sum_probs=75.7

Q ss_pred             CchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCeEE
Q 031713           13 SECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAE   92 (154)
Q Consensus        13 ~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~   92 (154)
                      --....+|..|++.|...+  .++..+++.++.....                ........-+-+..+.+.+++.|+++ 
T Consensus        48 Rl~DN~aL~~A~~~a~~~~--~~v~~vfi~dp~~~~~----------------~~~r~~Fl~~sL~~L~~~L~~~G~~L-  108 (482)
T 2xry_A           48 RAEDNWALLFSRAIAKEAN--VPVVVVFCLTDEFLEA----------------GIRQYEFMLKGLQELEVSLSRKKIPS-  108 (482)
T ss_dssp             CSSSCHHHHHHHHHHHHHT--SCEEEEEEECTTGGGS----------------CHHHHHHHHHHHHHHHHHHHHTTCCE-
T ss_pred             CccccHHHHHHHHHHHHcC--CcEEEEEEeChhhhcc----------------CHHHHHHHHHHHHHHHHHHHHcCCcE-
Confidence            3345678888888776544  5898999988753321                11233445566777778888888765 


Q ss_pred             EEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           93 TMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        93 ~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                       .+..|++.+.|.+++++.+++.|+...... ...+    .....+...+++++..+..
T Consensus       109 -~v~~g~~~~~l~~l~~~~~~~~V~~~~~~~-~~~~----~~~~~v~~~lgi~~~~~~~  161 (482)
T 2xry_A          109 -FFLRGDPGEKISRFVKDYNAGTLVTDFSPL-RIKN----QWIEKVISGISIPFFEVDA  161 (482)
T ss_dssp             -EEEESCHHHHHHHHHHHTTCSEEEEECCCS-HHHH----HHHHHHHHHCCSCEEEECC
T ss_pred             -EEEeCCHHHHHHHHHHHcCCCEEEEecccc-hhHH----HHHHHHHHHcCCEEEEEeC
Confidence             345799999999999999999999875432 1111    1224444555888877653

>4b4k_A N5-carboxyaminoimidazole ribonucleotide mutase; isomerase; 2.50A {Bacillus anthracis}

Probab=95.79  E-value=0.19  Score=32.20  Aligned_cols=69  Identities=16%  Similarity=0.215  Sum_probs=50.3

Q ss_pred             HHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHH---hcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           77 LGRAKEICAKHGVVAETMTEMG-DPKNVICEAAE---KHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        77 l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~---~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .+++.+.+++.|++++..+..- ...+.+.++++   +.+++.||.|+.+.+.+.        .-+.-.++.||+-||-.
T Consensus        38 ~~~a~~~L~~~gI~~e~~V~SAHRtp~~l~~~~~~a~~~g~~ViIa~AG~aahLp--------GvvAa~T~~PVIGVPv~  109 (181)
T 4b4k_A           38 MKYACDILDELNIPYEKKVVSAHRTPDYMFEYAETARERGLKVIIAGAGGAAHLP--------GMVAAKTNLPVIGVPVQ  109 (181)
T ss_dssp             HHHHHHHHHHTTCCEEEEECCTTTSHHHHHHHHHHTTTTTCCEEEEEECSSCCHH--------HHHHTTCCSCEEEEECC
T ss_pred             HHHHHHHHHHcCCCeeEEEEccccChHHHHHHHHHHHhcCceEEEEeccccccch--------hhHHhcCCCCEEEEecC
Confidence            4566677778899999999885 45556666654   568899999987655443        34566788999999865


Q ss_pred             C
Q 031713          153 V  153 (154)
Q Consensus       153 ~  153 (154)
                      +
T Consensus       110 s  110 (181)
T 4b4k_A          110 S  110 (181)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3g40_A Na-K-CL cotransporter; alpha/beta fold 10-stranded twisted beta sheet, transport protein; 1.90A {Methanosarcina acetivorans}

Probab=95.53  E-value=0.041  Score=38.08  Aligned_cols=99  Identities=16%  Similarity=0.088  Sum_probs=66.5

Q ss_pred             HHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEec
Q 031713           18 YALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEM   97 (154)
Q Consensus        18 ~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~v~~   97 (154)
                      -++-.|..+.+..+  +++.++.|++..                      ...+.+++.++++.+.++- +.... .+ .
T Consensus       180 LmlllAylL~~nW~--A~I~L~~vV~de----------------------~a~~~a~~~l~~Lv~~~Ri-~a~~~-vv-~  232 (294)
T 3g40_A          180 LALLIAYKLKSNWK--ASLSFMTFAPTA----------------------IQAQAAENFLQSLAELARI-PNVKM-QV-L  232 (294)
T ss_dssp             HHHHHHHHHHHHHT--CEEEEEEECSSH----------------------HHHHHHHHHHHHHHHHHTC-CSCEE-EE-E
T ss_pred             HHHHHHHHHhhCcC--CeEEEEEecCCH----------------------HHHHHHHHHHHHHHHHhcC-CceEE-Ee-c
Confidence            34445555555555  999999998873                      4566677888888887764 33332 23 3


Q ss_pred             CChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           98 GDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        98 g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      ++..+.|.+ +  .++||+++|-.....+.      +..+++..+...++.+++.
T Consensus       233 ~~F~~il~~-s--~~ADL~flGl~~~~df~------~~~~~~~~~~ssc~f~~ds  278 (294)
T 3g40_A          233 RENPIKSSK-L--PFASLHIFSLDPNPDLD------LARHLMEKAGSSCIFALDS  278 (294)
T ss_dssp             SSCTTTSSS-C--CCCSEEEEECCSSCCHH------HHHHHHHHHTSEEEEEECC
T ss_pred             CchHHHHhh-C--cCCCEEEEcCCCCCcHH------HHHHHHHhcCCeEEEEecC
Confidence            555555544 4  48999999986555444      5578888888888887654

>3umv_A Deoxyribodipyrimidine photo-lyase; CPD cyclobutane pyrimidine dimers, UV damaged DNA, DNA repai flavoprotein; HET: FAD; 1.71A {Oryza sativa japonica group}

Probab=95.28  E-value=0.3  Score=36.64  Aligned_cols=90  Identities=18%  Similarity=0.096  Sum_probs=63.3

Q ss_pred             cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCe
Q 031713           11 DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVV   90 (154)
Q Consensus        11 d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~   90 (154)
                      |..-....+|..|++.|...+  .+|..+++.++.....              ..........-+-|+++.+.+++.|++
T Consensus        47 DLRl~DN~AL~~A~~~a~~~~--~pVl~vfildp~~~~~--------------~~~~~r~~FL~~sL~dL~~~L~~lG~~  110 (506)
T 3umv_A           47 DQRLADNWALLHAAGLAAASA--SPLAVAFALFPRPFLL--------------SARRRQLGFLLRGLRRLAADAAARHLP  110 (506)
T ss_dssp             CCCSTTCHHHHHHHHHHHHHT--CCEEEEEECCCTTCGG--------------GCCHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             CcchhhcHHHHHHHHhhhhcC--CCEEEEEeccchhhcc--------------CCCHHHHHHHHHHHHHHHHHHHHcCCc
Confidence            334446778989998887655  6899999998752111              001133445556677777778777766


Q ss_pred             EEEEEecCChhhHHHHHHHhcCCCEEEEe
Q 031713           91 AETMTEMGDPKNVICEAAEKHKIQLLIVG  119 (154)
Q Consensus        91 ~~~~v~~g~~~~~i~~~a~~~~~dlivlg  119 (154)
                      .  .+..|++.+. .+++++.+++.|+..
T Consensus       111 L--~v~~G~p~~v-~~L~~~~~a~~V~~d  136 (506)
T 3umv_A          111 F--FLFTGGPAEI-PALVQRLGASTLVAD  136 (506)
T ss_dssp             E--EEESSCTTHH-HHHHHHTTCSEEEEC
T ss_pred             e--EEEecChHHH-HHHHHhcCCCEEEec
Confidence            4  5567999999 999999999999973

>2ywx_A Phosphoribosylaminoimidazole carboxylase catalyti; rossmann fold, structural genomics, NPPSFA; 2.31A {Methanocaldococcus jannaschii}

Probab=95.26  E-value=0.26  Score=30.91  Aligned_cols=68  Identities=16%  Similarity=0.180  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           76 LLGRAKEICAKHGVVAETMTEMG-DPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        76 ~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      ..+++...++..|++++..+..- ...+.+.+++++...+.||.++...+.+.        .-+.-.+++||+-||.
T Consensus        14 v~~~a~~~l~~~gi~~dv~V~saHR~p~~~~~~~~~a~~~ViIa~AG~aa~Lp--------gvva~~t~~PVIgVP~   82 (157)
T 2ywx_A           14 IAEKAVNILKEFGVEFEVRVASAHRTPELVEEIVKNSKADVFIAIAGLAAHLP--------GVVASLTTKPVIAVPV   82 (157)
T ss_dssp             HHHHHHHHHHHTTCCEEEEECCTTTCHHHHHHHHHHCCCSEEEEEEESSCCHH--------HHHHTTCSSCEEEEEE
T ss_pred             HHHHHHHHHHHcCCCeEEEEEcccCCHHHHHHHHHhcCCCEEEEEcCchhhhH--------HHHHhccCCCEEEecC
Confidence            34566777778899999999875 67788888988766699999987654443        4466677899998885

>4grd_A N5-CAIR mutase, phosphoribosylaminoimidazole carboxylase catalyti; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures; 1.85A {Burkholderia cenocepacia}

Probab=95.24  E-value=0.24  Score=31.50  Aligned_cols=68  Identities=19%  Similarity=0.240  Sum_probs=48.3

Q ss_pred             HHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHH---hcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           77 LGRAKEICAKHGVVAETMTEMG-DPKNVICEAAE---KHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        77 l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~---~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .+++...+++.|++++..+..- ...+.+.++++   +.+++.||.++.+.+.+.        .-+.-.+++||+-||-+
T Consensus        28 ~~~a~~~l~~~gi~~ev~V~saHR~p~~l~~~~~~a~~~g~~ViIa~AG~aahLp--------gvvA~~t~~PVIgVPv~   99 (173)
T 4grd_A           28 MKHAVAILQEFGVPYEAKVVSAHRMPDEMFDYAEKARERGLRAIIAGAGGAAHLP--------GMLAAKTTVPVLGVPVA   99 (173)
T ss_dssp             HHHHHHHHHHTTCCEEEEECCTTTSHHHHHHHHHHHTTTTCSEEEEEEESSCCHH--------HHHHHHCCSCEEEEEEC
T ss_pred             HHHHHHHHHHcCCCEEEEEEccccCHHHHHHHHHHHHhcCCeEEEEeccccccch--------hhheecCCCCEEEEEcC
Confidence            4566667778899999988775 45555555544   478899999987654443        34566778999999843

>3oow_A Phosphoribosylaminoimidazole carboxylase,catalyic; structural genomics, center for structural genomics of infec diseases, csgid; HET: MSE; 1.75A {Francisella tularensis subsp} SCOP: c.23.8.1 PDB: 3opq_A*

Probab=95.07  E-value=0.3  Score=30.90  Aligned_cols=68  Identities=16%  Similarity=0.228  Sum_probs=50.1

Q ss_pred             HHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHHh---cCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           77 LGRAKEICAKHGVVAETMTEMG-DPKNVICEAAEK---HKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        77 l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~~---~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .+++...++..|+.++..+..- ...+.+.+++++   .+++.||.++...+.+.        .-+.-.+++||+-||..
T Consensus        21 ~~~a~~~l~~~gi~~ev~V~SaHRtp~~l~~~~~~~~~~g~~ViIa~AG~aa~Lp--------gvvA~~t~~PVIgVP~~   92 (166)
T 3oow_A           21 MKECCDILDNLGIGYECEVVSAHRTPDKMFDYAETAKERGLKVIIAGAGGAAHLP--------GMVAAKTTLPVLGVPVK   92 (166)
T ss_dssp             HHHHHHHHHHTTCEEEEEECCTTTCHHHHHHHHHHTTTTTCCEEEEEECSSCCHH--------HHHHHTCSSCEEEEECC
T ss_pred             HHHHHHHHHHcCCCEEEEEEcCcCCHHHHHHHHHHHHhCCCcEEEEECCcchhhH--------HHHHhccCCCEEEeecC
Confidence            4566777778899999988775 556677777653   56899999987654443        44667788999999864

>1xmp_A PURE, phosphoribosylaminoimidazole carboxylase; purine biosynthesis, spine, lyase; 1.80A {Bacillus anthracis} SCOP: c.23.8.1

Probab=95.00  E-value=0.32  Score=30.88  Aligned_cols=68  Identities=16%  Similarity=0.218  Sum_probs=49.8

Q ss_pred             HHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHHh---cCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           77 LGRAKEICAKHGVVAETMTEMG-DPKNVICEAAEK---HKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        77 l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~~---~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .+++...+++.|++++..+..- ...+.+.+++++   .+++.||.++...+.+.        .-+.-.+++||+-||..
T Consensus        27 ~~~a~~~L~~~Gi~~dv~V~SaHR~p~~l~~~~~~a~~~g~~ViIa~AG~aa~Lp--------gvvA~~t~~PVIgVP~~   98 (170)
T 1xmp_A           27 MKYACDILDELNIPYEKKVVSAHRTPDYMFEYAETARERGLKVIIAGAGGAAHLP--------GMVAAKTNLPVIGVPVQ   98 (170)
T ss_dssp             HHHHHHHHHHTTCCEEEEECCTTTSHHHHHHHHHHTTTTTCCEEEEEEESSCCHH--------HHHHTTCCSCEEEEEEC
T ss_pred             HHHHHHHHHHcCCCEEEEEEeccCCHHHHHHHHHHHHhCCCcEEEEECCchhhhH--------HHHHhccCCCEEEeeCC
Confidence            4566677778899999988774 566777777654   45899999987654443        44667788999999864

>3trh_A Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit; purines, pyrimidines, nucleosides, nucleotides, lyase; 2.20A {Coxiella burnetii}

Probab=94.98  E-value=0.32  Score=30.81  Aligned_cols=68  Identities=12%  Similarity=0.062  Sum_probs=49.3

Q ss_pred             HHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHH---HhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           77 LGRAKEICAKHGVVAETMTEMG-DPKNVICEAA---EKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        77 l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a---~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .+++...+++.|++++..+..- ...+.+.+++   ++.+++.||.++...+.+.        .-+.-.+++||+-||-.
T Consensus        22 ~~~a~~~l~~~gi~~ev~V~SaHR~p~~~~~~~~~a~~~g~~ViIa~AG~aa~Lp--------gvvA~~t~~PVIgVP~~   93 (169)
T 3trh_A           22 METAFTELKSLGIPFEAHILSAHRTPKETVEFVENADNRGCAVFIAAAGLAAHLA--------GTIAAHTLKPVIGVPMA   93 (169)
T ss_dssp             HHHHHHHHHHTTCCEEEEECCTTTSHHHHHHHHHHHHHTTEEEEEEEECSSCCHH--------HHHHHTCSSCEEEEECC
T ss_pred             HHHHHHHHHHcCCCEEEEEEcccCCHHHHHHHHHHHHhCCCcEEEEECChhhhhH--------HHHHhcCCCCEEEeecC
Confidence            4566777778899999988774 4555566654   4578999999987554433        44667788999999864

>3kuu_A Phosphoribosylaminoimidazole carboxylase catalyti PURE; 3-layer (ABA) sandwich, rossmann fold, csgid, lyase, structu genomics; 1.41A {Yersinia pestis} SCOP: c.23.8.1 PDB: 1d7a_A* 1qcz_A 2ate_A* 2nsl_A* 2nsh_A* 2nsj_A*

Probab=94.87  E-value=0.36  Score=30.74  Aligned_cols=68  Identities=15%  Similarity=0.170  Sum_probs=49.8

Q ss_pred             HHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHH---hcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           77 LGRAKEICAKHGVVAETMTEMG-DPKNVICEAAE---KHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        77 l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~---~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .+++...+++.|++++..+..- ...+.+.++++   +.+++.||.++...+.+.        .-+.-.+++||+-||-.
T Consensus        28 ~~~a~~~L~~~Gi~~ev~V~SaHR~p~~~~~~~~~a~~~g~~ViIa~AG~aa~Lp--------gvvA~~t~~PVIgVP~~   99 (174)
T 3kuu_A           28 MQFAADVLTTLNVPFHVEVVSAHRTPDRLFSFAEQAEANGLHVIIAGNGGAAHLP--------GMLAAKTLVPVLGVPVQ   99 (174)
T ss_dssp             HHHHHHHHHHTTCCEEEEECCTTTCHHHHHHHHHHTTTTTCSEEEEEEESSCCHH--------HHHHHTCSSCEEEEEEC
T ss_pred             HHHHHHHHHHcCCCEEEEEEcccCCHHHHHHHHHHHHhCCCcEEEEECChhhhhH--------HHHHhccCCCEEEeeCC
Confidence            4566777778899999988775 56666777765   467899999987654443        44666788999998854

>3rg8_A Phosphoribosylaminoimidazole carboxylase, PURE PR; purine biosynthesis, lyase; 1.74A {Treponema denticola} SCOP: c.23.8.0 PDB: 3rgg_A*

Probab=94.57  E-value=0.48  Score=29.78  Aligned_cols=68  Identities=7%  Similarity=0.070  Sum_probs=49.1

Q ss_pred             HHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHHh---c-CCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           77 LGRAKEICAKHGVVAETMTEMG-DPKNVICEAAEK---H-KIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        77 l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~~---~-~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      .+++...+++.|++++..+..- ...+.+.+++++   . +++.||.++...+.+.        .-+...+++||+-||.
T Consensus        18 ~~~a~~~l~~~gi~~ev~V~saHR~p~~~~~~~~~a~~~~~~~ViIa~AG~aa~Lp--------gvvA~~t~~PVIgVP~   89 (159)
T 3rg8_A           18 AEKIASELKTFGIEYAIRIGSAHKTAEHVVSMLKEYEALDRPKLYITIAGRSNALS--------GFVDGFVKGATIACPP   89 (159)
T ss_dssp             HHHHHHHHHHTTCEEEEEECCTTTCHHHHHHHHHHHHTSCSCEEEEEECCSSCCHH--------HHHHHHSSSCEEECCC
T ss_pred             HHHHHHHHHHcCCCEEEEEEcccCCHHHHHHHHHHhhhcCCCcEEEEECCchhhhH--------HHHHhccCCCEEEeeC
Confidence            4566777778899999988775 566666666543   2 5899999987654443        4466678899999985


Q ss_pred             C
Q 031713          152 P  152 (154)
Q Consensus       152 ~  152 (154)
                      .
T Consensus        90 ~   90 (159)
T 3rg8_A           90 P   90 (159)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3ors_A N5-carboxyaminoimidazole ribonucleotide mutase; isomerase, isomerase,biosynthetic protein; 1.45A {Staphylococcus aureus subsp}

Probab=94.51  E-value=0.46  Score=29.96  Aligned_cols=68  Identities=12%  Similarity=0.169  Sum_probs=49.5

Q ss_pred             HHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHH---hcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           77 LGRAKEICAKHGVVAETMTEMG-DPKNVICEAAE---KHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        77 l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~---~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .+++...++..|++++..+..- ...+.+.++++   +.+++.||.++...+.+.        .-+.-.+++||+-||-.
T Consensus        19 ~~~a~~~l~~~gi~~ev~V~SaHR~p~~~~~~~~~a~~~g~~ViIa~AG~aa~Lp--------gvvA~~t~~PVIgVP~~   90 (163)
T 3ors_A           19 MQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLP--------GMVASLTTLPVIGVPIE   90 (163)
T ss_dssp             HHHHHHHHHHTTCCEEEEECCTTTSHHHHHHHHHHTTTTTCCEEEEEEESSCCHH--------HHHHHHCSSCEEEEEEC
T ss_pred             HHHHHHHHHHcCCCEEEEEECCcCCHHHHHHHHHHHHhCCCcEEEEECCchhhhH--------HHHHhccCCCEEEeeCC
Confidence            4566777788899999988774 56666666654   457899999987654443        44666788999999854

>1zun_A Sulfate adenylyltransferase subunit 2; beta barrel, switch domain, heterodimer, pyrophosphate, G protein; HET: GDP AGS; 2.70A {Pseudomonas syringae} SCOP: c.26.2.2

Probab=94.43  E-value=0.46  Score=33.56  Aligned_cols=93  Identities=11%  Similarity=0.044  Sum_probs=58.7

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKE   82 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~   82 (154)
                      +.+++|++.+...|..++..+.......+  .++.++|+.......                          +.++-+.+
T Consensus        46 ~~~ivVa~SGGkDS~vLL~Ll~~~~~~~~--~~i~vv~vDtg~~~~--------------------------et~~~v~~   97 (325)
T 1zun_A           46 FDNPVMLYSIGKDSAVMLHLARKAFFPGK--LPFPVMHVDTRWKFQ--------------------------EMYRFRDQ   97 (325)
T ss_dssp             CSSEEEECCSSHHHHHHHHHHHHHHTTSC--CSSCEEEECCSCCCH--------------------------HHHHHHHH
T ss_pred             CCCEEEEEcChHHHHHHHHHHHHhccccC--CCEEEEEEECCCCCH--------------------------HHHHHHHH
Confidence            46899999999999999988887765433  578889986553211                          11223334


Q ss_pred             HHHhcCCeEEEEEe-----cCC-hh-------------hHHHHHHHhcCCCEEEEecCCC
Q 031713           83 ICAKHGVVAETMTE-----MGD-PK-------------NVICEAAEKHKIQLLIVGSHSR  123 (154)
Q Consensus        83 ~~~~~~~~~~~~v~-----~g~-~~-------------~~i~~~a~~~~~dlivlg~~~~  123 (154)
                      .++..|+++.+.-.     .|. ..             ..+.+.+++.+++.++.|.+..
T Consensus        98 ~~~~~gi~l~v~~~~~~~~~G~~~~~~~~~~cc~~~K~~pL~~~l~e~g~~~i~tG~R~D  157 (325)
T 1zun_A           98 MVEEMGLDLITHINPDGVAQGINPFTHGSAKHTDIMKTEGLKQALDKHGFDAAFGGARRD  157 (325)
T ss_dssp             HHHTTTCCEEEECC--------------CCHHHHHHTHHHHHHHHHHHTCSEEECCCCTT
T ss_pred             HHHHcCCCEEEEeCchHHhcCCCccccChHHHHHHHHHHHHHHHHHHcCCCEEEEecccc
Confidence            45566777544321     121 11             2355667778999999998753

>1o4v_A Phosphoribosylaminoimidazole mutase PURE; structural genomics, joint center for structural genomics, J protein structure initiative, PSI; 1.77A {Thermotoga maritima} SCOP: c.23.8.1

Probab=94.39  E-value=0.47  Score=30.46  Aligned_cols=69  Identities=19%  Similarity=0.266  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHH---hcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           76 LLGRAKEICAKHGVVAETMTEMG-DPKNVICEAAE---KHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        76 ~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~---~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      ..+++...++..|++++..+..- ...+.+.++++   +.+++.||.++...+.+.        .-+...+++||+-||.
T Consensus        28 v~~~a~~~L~~~Gi~~dv~V~SaHR~p~~l~~~~~~a~~~g~~ViIa~AG~aa~Lp--------gvvA~~t~~PVIgVP~   99 (183)
T 1o4v_A           28 VMKQAAEILEEFGIDYEITIVSAHRTPDRMFEYAKNAEERGIEVIIAGAGGAAHLP--------GMVASITHLPVIGVPV   99 (183)
T ss_dssp             HHHHHHHHHHHTTCEEEEEECCTTTCHHHHHHHHHHTTTTTCCEEEEEEESSCCHH--------HHHHHHCSSCEEEEEE
T ss_pred             HHHHHHHHHHHcCCCeEEEEEcccCCHHHHHHHHHHHHhCCCcEEEEecCcccccH--------HHHHhccCCCEEEeeC
Confidence            34566777778899999999774 55666666655   456899999987654443        4466678899999986


Q ss_pred             C
Q 031713          152 P  152 (154)
Q Consensus       152 ~  152 (154)
                      .
T Consensus       100 ~  100 (183)
T 1o4v_A          100 K  100 (183)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1u11_A PURE (N5-carboxyaminoimidazole ribonucleotide MUT; acidophIle, protein stability, lyase; HET: CIT; 1.55A {Acetobacter aceti} SCOP: c.23.8.1 PDB: 2fwj_A* 2fw1_A* 2fwb_A 2fwa_A 2fw9_A 2fw7_A 2fw6_A 2fwp_A* 2fwi_A* 2fw8_A

Probab=94.34  E-value=0.51  Score=30.28  Aligned_cols=68  Identities=16%  Similarity=0.290  Sum_probs=49.8

Q ss_pred             HHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHHh---cCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           77 LGRAKEICAKHGVVAETMTEMG-DPKNVICEAAEK---HKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        77 l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~~---~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .+++...++..|++++..+..- ...+.+.+++++   .+++.||.++...+.+.        .-+.-.+++||+-||-.
T Consensus        37 ~~~a~~~L~~~Gi~~dv~V~SaHR~p~~l~~~~~~a~~~g~~ViIa~AG~aa~Lp--------gvvA~~t~~PVIgVP~~  108 (182)
T 1u11_A           37 MRHADALLTELEIPHETLIVSAHRTPDRLADYARTAAERGLNVIIAGAGGAAHLP--------GMCAAWTRLPVLGVPVE  108 (182)
T ss_dssp             HHHHHHHHHHTTCCEEEEECCTTTCHHHHHHHHHHTTTTTCCEEEEEEESSCCHH--------HHHHHHCSSCEEEEEEC
T ss_pred             HHHHHHHHHHcCCCeEEEEEcccCCHHHHHHHHHHHHhCCCcEEEEecCchhhhH--------HHHHhccCCCEEEeeCC
Confidence            4566677778899999988774 566777777664   45899999987654443        44666788999999854

>3lp6_A Phosphoribosylaminoimidazole carboxylase catalyti; alpha and beta protein, structural genomics, PSI-2, protein initiative; 1.70A {Mycobacterium tuberculosis} SCOP: c.23.8.0

Probab=94.29  E-value=0.48  Score=30.18  Aligned_cols=68  Identities=16%  Similarity=0.239  Sum_probs=48.9

Q ss_pred             HHHHHHHHHhcCCeEEEEEecC-ChhhHHHHH---HHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           77 LGRAKEICAKHGVVAETMTEMG-DPKNVICEA---AEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        77 l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~---a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .+++...++..|++++..+..- ...+.+.++   +++.+++.||.++...+.+.        .-+...+++||+-||-.
T Consensus        23 ~~~a~~~L~~~gi~~ev~V~SaHR~p~~~~~~~~~a~~~g~~ViIa~AG~aa~Lp--------gvvA~~t~~PVIgVP~~   94 (174)
T 3lp6_A           23 MADAAAALAEFDIPAEVRVVSAHRTPEAMFSYARGAAARGLEVIIAGAGGAAHLP--------GMVAAATPLPVIGVPVP   94 (174)
T ss_dssp             HHHHHHHHHHTTCCEEEEECCTTTCHHHHHHHHHHHHHHTCCEEEEEEESSCCHH--------HHHHHHCSSCEEEEEEC
T ss_pred             HHHHHHHHHHcCCCEEEEEECCCCCHHHHHHHHHHHHhCCCCEEEEecCchhhhH--------HHHHhccCCCEEEeeCC
Confidence            4566777778899999988774 445555555   55578999999987654443        44666788999999854

>1o97_C Electron transferring flavoprotein beta-subunit; FAD binding; HET: AMP FAD; 1.6A {Methylophilus methylotrophus} SCOP: c.26.2.3 PDB: 1o95_C* 1o96_A* 1o94_C* 3clr_C* 3cls_C* 3clt_C* 3clu_C*

Probab=93.95  E-value=0.79  Score=31.35  Aligned_cols=82  Identities=16%  Similarity=0.240  Sum_probs=52.4

Q ss_pred             EecCCchHHHHHHHHHHHcccCCCCC--eEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 031713            9 AIDESECRHYALQWALENLGDAISKS--DLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAK   86 (154)
Q Consensus         9 ~vd~~~~~~~~l~~a~~la~~~~~~~--~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   86 (154)
                      +...++.+..+++.|.+++...|  .  +++++.+=+...                           +..+.++    ..
T Consensus        32 ~~~lnp~d~~ale~A~~Lke~~g--~~~~V~av~~G~~~~---------------------------~~~lr~a----la   78 (264)
T 1o97_C           32 MYDLNEWDDFSLEEAMKIKESSD--TDVEVVVVSVGPDRV---------------------------DESLRKC----LA   78 (264)
T ss_dssp             EEEECHHHHHHHHHHHHHHHHCS--SCCEEEEEEESCGGG---------------------------HHHHHHH----HH
T ss_pred             CCccCHHHHHHHHHHHHHHHhcC--CCceEEEEEeCchhH---------------------------HHHHHHH----Hh
Confidence            34456779999999999988755  5  898887754211                           1122222    22


Q ss_pred             cCCeEEEEEec----C-C---hhhHHHHHHHhcCCCEEEEecCCC
Q 031713           87 HGVVAETMTEM----G-D---PKNVICEAAEKHKIQLLIVGSHSR  123 (154)
Q Consensus        87 ~~~~~~~~v~~----g-~---~~~~i~~~a~~~~~dlivlg~~~~  123 (154)
                      .|..--+.+..    + +   .+..|...+++.++|+|++|....
T Consensus        79 ~GaD~vi~v~d~~~~~~~~~~~a~~La~~i~~~~~dlVl~G~~s~  123 (264)
T 1o97_C           79 KGADRAVRVWDDAAEGSDAIVVGRILTEVIKKEAPDMVFAGVQSS  123 (264)
T ss_dssp             TTCSEEEEECCGGGTTCCHHHHHHHHHHHHHHHCCSEEEEESCCT
T ss_pred             cCCCEEEEEcCcccccCCHHHHHHHHHHHHHhcCCCEEEEcCCcc
Confidence            47664444422    1 2   344677788888999999998754

>2wq7_A RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A*

Probab=93.89  E-value=0.75  Score=34.85  Aligned_cols=128  Identities=9%  Similarity=-0.037  Sum_probs=81.0

Q ss_pred             EEEEEe--cCCchHHHHHHHHHHHccc--CCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAI--DESECRHYALQWALENLGD--AISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         5 ~iLv~v--d~~~~~~~~l~~a~~la~~--~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      .+|+=+  |..-....+|..|++.+..  .+  .+|..++++++.....       .      ..........-+-+..+
T Consensus        30 ~vl~WfrrDLRl~DN~aL~~A~~~~~~~~~~--~pv~~vfi~dp~~~~~-------~------~~~~~r~~Fl~~sL~~L   94 (543)
T 2wq7_A           30 TLVHWFRKGLRLHDNPALSHIFTAANAAPGR--YFVRPIFILDPGILDW-------M------QVGANRWRFLQQTLEDL   94 (543)
T ss_dssp             EEEEEESSCCCSTTCHHHHHHHHHHHHSTTT--EEEEEEEEECTTGGGC-------T------TSCHHHHHHHHHHHHHH
T ss_pred             eEEEEeCCCcCcchHHHHHHHHHhCccccCC--CeEEEEEEECchhhcc-------c------CCCHHHHHHHHHHHHHH
Confidence            335544  4455567788888877654  33  5799999988754321       0      00012333445667777


Q ss_pred             HHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           81 KEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        81 ~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      .+.+++.|+++.  +..|++.+.|.+++++.+++.|+....- ..... ....-....+....+++..+..
T Consensus        95 ~~~L~~~G~~L~--v~~g~~~~~l~~l~~~~~~~~v~~~~~~-~p~~~-~rd~~v~~~~~~~gi~~~~~~~  161 (543)
T 2wq7_A           95 DNQLRKLNSRLF--VVRGKPAEVFPRIFKSWRVEMLTFETDI-EPYSV-TRDAAVQKLAKAEGVRVETHCS  161 (543)
T ss_dssp             HHHHHHTTCCCE--EEESCHHHHHHHHHHHTTEEEEEEECCC-SHHHH-HHHHHHHHHHHHHTCEEEEECC
T ss_pred             HHHHHHCCCeEE--EEeCCHHHHHHHHHHHcCCCEEEEecCc-CHHHH-HHHHHHHHHHHHcCCEEEEecC
Confidence            777877787653  4579999999999999999999987542 22222 2223334556666788776654

>1ni5_A Putative cell cycle protein MESJ; structural genomics, ATPase, PP-type, putative cell cycle PR PSI, protein structure initiative; 2.65A {Escherichia coli} SCOP: b.153.1.2 c.26.2.5 d.229.1.1

Probab=93.77  E-value=0.51  Score=34.65  Aligned_cols=92  Identities=12%  Similarity=0.048  Sum_probs=59.5

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHccc-CCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGD-AISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~-~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      -++|+|++.+...|..++..+..+... .+  -++.++||.......                        ..+..+.+.
T Consensus        13 ~~~vlVa~SGG~DS~~Ll~ll~~~~~~~~g--~~v~avhvdhglr~~------------------------s~~~~~~v~   66 (433)
T 1ni5_A           13 SRQILVAFSGGLDSTVLLHQLVQWRTENPG--VALRAIHVHHGLSAN------------------------ADAWVTHCE   66 (433)
T ss_dssp             CSEEEEECCSBHHHHHHHHHHHHHHTTSTT--CEEEEEEECCSCCSS------------------------HHHHHHHHH
T ss_pred             CCEEEEEEcchHHHHHHHHHHHHHHHhcCC--CeEEEEEEECCCCcc------------------------cHHHHHHHH
Confidence            468999999999999999888877765 55  699999997653221                        122345566


Q ss_pred             HHHHhcCCeEEEEEec----CChhhHHH---------HHHHhcCCCEEEEecCC
Q 031713           82 EICAKHGVVAETMTEM----GDPKNVIC---------EAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        82 ~~~~~~~~~~~~~v~~----g~~~~~i~---------~~a~~~~~dlivlg~~~  122 (154)
                      +.|+..|+++.+.-..    |...+...         +.++  +++.|+.|++.
T Consensus        67 ~~~~~lgi~~~v~~~~~~~~~~~~e~~aR~~Ry~~l~~~a~--~~~~i~tgH~~  118 (433)
T 1ni5_A           67 NVCQQWQVPLVVERVQLAQEGLGIEAQARQARYQAFARTLL--PGEVLVTAQHL  118 (433)
T ss_dssp             HHHHHTTCCEEEECCCCCCSSSTTTTHHHHHHHHHHHHTCC--TTEEEECCCCH
T ss_pred             HHHHHcCCcEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHh--hCCeEEeeccc
Confidence            6777778886553322    21111111         2222  58899999863

>3ih5_A Electron transfer flavoprotein alpha-subunit; alpha-beta-alpha sandwich, structural genomics, PSI-2, protein structure initiative; 2.60A {Bacteroides thetaiotaomicron}

Probab=93.62  E-value=0.47  Score=31.45  Aligned_cols=87  Identities=9%  Similarity=0.055  Sum_probs=58.7

Q ss_pred             CCcEEEEEecC-----CchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDE-----SECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALAL   76 (154)
Q Consensus         2 ~~~~iLv~vd~-----~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   76 (154)
                      .|+.|||-++.     .+.+..++..|.+++...|  .+++++-+=+.. .                             
T Consensus         2 ~m~~ilV~~E~~~g~l~~~s~ell~~A~~La~~~g--~~v~av~~G~~~-~-----------------------------   49 (217)
T 3ih5_A            2 NANNLFVYCEIEEGIVADVSLELLTKGRSLANELN--CQLEAVVAGTGL-K-----------------------------   49 (217)
T ss_dssp             -CCCEEEECCEETTEECHHHHHHHHHHHHHHHHHT--CCEEEEEEESCC-T-----------------------------
T ss_pred             CcccEEEEEECcCCEECHHHHHHHHHHHHHHHhcC--CeEEEEEECCCH-H-----------------------------
Confidence            36789998875     4668999999999999877  788888774431 1                             


Q ss_pred             HHHHHHHHHhcCCeEEEEEec----C-C---hhhHHHHHHHhcCCCEEEEecCC
Q 031713           77 LGRAKEICAKHGVVAETMTEM----G-D---PKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        77 l~~~~~~~~~~~~~~~~~v~~----g-~---~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                        .+.+.+..+|..--+.+..    + +   .++.|.+.+++.++|+|++|+..
T Consensus        50 --~~~~~~~~~Gad~v~~v~~~~~~~~~~~~~a~~l~~~i~~~~p~~Vl~g~t~  101 (217)
T 3ih5_A           50 --EIEKQILPYGVDKLHVFDAEGLYPYTSLPHTSILVNLFKEEQPQICLMGATV  101 (217)
T ss_dssp             --TTHHHHGGGTCSEEEEEECGGGSSCCHHHHHHHHHHHHHHHCCSEEEEECSH
T ss_pred             --HHHHHHHhcCCCEEEEecCcccccCCHHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence              1112233457664344422    1 2   35678888999999999999753

>1efv_B Electron transfer flavoprotein; electron transport, glutaric acidemia type II; HET: FAD AMP; 2.10A {Homo sapiens} SCOP: c.26.2.3 PDB: 1t9g_S* 2a1u_B* 2a1t_S*

Probab=92.25  E-value=1.8  Score=29.38  Aligned_cols=96  Identities=16%  Similarity=0.154  Sum_probs=56.8

Q ss_pred             CchHHHHHHHHHHHcccCCCCC--eEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCe
Q 031713           13 SECRHYALQWALENLGDAISKS--DLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVV   90 (154)
Q Consensus        13 ~~~~~~~l~~a~~la~~~~~~~--~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~   90 (154)
                      ++.+..+++.|.++... |  .  +++++.+=+...                           +..+.++    ...|..
T Consensus        39 np~d~~Ale~A~~Lke~-g--~~~~V~av~~G~~~a---------------------------~~~lr~a----la~GaD   84 (255)
T 1efv_B           39 NPFCEIAVEEAVRLKEK-K--LVKEVIAVSCGPAQC---------------------------QETIRTA----LAMGAD   84 (255)
T ss_dssp             CHHHHHHHHHHHHHHHT-T--SCSEEEEEEEESTTH---------------------------HHHHHHH----HHHTCS
T ss_pred             CHHHHHHHHHHHHHHhc-C--CCceEEEEEeCChhH---------------------------HHHHHHH----HhcCCC
Confidence            34588999999999876 5  5  899888755321                           1222222    123666


Q ss_pred             EEEEEe------cC-C---hhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcE
Q 031713           91 AETMTE------MG-D---PKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPV  146 (154)
Q Consensus        91 ~~~~v~------~g-~---~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pv  146 (154)
                      --..+.      .+ +   .++.|...+++.++|+|++|........    +.+.-.+......|.
T Consensus        85 ~vi~v~~d~~~~~~~~~~~~A~~La~~i~~~~~dlVl~G~~s~d~d~----~~v~p~lA~~L~~~~  146 (255)
T 1efv_B           85 RGIHVEVPPAEAERLGPLQVARVLAKLAEKEKVDLVLLGKQAIDDDC----NQTGQMTAGFLDWPQ  146 (255)
T ss_dssp             EEEEEECCHHHHTTCCHHHHHHHHHHHHHHHTCSEEEEESCCTTTCC----CCHHHHHHHHHTCCE
T ss_pred             EEEEEecChhhcccCCHHHHHHHHHHHHHhcCCCEEEEeCcccCCch----hhHHHHHHHHhCCCc
Confidence            444443      13 2   3456777888889999999987543222    234444444444443

>1efp_B ETF, protein (electron transfer flavoprotein); electron transport, glutaric acidemia type II; HET: FAD AMP; 2.60A {Paracoccus denitrificans} SCOP: c.26.2.3

Probab=91.95  E-value=2  Score=29.14  Aligned_cols=78  Identities=13%  Similarity=0.135  Sum_probs=50.2

Q ss_pred             CCchHHHHHHHHHHHcccCCCCC--eEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 031713           12 ESECRHYALQWALENLGDAISKS--DLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGV   89 (154)
Q Consensus        12 ~~~~~~~~l~~a~~la~~~~~~~--~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   89 (154)
                      .++.+..+++.|.++... |  .  +++++.+=+...                           +..+.++    ...|.
T Consensus        35 lnp~d~~Ale~A~~Lke~-g--~~~~V~av~~G~~~a---------------------------~~~lr~a----la~Ga   80 (252)
T 1efp_B           35 MNPFDEIAVEEAIRLKEK-G--QAEEIIAVSIGVKQA---------------------------AETLRTA----LAMGA   80 (252)
T ss_dssp             ECHHHHHHHHHHHHHHTT-T--SCSEEEEEEEESGGG---------------------------HHHHHHH----HHHTC
T ss_pred             CCHHHHHHHHHHHHHHhc-C--CCceEEEEEeCChhH---------------------------HHHHHHH----HhcCC
Confidence            457789999999999876 5  5  899887754311                           1222222    12366


Q ss_pred             eEEEEEe------cC-C---hhhHHHHHHHhcCCCEEEEecCCC
Q 031713           90 VAETMTE------MG-D---PKNVICEAAEKHKIQLLIVGSHSR  123 (154)
Q Consensus        90 ~~~~~v~------~g-~---~~~~i~~~a~~~~~dlivlg~~~~  123 (154)
                      .--+.+.      .+ +   .++.|...+++.++|+|++|....
T Consensus        81 D~vi~v~~d~~~~~~~~~~~~a~~La~~i~~~~~dlVl~G~~s~  124 (252)
T 1efp_B           81 DRAILVVAADDVQQDIEPLAVAKILAAVARAEGTELIIAGKQAI  124 (252)
T ss_dssp             SEEEEEECCSSTTCCCCHHHHHHHHHHHHHHHTCSEEEEESCCT
T ss_pred             CEEEEEecChhhcccCCHHHHHHHHHHHHHhcCCCEEEEcCCcc
Confidence            6444443      12 2   345677788888999999998754

>3bl5_A Queuosine biosynthesis protein QUEC; PREQ1 biosynthesis, RNA modification, tRNA, hydrolase; 2.95A {Bacillus subtilis}

Probab=91.37  E-value=2  Score=27.97  Aligned_cols=38  Identities=24%  Similarity=0.370  Sum_probs=27.9

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccC
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPT   44 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~   44 (154)
                      |..++++|++.+.-.|..++..+.+.    +  .++..+|+...
T Consensus         1 m~~~~v~v~lSGG~DS~~ll~ll~~~----~--~~v~~~~~~~~   38 (219)
T 3bl5_A            1 MKKEKAIVVFSGGQDSTTCLLWALKE----F--EEVETVTFHYN   38 (219)
T ss_dssp             --CCEEEEECCSSHHHHHHHHHHHHH----C--SEEEEEEEESS
T ss_pred             CCCCCEEEEccCcHHHHHHHHHHHHc----C--CceEEEEEeCC
Confidence            67789999999998888777666542    3  48888988765

>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} SCOP: a.99.1.1 c.28.1.1

Probab=91.36  E-value=3.5  Score=30.75  Aligned_cols=130  Identities=12%  Similarity=-0.040  Sum_probs=76.1

Q ss_pred             cEEEEEe--cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            4 KKVMVAI--DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         4 ~~iLv~v--d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      +.+|+=+  |..-....+|..|++    .+  .++..|++.++........++....        .......-+-+..+.
T Consensus         6 ~~~l~WfrrDLRl~DN~aL~~A~~----~~--~~v~~vfi~dp~~~~~~~~~~~~~~--------~~r~~Fl~~sL~~L~   71 (489)
T 1np7_A            6 PTVLVWFRNDLRLHDHEPLHRALK----SG--LAITAVYCYDPRQFAQTHQGFAKTG--------PWRSNFLQQSVQNLA   71 (489)
T ss_dssp             CEEEEEESSCCCSTTCHHHHHHHH----TT--SEEEEEEEECGGGGSBCTTSCBSSC--------HHHHHHHHHHHHHHH
T ss_pred             CcEEEEeCCCCCcchHHHHHHHHh----cC--CCEEEEEEECchhhcccccccCCCC--------HHHHHHHHHHHHHHH
Confidence            3455555  444556778877764    22  4788888887643221000000001        122334455677777


Q ss_pred             HHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           82 EICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        82 ~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      +.+++.|+++.  +..|++.+.|.+++++.+++.|+..... .......- ....+.+...++++..+..
T Consensus        72 ~~L~~~G~~L~--v~~g~~~~~l~~l~~~~~~~~V~~~~~~-~~~~~~rd-~~v~~~l~~~gi~~~~~~~  137 (489)
T 1np7_A           72 ESLQKVGNKLL--VTTGLPEQVIPQIAKQINAKTIYYHREV-TQEELDVE-RNLVKQLTILGIEAKGYWG  137 (489)
T ss_dssp             HHHHHTTCCEE--EEESCHHHHHHHHHHHTTEEEEEEECCC-SHHHHHHH-HHHHHHHHHHTCEEEEECC
T ss_pred             HHHHHCCCcEE--EEECCHHHHHHHHHHHcCCCEEEEeccc-CHHHHHHH-HHHHHHHHhcCCeEEEecC
Confidence            77777787654  4579999999999999999999888543 22322222 2233444555677766543

>2nz2_A Argininosuccinate synthase; amino-acid biosynthesis, aspartate, citrulline, ST genomics, structural genomics consortium, SGC, ligase; HET: CIR; 2.40A {Homo sapiens}

Probab=91.00  E-value=3.5  Score=30.15  Aligned_cols=37  Identities=24%  Similarity=0.249  Sum_probs=28.5

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccC
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPT   44 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~   44 (154)
                      +.++++|++.+.-.|..++.++.+.    |  .++..+|+...
T Consensus         4 ~~~kVvvalSGGlDSsvll~lL~e~----G--~eV~av~vd~g   40 (413)
T 2nz2_A            4 SKGSVVLAYSGGLDTSCILVWLKEQ----G--YDVIAYLANIG   40 (413)
T ss_dssp             -CEEEEEECCSSHHHHHHHHHHHHT----T--EEEEEEEEESS
T ss_pred             CCCeEEEEEcChHHHHHHHHHHHHc----C--CEEEEEEEECC
Confidence            3578999999998888777766542    5  68999998665

>3k32_A Uncharacterized protein MJ0690; predicted subunit of tRNA methyltransferase, methanocaldococcus jannaschii DSM , PSI- 2; 2.50A {Methanocaldococcus jannaschii}

Probab=90.77  E-value=2.3  Score=27.63  Aligned_cols=38  Identities=11%  Similarity=-0.088  Sum_probs=27.5

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccC
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPT   44 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~   44 (154)
                      |.+++++|++.+...|..++..+.    ..|  .++.++|+...
T Consensus         4 m~~~kv~v~~SGG~DS~~ll~ll~----~~g--~~v~~~~v~~~   41 (203)
T 3k32_A            4 MKLMDVHVLFSGGKDSSLSAVILK----KLG--YNPHLITINFG   41 (203)
T ss_dssp             --CEEEEEECCCSHHHHHHHHHHH----HTT--EEEEEEEEECS
T ss_pred             ccCCeEEEEEECcHHHHHHHHHHH----HcC--CCeEEEEEeCC
Confidence            677899999999988887765443    345  68999998654

>3p9x_A Phosphoribosylglycinamide formyltransferase; structural genomics, PSI-biology, protein STRU initiative; 1.90A {Bacillus halodurans}

Probab=90.48  E-value=2.6  Score=27.79  Aligned_cols=85  Identities=9%  Similarity=0.137  Sum_probs=54.8

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKE   82 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~   82 (154)
                      |+||.|-+.++.++..++-.+.+- ..  .++++.++-...+.                                ..+.+
T Consensus         2 m~riavl~Sg~Gsnl~ali~~~~~-~~--l~~eI~~Visn~~~--------------------------------a~v~~   46 (211)
T 3p9x_A            2 MKRVAIFASGSGTNAEAIIQSQKA-GQ--LPCEVALLITDKPG--------------------------------AKVVE   46 (211)
T ss_dssp             -CEEEEECCTTCHHHHHHHHHHHT-TC--CSSEEEEEEESCSS--------------------------------SHHHH
T ss_pred             CCEEEEEEeCCchHHHHHHHHHHc-CC--CCcEEEEEEECCCC--------------------------------cHHHH
Confidence            478999999998888887766542 22  22677665543221                                13445


Q ss_pred             HHHhcCCeEEEEEec--CC---hhhHHHHHHHhcCCCEEEEecCC
Q 031713           83 ICAKHGVVAETMTEM--GD---PKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        83 ~~~~~~~~~~~~v~~--g~---~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      .+++.|+++...-..  .+   ...++.+..++.++|++|+...+
T Consensus        47 ~A~~~gIp~~~~~~~~~~~r~~~d~~~~~~l~~~~~Dliv~agy~   91 (211)
T 3p9x_A           47 RVKVHEIPVCALDPKTYPSKEAYEIEVVQQLKEKQIDFVVLAGYM   91 (211)
T ss_dssp             HHHTTTCCEEECCGGGSSSHHHHHHHHHHHHHHTTCCEEEESSCC
T ss_pred             HHHHcCCCEEEeChhhcCchhhhHHHHHHHHHhcCCCEEEEeCch
Confidence            566778886442211  11   14688899999999999998764

>1iv0_A Hypothetical protein; rnaseh-like, YQGF, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Thermus thermophilus} SCOP: c.55.3.8

Probab=90.41  E-value=0.98  Score=25.89  Aligned_cols=52  Identities=10%  Similarity=0.068  Sum_probs=35.4

Q ss_pred             ChhhHHHHHHHhcCCCEEEEecCC----CCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           99 DPKNVICEAAEKHKIQLLIVGSHS----RGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        99 ~~~~~i~~~a~~~~~dlivlg~~~----~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      ...+.|.+++++.+++.||+|-..    .........-.++++|-.. +.||..+-+
T Consensus        38 ~~~~~l~~li~e~~v~~iVvGlP~~mdGt~~~~~~~~~~f~~~L~~~-~lpV~~~DE   93 (98)
T 1iv0_A           38 EDVEALLDFVRREGLGKLVVGLPLRTDLKESAQAGKVLPLVEALRAR-GVEVELWDE   93 (98)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEECCCCCCSSSCCCSSTTHHHHHHHHHT-TCEEEEECC
T ss_pred             HHHHHHHHHHHHcCCCEEEEeeccCCCCCcCHHHHHHHHHHHHHhcC-CCCEEEECC
Confidence            356788999999999999999532    1111112333456777766 899988754

>3da8_A Probable 5'-phosphoribosylglycinamide formyltransferase PURN; glycinamide ribonucleotide transformylase, structure; 1.30A {Mycobacterium tuberculosis} PDB: 3dcj_A*

Probab=90.18  E-value=2.8  Score=27.70  Aligned_cols=84  Identities=19%  Similarity=0.137  Sum_probs=52.9

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      +..||.|.+.++.++..++-.+..  ...+  .++.++-..++  .                               ...
T Consensus        11 ~~~ri~vl~SG~gsnl~all~~~~--~~~~--~eI~~Vis~~~--a-------------------------------~~~   53 (215)
T 3da8_A           11 APARLVVLASGTGSLLRSLLDAAV--GDYP--ARVVAVGVDRE--C-------------------------------RAA   53 (215)
T ss_dssp             SSEEEEEEESSCCHHHHHHHHHSS--TTCS--EEEEEEEESSC--C-------------------------------HHH
T ss_pred             CCcEEEEEEeCChHHHHHHHHHHh--ccCC--CeEEEEEeCCc--h-------------------------------HHH
Confidence            456899999999888777755542  2222  56655533222  1                               113


Q ss_pred             HHHHhcCCeEEEEEec--CC---hhhHHHHHHHhcCCCEEEEecCC
Q 031713           82 EICAKHGVVAETMTEM--GD---PKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        82 ~~~~~~~~~~~~~v~~--g~---~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      +.++++|+++...-..  .+   ..+++.+..++.++|++|+...+
T Consensus        54 ~~A~~~gIp~~~~~~~~~~~r~~~d~~~~~~l~~~~~Dlivlagy~   99 (215)
T 3da8_A           54 EIAAEASVPVFTVRLADHPSRDAWDVAITAATAAHEPDLVVSAGFM   99 (215)
T ss_dssp             HHHHHTTCCEEECCGGGSSSHHHHHHHHHHHHHTTCCSEEEEEECC
T ss_pred             HHHHHcCCCEEEeCcccccchhhhhHHHHHHHHhhCCCEEEEcCch
Confidence            4556678886554211  11   24678889999999999998764

>2hma_A Probable tRNA (5-methylaminomethyl-2-thiouridylat methyltransferase; alpha-beta, beta barrel, structural genomics, PSI-2; HET: MSE SAM; 2.41A {Streptococcus pneumoniae}

Probab=89.68  E-value=4.4  Score=29.18  Aligned_cols=96  Identities=11%  Similarity=0.006  Sum_probs=55.6

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKE   82 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~   82 (154)
                      .++|+|++.+...|..++..+.+    .|  -++..+|+........         ..    .     -...+..+.+..
T Consensus         9 ~~kVlVa~SGGvDSsv~a~lL~~----~G--~~V~~v~~~~~~~~~~---------~~----~-----c~~~~d~~~a~~   64 (376)
T 2hma_A            9 KTRVVVGMSGGVDSSVTALLLKE----QG--YDVIGIFMKNWDDTDE---------NG----V-----CTATEDYKDVVA   64 (376)
T ss_dssp             GSEEEEECCSSHHHHHHHHHHHH----TT--CEEEEEEEECCCCCC----------------------CHHHHHHHHHHH
T ss_pred             CCeEEEEEeCHHHHHHHHHHHHH----cC--CcEEEEEEECCCcccc---------cc----c-----CCCHHHHHHHHH
Confidence            46899999999888766655443    35  6899999865421100         00    0     000112344444


Q ss_pred             HHHhcCCeEEEEEec-----------------CC------------hhhHHHHHHHhcCCCEEEEecCC
Q 031713           83 ICAKHGVVAETMTEM-----------------GD------------PKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        83 ~~~~~~~~~~~~v~~-----------------g~------------~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      .++..|++..+.-..                 |.            -...+.++|++.++|.|+.|++.
T Consensus        65 va~~lGIp~~vv~~~~~~~~~v~~~~l~~y~~G~tpnpc~~C~r~ik~~~l~~~A~~~G~d~IatGH~a  133 (376)
T 2hma_A           65 VADQIGIPYYSVNFEKEYWDRVFEYFLAEYRAGRTPNPDVMCNKEIKFKAFLDYAITLGADYVATGHYA  133 (376)
T ss_dssp             HHHHHTCCEEEEECHHHHHHHTHHHHHHHHHTTCCCCHHHHHHHHTTTTHHHHHHHTTTCSEEECCCSE
T ss_pred             HHHHhCCcEEEEeChHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCCCEEEECcch
Confidence            555556665443321                 10            13456788999999999999853

>4ds3_A Phosphoribosylglycinamide formyltransferase; structural genomics, seattle structural genomics center for infectious disease, ssgcid; 1.85A {Brucella melitensis BV}

Probab=89.64  E-value=3.1  Score=27.38  Aligned_cols=87  Identities=13%  Similarity=0.161  Sum_probs=53.6

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      |+.+||.|.+.++.+...++-.++. ...  .+.++.++-...+.  ..                              .
T Consensus         5 m~~~ri~vl~SG~gsnl~all~~~~-~~~--l~~~I~~Visn~~~--a~------------------------------~   49 (209)
T 4ds3_A            5 MKRNRVVIFISGGGSNMEALIRAAQ-APG--FPAEIVAVFSDKAE--AG------------------------------G   49 (209)
T ss_dssp             -CCEEEEEEESSCCHHHHHHHHHHT-STT--CSEEEEEEEESCTT--CT------------------------------H
T ss_pred             CCCccEEEEEECCcHHHHHHHHHHH-cCC--CCcEEEEEEECCcc--cH------------------------------H
Confidence            5667899999999888777766652 122  22455554442221  11                              0


Q ss_pred             HHHHHhcCCeEEEEEec--CC---hhhHHHHHHHhcCCCEEEEecCC
Q 031713           81 KEICAKHGVVAETMTEM--GD---PKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        81 ~~~~~~~~~~~~~~v~~--g~---~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      .+.+++.|+++...-..  .+   ..+++.+..++.++|++|+...+
T Consensus        50 l~~A~~~gIp~~~~~~~~~~~r~~~d~~~~~~l~~~~~Dliv~agy~   96 (209)
T 4ds3_A           50 LAKAEAAGIATQVFKRKDFASKEAHEDAILAALDVLKPDIICLAGYM   96 (209)
T ss_dssp             HHHHHHTTCCEEECCGGGSSSHHHHHHHHHHHHHHHCCSEEEESSCC
T ss_pred             HHHHHHcCCCEEEeCccccCCHHHHHHHHHHHHHhcCCCEEEEeccc
Confidence            14456678886543221  12   24688899999999999998764

>3kcq_A Phosphoribosylglycinamide formyltransferase; structural genomics, niaid, seattle structural center for infectious disease, ssgcid; 2.20A {Anaplasma phagocytophilum} SCOP: c.65.1.0

Probab=88.34  E-value=4  Score=26.98  Aligned_cols=86  Identities=14%  Similarity=0.044  Sum_probs=51.6

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      ..+||.|-+.++.+...++-.++   +..+.+.++.++  +.......                              ..
T Consensus         7 ~~~ri~vl~SG~gsnl~all~~~---~~~~~~~~I~~V--is~~~~a~------------------------------~l   51 (215)
T 3kcq_A            7 KELRVGVLISGRGSNLEALAKAF---STEESSVVISCV--ISNNAEAR------------------------------GL   51 (215)
T ss_dssp             CCEEEEEEESSCCHHHHHHHHHT---CCC-CSEEEEEE--EESCTTCT------------------------------HH
T ss_pred             CCCEEEEEEECCcHHHHHHHHHH---HcCCCCcEEEEE--EeCCcchH------------------------------HH
Confidence            35689999999988877665554   221111454444  43321111                              02


Q ss_pred             HHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCC
Q 031713           82 EICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        82 ~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      +.+++.|+++...-...-...++.+..++.++|++|+...+
T Consensus        52 ~~A~~~gIp~~~~~~~~~~~~~~~~~L~~~~~Dlivlagy~   92 (215)
T 3kcq_A           52 LIAQSYGIPTFVVKRKPLDIEHISTVLREHDVDLVCLAGFM   92 (215)
T ss_dssp             HHHHHTTCCEEECCBTTBCHHHHHHHHHHTTCSEEEESSCC
T ss_pred             HHHHHcCCCEEEeCcccCChHHHHHHHHHhCCCEEEEeCCc
Confidence            34566788865422222124788899999999999998764

>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana}

Probab=88.21  E-value=2.8  Score=31.76  Aligned_cols=121  Identities=15%  Similarity=0.110  Sum_probs=70.0

Q ss_pred             cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhc----ccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 031713           11 DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQ----ASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAK   86 (154)
Q Consensus        11 d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   86 (154)
                      |..-....+|..|++    .+  .+|..|+|.++......    ..+....+        ........+-|..+.+.+++
T Consensus        14 DLRl~DN~AL~~A~~----~~--~~vlpvfi~dp~~~~~~~~~~~~g~~~~g--------~~r~~Fl~~sL~~L~~~L~~   79 (537)
T 3fy4_A           14 GLRVHDNPALEYASK----GS--EFMYPVFVIDPHYMESDPSAFSPGSSRAG--------VNRIRFLLESLKDLDSSLKK   79 (537)
T ss_dssp             CCCSTTCHHHHHHHT----TC--SCEEEEEEECHHHHSCCTTSSSSBCSSCB--------HHHHHHHHHHHHHHHHHHHH
T ss_pred             CcccchhHHHHHHHh----cC--CCEEEEEEeChhhhcccccccccccccCC--------HHHHHHHHHHHHHHHHHHHH
Confidence            455556778877764    23  58999999886432210    00000011        12333445566777777777


Q ss_pred             cCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEE
Q 031713           87 HGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVV  149 (154)
Q Consensus        87 ~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv  149 (154)
                      .|++.  .++.|++.+.|.+++++.+++-|+..... ...... ........+....+++..+
T Consensus        80 ~G~~L--~v~~G~~~~vl~~L~~~~~~~~V~~n~~~-~p~~~~-RD~~v~~~l~~~gI~~~~~  138 (537)
T 3fy4_A           80 LGSRL--LVFKGEPGEVLVRCLQEWKVKRLCFEYDT-DPYYQA-LDVKVKDYASSTGVEVFSP  138 (537)
T ss_dssp             TTCCC--EEEESCHHHHHHHHHTTSCEEEEEECCCC-SHHHHH-HHHHHHHHHHHTTCEEECC
T ss_pred             cCCce--EEEECCHHHHHHHHHHHcCCCEEEEeccc-cHHHHH-HHHHHHHHHHHcCCeEEEe
Confidence            77654  45579999999999999999999887542 222221 1222334445555555443

>2e0i_A 432AA long hypothetical deoxyribodipyrimidine PHO; photolyase, FAD, DNA repair, lyase; HET: FAD; 2.80A {Sulfolobus tokodaii}

Probab=87.58  E-value=3.5  Score=30.38  Aligned_cols=117  Identities=12%  Similarity=0.067  Sum_probs=71.7

Q ss_pred             cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCe
Q 031713           11 DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVV   90 (154)
Q Consensus        11 d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~   90 (154)
                      |..-....+|..|++.    +  .+|..+++.++......     .       ..........-+-+..+.+.+++.|++
T Consensus        10 DLRl~DN~aL~~A~~~----~--~~v~~vfi~dp~~~~~~-----~-------~~~~~r~~Fl~~sL~~L~~~L~~~G~~   71 (440)
T 2e0i_A           10 DLRLEDNTGLNYALSE----C--DRVIPVFIADPRQLINN-----P-------YKSEFAVSFMINSLLELDDELRKKGSR   71 (440)
T ss_dssp             CCCSSSCHHHHHHHHH----S--SEEEEEEEECHHHHSSC-----T-------TCCHHHHHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCccchhHHHHHHHhc----C--CCEEEEEEeChhhhccC-----C-------cCCHHHHHHHHHHHHHHHHHHHHcCCe
Confidence            3444456678777762    3  58999999886432110     0       000123344556677777888877876


Q ss_pred             EEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           91 AETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        91 ~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      +.  +..|++.+.|.++++  +++.|+..... ....... .....+.+...++++..+..
T Consensus        72 L~--v~~g~~~~~l~~l~~--~~~~v~~~~~~-~~~~~~r-d~~v~~~l~~~gi~~~~~~~  126 (440)
T 2e0i_A           72 LN--VFFGEAEKVVSRFFN--KVDAIYVNEDY-TPFSISR-DEKIRKVCEENGIEFKAYED  126 (440)
T ss_dssp             CE--EEESCHHHHHHHHCT--TCSEEEEECCC-SHHHHHH-HHHHHHHHHTTTCEEEEECC
T ss_pred             EE--EEECCHHHHHHHHHc--CCCEEEEeccc-ChHHHHH-HHHHHHHHHHcCceEEEecC
Confidence            53  457999999999999  99999887542 2233222 23334455666788776653

>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus} SCOP: a.99.1.1 c.28.1.1 PDB: 1owm_A* 1own_A* 1owo_A* 1owp_A* 1qnf_A* 1tez_A*

Probab=87.36  E-value=3.8  Score=30.53  Aligned_cols=118  Identities=14%  Similarity=0.104  Sum_probs=72.4

Q ss_pred             cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCe
Q 031713           11 DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVV   90 (154)
Q Consensus        11 d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~   90 (154)
                      |..-....+|..|++.   .   .+|..+++.++.....       .      ..........-+-+..+.+.+++.|++
T Consensus        12 DLRl~Dn~aL~~A~~~---~---~~v~~vfi~dp~~~~~-------~------~~~~~r~~fl~~sL~~L~~~L~~~G~~   72 (484)
T 1owl_A           12 DLRLSDNIGLAAARAQ---S---AQLIGLFCLDPQILQS-------A------DMAPARVAYLQGCLQELQQRYQQAGSR   72 (484)
T ss_dssp             CCCSSSCHHHHHHHHH---C---SCEEEEEEECHHHHTC-------T------TCCHHHHHHHHHHHHHHHHHHHHHTSC
T ss_pred             CCCcchhHHHHHHHhc---C---CCEEEEEEEcchhhcC-------C------CCCHHHHHHHHHHHHHHHHHHHHCCCe
Confidence            3444456677777653   1   3688888887643210       0      000123334455667777777777876


Q ss_pred             EEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           91 AETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        91 ~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      +.  +..|++.+.|.+++++.+++.|+..... ....... .....+.+...++++..+..
T Consensus        73 L~--v~~g~~~~~l~~l~~~~~~~~v~~~~~~-~p~~~~r-d~~v~~~l~~~gi~~~~~~~  129 (484)
T 1owl_A           73 LL--LLQGDPQHLIPQLAQQLQAEAVYWNQDI-EPYGRDR-DGQVAAALKTAGIRAVQLWD  129 (484)
T ss_dssp             EE--EEESCHHHHHHHHHHHTTCSEEEEECCC-SHHHHHH-HHHHHHHHHHTTCEEEEECC
T ss_pred             EE--EEeCCHHHHHHHHHHHcCCCEEEEeccC-ChhHHHH-HHHHHHHHHHcCcEEEEecC
Confidence            53  4579999999999999999999987543 2233222 23334455666788777643

>1k92_A Argininosuccinate synthase, argininosuccinate SY; N-type ATP pyrophosphatase, ligase; 1.60A {Escherichia coli} SCOP: c.26.2.1 d.210.1.1 PDB: 1k97_A* 1kp2_A* 1kp3_A*

Probab=86.25  E-value=8.5  Score=28.55  Aligned_cols=37  Identities=16%  Similarity=0.121  Sum_probs=29.5

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccC
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPT   44 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~   44 (154)
                      ..++|+|++.+.-.|..++.++.+.    |  .+++.+|+...
T Consensus         9 ~~~KVvVA~SGGlDSSvll~~L~e~----G--~eViavtvd~G   45 (455)
T 1k92_A            9 VGQRIGIAFSGGLDTSAALLWMRQK----G--AVPYAYTANLG   45 (455)
T ss_dssp             TTSEEEEECCSSHHHHHHHHHHHHT----T--CEEEEEEEECC
T ss_pred             CCCeEEEEEcChHHHHHHHHHHHHc----C--CEEEEEEEEcC
Confidence            3578999999999888888777552    5  69999999665

>2h31_A Multifunctional protein ADE2; alpha-beta-alpha, ligase, lyase; 2.80A {Homo sapiens}

Probab=85.92  E-value=5  Score=29.45  Aligned_cols=69  Identities=13%  Similarity=0.168  Sum_probs=47.5

Q ss_pred             HHHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHH---HhcCC-CEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           76 LLGRAKEICAKHGVVAETMTEMG-DPKNVICEAA---EKHKI-QLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        76 ~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a---~~~~~-dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      ..+++...++..|++++..|..- ...+.+.+++   ++.++ +.||.++...+.+.        .-+...+++||+-||
T Consensus       280 ~~~~a~~~l~~~gi~~~v~V~saHR~p~~~~~~~~~~~~~g~~~viIa~AG~~a~Lp--------gvva~~t~~PVIgvP  351 (425)
T 2h31_A          280 HCEKIKKACGNFGIPCELRVTSAHKGPDETLRIKAEYEGDGIPTVFVAVAGRSNGLG--------PVMSGNTAYPVISCP  351 (425)
T ss_dssp             HHHHHHHHHHHTTCCEEEEECCTTTCHHHHHHHHHHHHTTCCCEEEEEECCSSCCHH--------HHHHHHCSSCEEECC
T ss_pred             HHHHHHHHHHHcCCceEEeeeeccCCHHHHHHHHHHHHHCCCCeEEEEEcCcccchH--------hHHhccCCCCEEEee
Confidence            35566777778899999988774 4455555554   45667 58888876544333        446667889999998


Q ss_pred             CC
Q 031713          151 KP  152 (154)
Q Consensus       151 ~~  152 (154)
                      ..
T Consensus       352 ~~  353 (425)
T 2h31_A          352 PL  353 (425)
T ss_dssp             CC
T ss_pred             Cc
Confidence            63

>1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon, lyase (carbon-carbon); HET: DNA FAD MHF; 2.30A {Escherichia coli} SCOP: a.99.1.1 c.28.1.1

Probab=85.27  E-value=1.5  Score=32.66  Aligned_cols=91  Identities=11%  Similarity=0.061  Sum_probs=59.0

Q ss_pred             CchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCeEE
Q 031713           13 SECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAE   92 (154)
Q Consensus        13 ~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~   92 (154)
                      .-....+|..|++.  ..   .+|..++|.++.....             ...........-+-|..+.+.+++.|+++.
T Consensus        12 Rl~DN~aL~~A~~~--~~---~~v~~vfi~dp~~~~~-------------~~~~~~r~~fl~~sL~~L~~~L~~~G~~L~   73 (471)
T 1dnp_A           12 RLHDNLALAAACRN--SS---ARVLALYIATPRQWAT-------------HNMSPRQAELINAQLNGLQIALAEKGIPLL   73 (471)
T ss_dssp             CSTTCHHHHHHSSS--TT---SEEEEEEEECHHHHHH-------------TTCCHHHHHHHHHHHHHHHHHHHHTTCCEE
T ss_pred             cccchHHHHHHHhC--CC---CCEEEEEEECchhhcc-------------CCCCHHHHHHHHHHHHHHHHHHHHCCCeEE
Confidence            33455577666542  12   4899999988643210             000122334455667777778888887764


Q ss_pred             EEEe--cCChhhHHHHHHHhcCCCEEEEecC
Q 031713           93 TMTE--MGDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        93 ~~v~--~g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      +...  .|++.+.|.+++++.+++.|+....
T Consensus        74 v~~~~~~g~~~~~l~~l~~~~~~~~v~~~~~  104 (471)
T 1dnp_A           74 FREVDDFVASVEIVKQVCAENSVTHLFYNYQ  104 (471)
T ss_dssp             EEECSSHHHHHHHHHHHHHHHTCCEEEEECC
T ss_pred             EEEccCCCCHHHHHHHHHHHcCCCEEEEecc
Confidence            4322  6899999999999999999998654

>1sur_A PAPS reductase; assimilatory sulfate reduction, 3-phospho-adenylyl-sulfate reductase, oxidoreductase; 2.00A {Escherichia coli} SCOP: c.26.2.2

Probab=85.14  E-value=5.9  Score=25.76  Aligned_cols=36  Identities=6%  Similarity=-0.042  Sum_probs=27.6

Q ss_pred             cEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCC
Q 031713            4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTE   45 (154)
Q Consensus         4 ~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~   45 (154)
                      .+|+|++.+...|..++..+.++.      .++.++|+....
T Consensus        45 ~~v~Va~SGGkDS~vLL~ll~~~~------~~v~~v~vd~g~   80 (215)
T 1sur_A           45 GEYVLSSSFGIQAAVSLHLVNQIR------PDIPVILTDTGY   80 (215)
T ss_dssp             SEEEEECCCCTTHHHHHHHHHHHS------TTCEEEEEECSC
T ss_pred             CCEEEEecCCHHHHHHHHHHHHhC------CCCeEEEeeCCC
Confidence            489999999999998887766552      367888886653

>2j07_A Deoxyribodipyrimidine photo-lyase; flavoprotein, nucleotide-binding, DNA repair; HET: FAD HDF; 1.95A {Thermus thermophilus} SCOP: a.99.1.1 c.28.1.1 PDB: 1iqu_A* 1iqr_A* 2j08_A* 2j09_A*

Probab=84.74  E-value=9.6  Score=27.82  Aligned_cols=111  Identities=16%  Similarity=0.079  Sum_probs=68.6

Q ss_pred             cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCe
Q 031713           11 DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVV   90 (154)
Q Consensus        11 d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~   90 (154)
                      |..-....+|..|++    .   +++..+++.++....               . ........-+-+.++.+.+++.|++
T Consensus        11 DlRl~Dn~aL~~A~~----~---~~v~~vfi~d~~~~~---------------~-~~~r~~fl~~sL~~l~~~L~~~g~~   67 (420)
T 2j07_A           11 DLRLHDHPALLEALA----R---GPVVGLVVLDPNNLK---------------T-TPRRRAWFLENVRALREAYRARGGA   67 (420)
T ss_dssp             CCCSTTCHHHHHHHT----T---SCEEEEEEECHHHHS---------------S-CHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             CCCccccHHHHHHHh----C---CCEEEEEEECCcccc---------------C-CHHHHHHHHHHHHHHHHHHHHCCCe
Confidence            444455667776653    2   268888887653210               0 1233344556677777888888876


Q ss_pred             EEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           91 AETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        91 ~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      +  .+..|++.+.|.+++++.+++.|+..... .......-    ..|-..+++++..+..
T Consensus        68 l--~~~~g~~~~~l~~l~~~~~~~~v~~~~~~-~~~~~~rd----~~v~~~l~i~~~~~~~  121 (420)
T 2j07_A           68 L--WVLEGLPWEKVPEAARRLKAKAVYALTSH-TPYGRYRD----GRVREALPVPLHLLPA  121 (420)
T ss_dssp             E--EEEESCHHHHHHHHHHHTTCSEEEEECCC-SHHHHHHH----HHHHHHCSSCEEEECC
T ss_pred             E--EEEeCCHHHHHHHHHHHcCCCEEEEeccc-ChhHHHHH----HHHHHHcCCeEEEeCC
Confidence            5  44579999999999999999999987543 22232222    2333333777776643

>3s40_A Diacylglycerol kinase; structural genomics, the center for structural genomics of infectious diseases, csgid, transfer; 2.10A {Bacillus anthracis} PDB: 3t5p_A

Probab=84.29  E-value=4  Score=28.26  Aligned_cols=70  Identities=13%  Similarity=0.083  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhh-cCCCcEEEEcCC
Q 031713           76 LLGRAKEICAKHGVVAETMTEMG-DPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVH-NAKCPVLVVRKP  152 (154)
Q Consensus        76 ~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~-~~~~pvliv~~~  152 (154)
                      ..+++...++..+++++...... ..+..+.+.+.+ ++|.||+.- |.+.+     ..+++.+.. ...+|+.++|-.
T Consensus        27 ~~~~i~~~l~~~~~~~~~~~t~~~~~a~~~~~~~~~-~~d~vv~~G-GDGTl-----~~v~~~l~~~~~~~~l~iiP~G   98 (304)
T 3s40_A           27 NLTKIVPPLAAAFPDLHILHTKEQGDATKYCQEFAS-KVDLIIVFG-GDGTV-----FECTNGLAPLEIRPTLAIIPGG   98 (304)
T ss_dssp             HHHHHHHHHHHHCSEEEEEECCSTTHHHHHHHHHTT-TCSEEEEEE-CHHHH-----HHHHHHHTTCSSCCEEEEEECS
T ss_pred             HHHHHHHHHHHcCCeEEEEEccCcchHHHHHHHhhc-CCCEEEEEc-cchHH-----HHHHHHHhhCCCCCcEEEecCC
Confidence            34556667777788887766554 455566655543 788877653 22322     234455554 256899999865

>2ywb_A GMP synthase [glutamine-hydrolyzing]; GMP synthetase, XMP binding, ATP binding, purine nucleotide biosynthetic pathway, structural genomics; 2.10A {Thermus thermophilus} PDB: 2ywc_A*

Probab=84.16  E-value=11  Score=28.22  Aligned_cols=35  Identities=9%  Similarity=-0.016  Sum_probs=27.3

Q ss_pred             cEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccC
Q 031713            4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPT   44 (154)
Q Consensus         4 ~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~   44 (154)
                      ++++|++.+...|..++..+.+.    |  .++.++|+...
T Consensus       210 ~kvvvalSGGvDSsvla~ll~~~----g--~~v~av~vd~g  244 (503)
T 2ywb_A          210 DRVLLAVSGGVDSSTLALLLAKA----G--VDHLAVFVDHG  244 (503)
T ss_dssp             SEEEEEECSSHHHHHHHHHHHHH----T--CEEEEEEEECS
T ss_pred             ccEEEEecCCcchHHHHHHHHHc----C--CeEEEEEEeCC
Confidence            68999999998888777665543    5  58999998654

>3fni_A Putative diflavin flavoprotein A 3; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium; 2.30A {Nostoc SP} PDB: 2klb_A

Probab=83.92  E-value=5.7  Score=24.59  Aligned_cols=49  Identities=14%  Similarity=0.060  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEEecCC-hhhHHHHHHHhcCCCEEEEecCCCC
Q 031713           74 LALLGRAKEICAKHGVVAETMTEMGD-PKNVICEAAEKHKIQLLIVGSHSRG  124 (154)
Q Consensus        74 ~~~l~~~~~~~~~~~~~~~~~v~~g~-~~~~i~~~a~~~~~dlivlg~~~~~  124 (154)
                      +++.+.+.+.+.+.|++++..-.... ....+.....  ++|.||+|+....
T Consensus        19 ~~iA~~ia~~l~~~g~~v~~~~~~~~~~~~~~~~~~~--~~d~ii~Gspty~   68 (159)
T 3fni_A           19 DRLAQAIINGITKTGVGVDVVDLGAAVDLQELRELVG--RCTGLVIGMSPAA   68 (159)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEESSSCCCHHHHHHHHH--TEEEEEEECCBTT
T ss_pred             HHHHHHHHHHHHHCCCeEEEEECcCcCCHHHHHHHHH--hCCEEEEEcCcCC
Confidence            44555666666667887665444444 4556666666  7999999987544

>2j4d_A Cryptochrome 3, cryptochrome DASH; DNA-binding protein, flavoprotein, FAD, mitochondrion, plastid, chromophore, chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana} PDB: 2vtb_A* 2ijg_X* 2vtb_B*

Probab=83.80  E-value=12  Score=28.21  Aligned_cols=129  Identities=9%  Similarity=0.037  Sum_probs=74.6

Q ss_pred             EEEEEe--cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhccc-CCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAI--DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQAS-MFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         5 ~iLv~v--d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      .+|+=+  |.--....+|..|++.    +  .+|..++++++........ ++....        .......-+-|..+.
T Consensus        41 ~~l~WfrrDLRl~DN~AL~~A~~~----~--~~v~~vfi~dp~~~~~~~~~~~~~~~--------~~r~~Fl~~sL~~L~  106 (525)
T 2j4d_A           41 VTILWFRNDLRVLDNDALYKAWSS----S--DTILPVYCLDPRLFHTTHFFNFPKTG--------ALRGGFLMECLVDLR  106 (525)
T ss_dssp             EEEEEESSCCCSTTCHHHHHHHHT----C--SEEEEEEEECGGGGSBCTTTCCBSSC--------HHHHHHHHHHHHHHH
T ss_pred             eEEEEeCCCcCcchhHHHHHHHhc----C--CcEEEEEEECchhhcccccccCCCCC--------HHHHHHHHHHHHHHH
Confidence            344444  3444566677777642    2  4788888887643211000 000001        123334455667777


Q ss_pred             HHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCC--CcEEEEcC
Q 031713           82 EICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAK--CPVLVVRK  151 (154)
Q Consensus        82 ~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~--~pvliv~~  151 (154)
                      +.+++.|+.+.  ++.|++.+.|.+++++.+++.|+..... ........ ....+.+....  +++..+..
T Consensus       107 ~~L~~~G~~L~--v~~g~~~~~l~~l~~~~~~~~V~~~~~~-~p~~~~rd-~~v~~~l~~~gv~i~~~~~~~  174 (525)
T 2j4d_A          107 KNLMKRGLNLL--IRSGKPEEILPSLAKDFGARTVFAHKET-CSEEVDVE-RLVNQGLKRVGNSTKLELIWG  174 (525)
T ss_dssp             HHHHHTTCCCE--EEESCHHHHHHHHHHHHTCSEEEEECCC-SHHHHHHH-HHHHHHHHTTCSSCEEEEECC
T ss_pred             HHHHHcCCeEE--EEeCCHHHHHHHHHHHcCCCEEEEeccC-CHHHHHHH-HHHHHHHHhcCCceEEEEecC
Confidence            77777787653  4579999999999999999999987543 22333222 23344455555  67766543

>2qv7_A Diacylglycerol kinase DGKB; alpha-beta domain 1, beta sandwich domain 2, protein-ADP COM transferase; HET: ADP; 2.30A {Staphylococcus aureus} SCOP: e.52.1.2 PDB: 2qvl_A

Probab=83.79  E-value=4  Score=28.71  Aligned_cols=72  Identities=17%  Similarity=0.106  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHh-hcCCCcEEEEcCC
Q 031713           75 ALLGRAKEICAKHGVVAETMTEMG-DPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCV-HNAKCPVLVVRKP  152 (154)
Q Consensus        75 ~~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~-~~~~~pvliv~~~  152 (154)
                      +..+++...+++.|+++....... ..+..+.+.+...++|+||+.- |.+.+     ..+++.++ ....+|+.++|-.
T Consensus        42 ~~~~~i~~~L~~~g~~~~~~~t~~~~~a~~~~~~~~~~~~d~vvv~G-GDGTv-----~~v~~~l~~~~~~~pl~iIP~G  115 (337)
T 2qv7_A           42 RELPDALIKLEKAGYETSAYATEKIGDATLEAERAMHENYDVLIAAG-GDGTL-----NEVVNGIAEKPNRPKLGVIPMG  115 (337)
T ss_dssp             HHHHHHHHHHHHTTEEEEEEECCSTTHHHHHHHHHTTTTCSEEEEEE-CHHHH-----HHHHHHHTTCSSCCEEEEEECS
T ss_pred             HHHHHHHHHHHHcCCeEEEEEecCcchHHHHHHHHhhcCCCEEEEEc-CchHH-----HHHHHHHHhCCCCCcEEEecCC
Confidence            344566777777787776655444 3445555555556788777653 32322     23555554 3456899999864

>1kor_A Argininosuccinate synthetase; ligase, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: ANP ARG; 1.95A {Thermus thermophilus} SCOP: c.26.2.1 d.210.1.1 PDB: 1j1z_A* 1j21_A* 1kh1_A 1kh2_A* 1kh3_A* 1j20_A*

Probab=83.43  E-value=11  Score=27.42  Aligned_cols=37  Identities=24%  Similarity=0.330  Sum_probs=28.0

Q ss_pred             cEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCC
Q 031713            4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTE   45 (154)
Q Consensus         4 ~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~   45 (154)
                      ++++|++.+...|..++.++.+.   ++  .++..+|+....
T Consensus         1 ~kVvva~SGG~DSsvll~ll~~~---~g--~~V~av~vd~g~   37 (400)
T 1kor_A            1 MKIVLAYSGGLDTSIILKWLKET---YR--AEVIAFTADIGQ   37 (400)
T ss_dssp             CEEEEECCSSHHHHHHHHHHHHH---HT--CEEEEEEEESSC
T ss_pred             CcEEEEEeChHHHHHHHHHHHHh---hC--CcEEEEEEeCCC
Confidence            47999999998888888776542   35  589999986653

>3hly_A Flavodoxin-like domain; Q5MZP6_SYNP6, flavoprotein, DFA1, SNR135D, NESG, structural genomics, PSI-2; 2.40A {Synechococcus elongatus pcc 6301}

Probab=83.09  E-value=5.2  Score=24.75  Aligned_cols=49  Identities=16%  Similarity=0.104  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCC
Q 031713           74 LALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRG  124 (154)
Q Consensus        74 ~~~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~  124 (154)
                      ++..+.+.+.+.+.|++++..-........+.....  ++|.||+|+...+
T Consensus        15 ~~~A~~ia~~l~~~g~~v~~~~~~~~~~~~~~~~~~--~~d~ii~Gspty~   63 (161)
T 3hly_A           15 DRLSQAIGRGLVKTGVAVEMVDLRAVDPQELIEAVS--SARGIVLGTPPSQ   63 (161)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEEETTTCCHHHHHHHHH--HCSEEEEECCBSS
T ss_pred             HHHHHHHHHHHHhCCCeEEEEECCCCCHHHHHHHHH--hCCEEEEEcCCcC
Confidence            445555666666678776654444444455555555  7999999987543

>1nu0_A Hypothetical protein YQGF; structural genomics, structure 2 function project, S2F, unknown function; 1.60A {Escherichia coli} SCOP: c.55.3.8 PDB: 1nmn_A 1ovq_A

Probab=83.00  E-value=1.4  Score=26.96  Aligned_cols=52  Identities=15%  Similarity=-0.007  Sum_probs=35.2

Q ss_pred             ChhhHHHHHHHhcCCCEEEEecCC----CCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           99 DPKNVICEAAEKHKIQLLIVGSHS----RGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        99 ~~~~~i~~~a~~~~~dlivlg~~~----~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      ...+.|.+++++.+++.||+|-..    .........-.+++.|-...+.||..+-
T Consensus        40 ~~~~~l~~li~e~~v~~iVvGlP~~mdGt~~~~~~~~~~f~~~L~~~~~lpV~~~D   95 (138)
T 1nu0_A           40 PDWNIIERLLKEWQPDEIIVGLPLNMDGTEQPLTARARKFANRIHGRFGVEVKLHD   95 (138)
T ss_dssp             ECHHHHHHHHHHHCCSEEEEEEEECTTSCBCHHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             hHHHHHHHHHHHcCCCEEEEecccCCCcCcCHHHHHHHHHHHHHHHHhCCCEEEEc
Confidence            357899999999999999999542    1111112223456666666688998874

>3rjz_A N-type ATP pyrophosphatase superfamily; structural genomics, PSI-biology, northeast structural genom consortium, NESG, alpha-beta protein; 2.30A {Pyrococcus furiosus} SCOP: c.26.2.1 PDB: 3h7e_A 3rk0_A* 3rk1_A* 1ru8_A 2d13_A

Probab=82.03  E-value=1.8  Score=29.10  Aligned_cols=91  Identities=15%  Similarity=0.101  Sum_probs=49.7

Q ss_pred             cEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCch-hhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFI-YVQASMFGAAPPDLLMSIQENQKKAALALLGRAKE   82 (154)
Q Consensus         4 ~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~   82 (154)
                      .+++|.+++...|..++-.    +...|  -++..++....... ..   .+.                  ....+.+..
T Consensus         5 MKvvvl~SGGkDSs~al~~----l~~~G--~eV~~L~~~~~~~~~s~---~~h------------------~~~~e~a~~   57 (237)
T 3rjz_A            5 ADVAVLYSGGKDSNYALYW----AIKNR--FSVKFLVTMVSENEESY---MYH------------------TINANLTDL   57 (237)
T ss_dssp             SEEEEECCSSHHHHHHHHH----HHHTT--CEEEEEEEEECC-----------------------------CCSSSHHHH
T ss_pred             CEEEEEecCcHHHHHHHHH----HHHcC--CeEEEEEEEcCCCCCcc---ccC------------------CccHHHHHH
Confidence            5899999998888755543    44445  57776654333211 00   000                  011123334


Q ss_pred             HHHhcCCeEEEEEecCC---hhhHHHHHHHhcCCCEEEEecC
Q 031713           83 ICAKHGVVAETMTEMGD---PKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        83 ~~~~~~~~~~~~v~~g~---~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      .++..|++....-..|.   -.+.+.+..++.+++-+|.|.-
T Consensus        58 ~A~~LGIpl~~v~~~g~~~~e~e~l~~~l~~~~i~~vv~Gdi   99 (237)
T 3rjz_A           58 QARALGIPLVKGFTQGEKEKEVEDLKRVLSGLKIQGIVAGAL   99 (237)
T ss_dssp             HHHHHTCCEEEEEC------CHHHHHHHHTTSCCSEEECC--
T ss_pred             HHHHcCCCEEEEECCCCchHHHHHHHHHHHhcCCcEEEECCc
Confidence            45556888666555553   4556666777778999999974

>2l69_A Rossmann 2X3 fold protein; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Artificial gene}

Probab=81.14  E-value=5.5  Score=22.49  Aligned_cols=38  Identities=16%  Similarity=0.087  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcC
Q 031713           75 ALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHK  112 (154)
Q Consensus        75 ~~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~  112 (154)
                      ..++++....+..|.++.+.....+..+.+.+..++.+
T Consensus        88 nrleefsrevrrrgfevrtvtspddfkkslerlirevg  125 (134)
T 2l69_A           88 NRLEEFSREVRRRGFEVRTVTSPDDFKKSLERLIREVG  125 (134)
T ss_dssp             HHHHHHHHHHHHTTCCEEEESSHHHHHHHHHHHHHHHC
T ss_pred             hHHHHHHHHHHhcCceEEEecChHHHHHHHHHHHHHhc
Confidence            44566777777778777665444567777777777543

---

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	154
d2gm3a1	171	c.26.2.4 (A:5-175) Putative ethylene-responsive pr	1e-32
d1mjha_	160	c.26.2.4 (A:) "Hypothetical" protein MJ0577 {Archa	1e-24
d1tq8a_	147	c.26.2.4 (A:) Hypothetical protein Rv1636 {Mycobac	9e-23
d2z3va1	135	c.26.2.4 (A:2-136) Hypothetical protein TTHA0895 {	2e-21
d1jmva_	140	c.26.2.4 (A:) Universal stress protein A, UspA {Ha	2e-17
d1q77a_	138	c.26.2.4 (A:) Hypothetical protein Aq_178 {Aquifex	2e-09

>d2gm3a1 c.26.2.4 (A:5-175) Putative ethylene-responsive protein AT3g01520/F4P13_7 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 171

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: Putative ethylene-responsive protein AT3g01520/F4P13 7
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score =  111 bits (279), Expect = 1e-32
 Identities = 44/161 (27%), Positives = 80/161 (49%), Gaps = 10/161 (6%)

Query: 4   KKVMVAIDESECRHY---------ALQWALENLGDAISK-SDLIIFTARPTEFIYVQASM 53
            KVMVA++ S  + Y         A +W LE +  + +    +++   +  +        
Sbjct: 2   TKVMVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQVVDEDGFDDVD 61

Query: 54  FGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKI 113
              A P+    ++++ K   L LL      C + GV  E   + GDPK+VIC+  ++ + 
Sbjct: 62  SIYASPEDFRDMRQSNKAKGLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRP 121

Query: 114 QLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKPVE 154
             L+VGS   G  Q+ F+G+VS +CV +A+CPV+ +++  +
Sbjct: 122 DFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVMTIKRNAD 162

>d1mjha_ c.26.2.4 (A:) "Hypothetical" protein MJ0577 {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 160

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: "Hypothetical" protein MJ0577
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 90.8 bits (224), Expect = 1e-24
 Identities = 30/155 (19%), Positives = 61/155 (39%), Gaps = 6/155 (3%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLI------IFTARPTEFIYVQASMFGAA 57
           KK++   D SE    AL+           +  L+          R    + +  +    +
Sbjct: 4   KKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNKS 63

Query: 58  PPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLI 117
             +    ++    + A   +   K+     G   + +  +G P   I + AE   + ++I
Sbjct: 64  VEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIII 123

Query: 118 VGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP 152
           +GSH +  ++   LGSV+   +  +  PVLVV++ 
Sbjct: 124 MGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRK 158

>d1tq8a_ c.26.2.4 (A:) Hypothetical protein Rv1636 {Mycobacterium tuberculosis [TaxId: 1773]} Length = 147

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: Hypothetical protein Rv1636
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score = 85.8 bits (211), Expect = 9e-23
 Identities = 40/148 (27%), Positives = 57/148 (38%), Gaps = 9/148 (6%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
           K V+V  D S+    A+  A +    A + + LII +A        Q     AA      
Sbjct: 6   KTVVVGTDGSDSSMRAVDRAAQI---AGADAKLIIASA-----YLPQHEDARAADILKDE 57

Query: 64  SIQENQKKAALALLGRAKEICAKHG-VVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHS 122
           S +         +L  AKE     G    E    +G P + +   A++ K  LL+VG+  
Sbjct: 58  SYKVTGTAPIYEILHDAKERAHNAGAKNVEERPIVGAPVDALVNLADEEKADLLVVGNVG 117

Query: 123 RGPIQRAFLGSVSNYCVHNAKCPVLVVR 150
              I    LGSV       AK  VL+V 
Sbjct: 118 LSTIAGRLLGSVPANVSRRAKVDVLIVH 145

>d2z3va1 c.26.2.4 (A:2-136) Hypothetical protein TTHA0895 {Thermus thermophilus [TaxId: 274]} Length = 135

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: Hypothetical protein TTHA0895
species: Thermus thermophilus [TaxId: 274]

 Score = 81.8 bits (201), Expect = 2e-21
 Identities = 33/146 (22%), Positives = 56/146 (38%), Gaps = 12/146 (8%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
           K +++A D SE    A + A          + LI+        ++    +          
Sbjct: 2   KTILLAYDGSEHARRAAEVAKAEA--EAHGARLIV--------VHAYEPVPDYLGEPFFE 51

Query: 64  SIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSR 123
                + + A  +L  A+ +        + +   G P   I +AA   K  L+++G+   
Sbjct: 52  EALRRRLERAEGVLEEARALTG--VPKEDALLLEGVPAEAILQAARAEKADLIVMGTRGL 109

Query: 124 GPIQRAFLGSVSNYCVHNAKCPVLVV 149
           G +   FLGS S   V  A CPVL+V
Sbjct: 110 GALGSLFLGSQSQRVVAEAPCPVLLV 135

>d1jmva_ c.26.2.4 (A:) Universal stress protein A, UspA {Haemophilus influenzae [TaxId: 727]} Length = 140

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: Universal stress protein A, UspA
species: Haemophilus influenzae [TaxId: 727]

 Score = 71.6 bits (174), Expect = 2e-17
 Identities = 30/147 (20%), Positives = 55/147 (37%), Gaps = 12/147 (8%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
           K ++VA+D SE     L+ A+       +K  +I             + ++       + 
Sbjct: 3   KHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIHV-------DVNFSDLYTGLIDVNMS 55

Query: 64  SIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSR 123
           S+Q+         L    E         E ++  GD   V+ +A E++ + LL+ G H  
Sbjct: 56  SMQDRISTETQKALLDLAESVDYPIS--EKLSGSGDLGQVLSDAIEQYDVDLLVTGHHQD 113

Query: 124 GPIQRAFLGSVSNYCVHNAKCPVLVVR 150
                  L S +   ++  K  +LVV 
Sbjct: 114 FWS---KLMSSTRQVMNTIKIDMLVVP 137

>d1q77a_ c.26.2.4 (A:) Hypothetical protein Aq_178 {Aquifex aeolicus [TaxId: 63363]} Length = 138

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: Hypothetical protein Aq 178
species: Aquifex aeolicus [TaxId: 63363]

 Score = 50.9 bits (120), Expect = 2e-09
 Identities = 20/147 (13%), Positives = 40/147 (27%), Gaps = 13/147 (8%)

Query: 4   KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLM 63
           K ++V  D       A+ +A+        K    +      E +Y               
Sbjct: 5   KVLLVLTDAYSDCEKAITYAVNF----SEKLGAELDILAVLEDVYNLERANVTFGLPFPP 60

Query: 64  SIQENQKKAALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSR 123
            I+E  KK     L    E       +      +G     + +  E    +L++   +  
Sbjct: 61  EIKEESKKRIERRLREVWEKLTGSTEIPGVEYRIGPLSEEVKKFVEGKGYELVVWACYPS 120

Query: 124 GPIQRAFLGSVSNYCVHNAKCPVLVVR 150
             + +   G              L+V+
Sbjct: 121 AYLCKVIDGL---------NLASLIVK 138

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	154
d1mjha_	160	"Hypothetical" protein MJ0577 {Archaeon Methanococ	100.0
d2z3va1	135	Hypothetical protein TTHA0895 {Thermus thermophilu	99.97
d2gm3a1	171	Putative ethylene-responsive protein AT3g01520/F4P	99.97
d1tq8a_	147	Hypothetical protein Rv1636 {Mycobacterium tubercu	99.97
d1jmva_	140	Universal stress protein A, UspA {Haemophilus infl	99.95
d1q77a_	138	Hypothetical protein Aq_178 {Aquifex aeolicus [Tax	99.94
d1wy5a1	216	TilS-like protein Aq_1887 {Aquifex aeolicus [TaxId	97.32
d3clsc1	262	Small, beta subunit of electron transfer flavoprot	96.61
d1u11a_	159	N5-CAIR mutase (phosphoribosylaminoimidazole carbo	95.94
d1efpb_	246	Small, beta subunit of electron transfer flavoprot	95.93
d1xmpa_	155	N5-CAIR mutase (phosphoribosylaminoimidazole carbo	95.87
d1qcza_	163	N5-CAIR mutase (phosphoribosylaminoimidazole carbo	95.85
d1np7a2	204	Cryptochrome {Synechocystis sp., pcc 6803 [TaxId:	95.64
d1o4va_	169	N5-CAIR mutase (phosphoribosylaminoimidazole carbo	95.51
d1ni5a1	227	tRNA-Ile-lysidine synthetase, TilS, N-terminal dom	95.01
d2j07a2	170	DNA photolyase {Thermus thermophilus [TaxId: 274]}	94.78
d1owla2	202	DNA photolyase {Synechococcus elongatus [TaxId: 32	94.7
d1efvb_	252	Small, beta subunit of electron transfer flavoprot	92.7
d1u3da2	185	Cryptochrome {Thale cress (Arabidopsis thaliana) [	92.45
d1vbka1	132	Hypothetical protein PH1313, C-terminal domain {Ar	92.36
d1ycga1	149	Nitric oxide reductase C-terminal domain {Moorella	90.18
d1ls1a2	207	GTPase domain of the signal sequence recognition p	89.17
d2c5sa1	218	Thiamine biosynthesis protein ThiI, C-terminal dom	88.49
d1e5da1	152	Rubredoxin oxygen:oxidoreductase (ROO), C-terminal	88.23
d2qy9a2	211	GTPase domain of the signal recognition particle r	87.35
d3clsd1	192	Large, alpha subunit of electron transfer flavopro	86.45
d1dnpa2	200	DNA photolyase {Escherichia coli [TaxId: 562]}	85.86
d2bona1	295	Lipid kinase YegS {Escherichia coli [TaxId: 562]}	85.69
d2qv7a1	312	Diacylglycerol kinase DgkB {Staphylococcus aureus	85.18
d1p3y1_	183	MrsD {Bacillus sp. hil-y85/54728 [TaxId: 69002]}	85.16
d1nu0a_	138	Hypothetical protein YqgF (RuvX) {Escherichia coli	84.21
d2a9pa1	117	DNA-binding response regulator MicA, N-terminal do	83.04
d1gsoa2	105	Glycinamide ribonucleotide synthetase (GAR-syn), N	81.97
d1okkd2	207	GTPase domain of the signal recognition particle r	81.78
d3bzka5	149	Transcriptional accessory factor Tex {Pseudomonas	80.26
d1s8na_	190	Probable two-component system transcriptional regu	80.08

>d1mjha_ c.26.2.4 (A:) "Hypothetical" protein MJ0577 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: "Hypothetical" protein MJ0577
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=100.00  E-value=6.9e-35  Score=186.56  Aligned_cols=151  Identities=21%  Similarity=0.283  Sum_probs=130.5

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcc--c------CCCCCchHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQA--S------MFGAAPPDLLMSIQENQKKA   72 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~--~------~~~~~~~~~~~~~~~~~~~~   72 (154)
                      |||+|||||+|+|+.+.+++++|..+|+..+  ++|+++||.++.......  .      .+............+...++
T Consensus         1 ~m~~~ILvavD~s~~s~~al~~a~~la~~~~--a~l~llhV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (160)
T d1mjha_           1 VMYKKILYPTDFSETAEIALKHVKAFKTLKA--EEVILLHVIDEREIKKRDIFSLLLGVAGLNKSVEEFENELKNKLTEE   78 (160)
T ss_dssp             CCCCEEEEECCSCHHHHHHHHHHHHTCCSSC--CEEEEEEEEEGGGTC-----------------CHHHHHHHHHHHHHH
T ss_pred             CCcCeEEEEECCCHHHHHHHHHHHHHHHhcC--CEEEEEEecccccccccccccccccccccchhHHHHHHHHHHHHHHH
Confidence            8999999999999999999999999999987  999999998775533210  0      01122345555677777888


Q ss_pred             HHHHHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           73 ALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        73 ~~~~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      +++.++++...+...|+++++.+..|++.+.|++++++.++||||||+++++.+.++|+||++++|+++++|||++||++
T Consensus        79 ~~~~l~~~~~~~~~~gv~~~~~~~~G~~~~~I~~~a~~~~~dliV~G~~~~~~~~~~~~GS~a~~vl~~s~~pVlvV~~~  158 (160)
T d1mjha_          79 AKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRK  158 (160)
T ss_dssp             HHHHHHHHHHHHHHTTCEEEEEEEEECHHHHHHHHHHHTTCSEEEEESCCSSCCTTCSSCHHHHHHHHHCCSCEEEECCC
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEEeccHHHHHhhhhhccccceEEeccCCCCcccccccCcHHHHHHhcCCCCEEEEcCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             C
Q 031713          153 V  153 (154)
Q Consensus       153 ~  153 (154)
                      .
T Consensus       159 ~  159 (160)
T d1mjha_         159 N  159 (160)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d2z3va1 c.26.2.4 (A:2-136) Hypothetical protein TTHA0895 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: Hypothetical protein TTHA0895
species: Thermus thermophilus [TaxId: 274]

Probab=99.97  E-value=6.5e-30  Score=158.97  Aligned_cols=134  Identities=28%  Similarity=0.368  Sum_probs=109.2

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKE   82 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~   82 (154)
                      |++||||+|+|+.+.+++++|+++|+..+  ++|+++||+++.....        .....+...+...+..++.++++.+
T Consensus         1 yk~Ilv~~D~s~~s~~a~~~a~~~a~~~~--~~l~ll~V~~~~~~~~--------~~~~~~~~~~~~~~~~~~~l~~~~~   70 (135)
T d2z3va1           1 FKTILLAYDGSEHARRAAEVAKAEAEAHG--ARLIVVHAYEPVPDYL--------GEPFFEEALRRRLERAEGVLEEARA   70 (135)
T ss_dssp             CCEEEEECCSSHHHHHHHHHHHHHHHHHT--CEEEEEEEECCCCTTC--------CTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCHHHHHHHHHHHHHHHHcC--CEEEEEEEecCCcccc--------ccchhHHHHHHHHHHHHHHHHHHHH
Confidence            79999999999999999999999999987  9999999998654322        2223333334445555556655554


Q ss_pred             HHHhcCCe-EEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEE
Q 031713           83 ICAKHGVV-AETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVV  149 (154)
Q Consensus        83 ~~~~~~~~-~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv  149 (154)
                      .   .+.. .+..+..|++.++|++++++.++|+||||+++++.+.++++|+++++++++++|||++|
T Consensus        71 ~---~~~~~~~~~~~~g~~~~~I~~~a~~~~~dliV~G~~~~~~~~~~~~Gs~~~~ll~~~~~pVlvV  135 (135)
T d2z3va1          71 L---TGVPKEDALLLEGVPAEAILQAARAEKADLIVMGTRGLGALGSLFLGSQSQRVVAEAPCPVLLV  135 (135)
T ss_dssp             H---HCCCGGGEEEEESCHHHHHHHHHHHTTCSEEEEESSCSSSCBCSSCBHHHHHHHHHCSSCEEEE
T ss_pred             h---cCCCeEEEEEEcCChHHHHHHHhhhhheeeEEeccCCCCcccccccCcHHHHHHHhCCCCEEeC
Confidence            3   3443 55667789999999999999999999999999999999999999999999999999997

>d2gm3a1 c.26.2.4 (A:5-175) Putative ethylene-responsive protein AT3g01520/F4P13_7 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: Putative ethylene-responsive protein AT3g01520/F4P13 7
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.97  E-value=8.8e-30  Score=164.34  Aligned_cols=150  Identities=29%  Similarity=0.529  Sum_probs=115.0

Q ss_pred             CcEEEEEecCCc---------hHHHHHHHHHHHcccCCC-CCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESE---------CRHYALQWALENLGDAIS-KSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKA   72 (154)
Q Consensus         3 ~~~iLv~vd~~~---------~~~~~l~~a~~la~~~~~-~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   72 (154)
                      .+||||++|+|.         .|++|++||+.++.+.+. ...|+++|+.+.........+......+......+...+.
T Consensus         1 p~ki~vavd~s~~~~~~~~~~~S~~Al~wal~~~~~~~~~~~~L~~vhv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (171)
T d2gm3a1           1 PTKVMVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQVVDEDGFDDVDSIYASPEDFRDMRQSNKAK   80 (171)
T ss_dssp             CEEEEEECCBCSSSCTTCBCHHHHHHHHHHHHHTTTTCTTSEEEEEEEEEC----------CCCCSHHHHHHHTTSHHHH
T ss_pred             CCEEEEEEcCCcccCCCCCCHHHHHHHHHHHHHHHHCCCCCcEEEEEEeccccccccccccccccCHHHHHHHHHHHHHH
Confidence            369999999986         799999999999887541 1269999998876543322222244556666667777788


Q ss_pred             HHHHHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           73 ALALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        73 ~~~~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .++.++++...+...|++++..+..|++.++|++++++.++|+||||+++++.+.++++||++++++++++|||++||+.
T Consensus        81 ~~~~l~~~~~~~~~~~~~~~~~v~~G~~~~~I~~~a~~~~~dlIV~G~~g~~~~~~~~lGSv~~~vi~~~~cpVlvV~~~  160 (171)
T d2gm3a1          81 GLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVMTIKRN  160 (171)
T ss_dssp             HHHHHHHHHHHHHHHTCEEEEEEEESCHHHHHHHHHHHHCCSEEEEEECCCC--------CHHHHHHHHCSSCEEEEECC
T ss_pred             HHHHHHHHHHHHHhcCCceEEEEEeCChHHHHHHHHhhcCCcEEEeccCCccccccCccCcHHHHHHhCCCCCEEEEeCC
Confidence            88999999999999999999999999999999999999999999999999999999999999999999999999999865

>d1tq8a_ c.26.2.4 (A:) Hypothetical protein Rv1636 {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: Hypothetical protein Rv1636
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=99.97  E-value=6.2e-30  Score=161.14  Aligned_cols=144  Identities=26%  Similarity=0.242  Sum_probs=110.2

Q ss_pred             CCCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            1 MDKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         1 m~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      +.|++||||+|+|+.+..++++|+.+|+..+  +.+.++++.+......      .......+......++..++.++++
T Consensus         3 ~~yk~ILv~vD~s~~s~~al~~A~~la~~~~--~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~l~~~   74 (147)
T d1tq8a_           3 SAYKTVVVGTDGSDSSMRAVDRAAQIAGADA--KLIIASAYLPQHEDAR------AADILKDESYKVTGTAPIYEILHDA   74 (147)
T ss_dssp             CCCCEEEEECCSSHHHHHHHHHHHHHHTTTS--EEEEEEECCC--------------------------CCTHHHHHHHH
T ss_pred             cCCCEEEEEECCCHHHHHHHHHHHHHHhcCC--CEEEEEEEeccccccc------ccccchhhhHHHHHHHHHHHHHHHH
Confidence            1699999999999999999999999999765  5565555544433221      1111222334455556677888888


Q ss_pred             HHHHHhcCCe-EEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           81 KEICAKHGVV-AETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        81 ~~~~~~~~~~-~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .+.+.+.|+. ++..+..|++.+.|++++++.++|+||+|+++++.+.++++||++++|+++++||||+|++.
T Consensus        75 ~~~~~~~~~~~~~~~~~~G~~~~~i~~~a~~~~~dlIv~g~~~~~~~~~~l~Gs~~~~ll~~~~~pVlvV~~~  147 (147)
T d1tq8a_          75 KERAHNAGAKNVEERPIVGAPVDALVNLADEEKADLLVVGNVGLSTIAGRLLGSVPANVSRRAKVDVLIVHTT  147 (147)
T ss_dssp             HHHHHTTTCCEEEEEEECSSHHHHHHHHHHHTTCSEEEEECCCCCSHHHHHTBBHHHHHHHHTTCEEEEECCC
T ss_pred             HHHHHHcCCCcEEEEEEecChHHHHHHhhhccceeEEEecCCCCCcccccccccHHHHHHHhCCCCEEEEecC
Confidence            8888888876 78889999999999999999999999999999999999999999999999999999999874

>d1jmva_ c.26.2.4 (A:) Universal stress protein A, UspA {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: Universal stress protein A, UspA
species: Haemophilus influenzae [TaxId: 727]

Probab=99.95  E-value=2.6e-28  Score=152.46  Aligned_cols=138  Identities=22%  Similarity=0.134  Sum_probs=105.3

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      ||++||||+|+++.+..+++||..+|+..+  ++|+++||++......     ........+...+...+...+.+++..
T Consensus         1 myk~ILv~vD~s~~s~~al~~A~~~a~~~~--~~v~~lhv~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~   73 (140)
T d1jmva_           1 MYKHILVAVDLSEESPILLKKAVGIAKRHD--AKLSIIHVDVNFSDLY-----TGLIDVNMSSMQDRISTETQKALLDLA   73 (140)
T ss_dssp             CCSEEEEEECCSTTHHHHHHHHHHHHHHHT--CEEEEEEEEECCGGGC-----CCCEEHHHHHHTTCCCCHHHHHHHHHH
T ss_pred             CCCeEEEEECCCHHHHHHHHHHHHHHHHcC--CeEEEEEEeeeccccc-----ccccccchHHHHHHHHHHHHHHHHHHH
Confidence            799999999999999999999999999987  9999999988765432     112222233333333334444444443


Q ss_pred             HHHHhcCCe-EEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           82 EICAKHGVV-AETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        82 ~~~~~~~~~-~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      .   ..+.. .+..+..|++.+.|.+++++.++|+||||+++++..   .+||++++++++++|||++||..
T Consensus        74 ~---~~~~~~~~~~~~~~~~~~~I~~~a~~~~~dliV~G~~~~~~~---~lgs~~~~li~~~~~pVliVp~~  139 (140)
T d1jmva_          74 E---SVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHHQDFWS---KLMSSTRQVMNTIKIDMLVVPLR  139 (140)
T ss_dssp             H---HSSSCCCCEEEEEECHHHHHHHHHHHTTCCEEEEEECCCCHH---HHHHHHHHHHTTCCSEEEEEECC
T ss_pred             H---hcCCceEEEEEEecCHHHHHHHhhhhchhhEEEeccCCCCCC---CcccHHHHHHhccCCCEEEEecC
Confidence            3   33444 445666789999999999999999999999876543   48999999999999999999975

>d1q77a_ c.26.2.4 (A:) Hypothetical protein Aq_178 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: Hypothetical protein Aq 178
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.94  E-value=2.3e-27  Score=147.67  Aligned_cols=135  Identities=16%  Similarity=0.126  Sum_probs=106.9

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcc-cCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQA-SMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      ++|+||||+|+|+.+..|+++|.++|+.++  ++++++||+++....... ....   ........+..++..++.++++
T Consensus         3 ~mk~ILv~~D~S~~s~~al~~A~~~a~~~~--a~l~llhv~~~~~~~~~~~~~~~---~~~~~~~~e~~~~~~~~~l~~~   77 (138)
T d1q77a_           3 AMKVLLVLTDAYSDCEKAITYAVNFSEKLG--AELDILAVLEDVYNLERANVTFG---LPFPPEIKEESKKRIERRLREV   77 (138)
T ss_dssp             CCEEEEEEESTTCCCHHHHHHHHHHHTTTC--CEEEEEEECHHHHHHHHHHHHHC---CCCCTHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEeCCHHHHHHHHHHHHhhhhcc--ceEEEEEEccCcccccccccccc---cchhhhhhhhhhhhccccchhh
Confidence            689999999999999999999999999988  999999998754322110 0000   0112234445556677778888


Q ss_pred             HHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           81 KEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        81 ~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      .+.+...+..++..+..|++.+.|.+++++.++||||||+++++.+         .+++..+.||+|||+
T Consensus        78 ~~~~~~~~~~~~~~v~~G~~~~~I~~~a~~~~~DLIV~Gs~g~~~l---------~r~l~g~~~~~livk  138 (138)
T d1q77a_          78 WEKLTGSTEIPGVEYRIGPLSEEVKKFVEGKGYELVVWACYPSAYL---------CKVIDGLNLASLIVK  138 (138)
T ss_dssp             HHHHHSCCCCCCEEEECSCHHHHHHHHHTTSCCSEEEECSCCGGGT---------HHHHHHSSSEEEECC
T ss_pred             cccccccceeEEEeeecchhHHHHHHhhhhccCCEEEEecCCCcHH---------HHHhcCCCCCEEEeC
Confidence            8888888889999999999999999999999999999999987655         457777899999985

>d1wy5a1 c.26.2.5 (A:1-216) TilS-like protein Aq_1887 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: PP-loop ATPase
domain: TilS-like protein Aq 1887
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.32  E-value=0.0021  Score=41.14  Aligned_cols=95  Identities=11%  Similarity=-0.049  Sum_probs=64.2

Q ss_pred             CcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKE   82 (154)
Q Consensus         3 ~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~   82 (154)
                      -++|+|++.|...|..++..+..+....+. ..+.++||.......                        .....+.+..
T Consensus        24 ~~kv~Va~SGG~DS~~Ll~lL~~~~~~~~~-~~i~~~~vdh~~r~~------------------------s~~~~~~~~~   78 (216)
T d1wy5a1          24 ERRVLIAFSGGVDSVVLTDVLLKLKNYFSL-KEVALAHFNHMLRES------------------------AERDEEFCKE   78 (216)
T ss_dssp             CCEEEEECCSSHHHHHHHHHHHHSTTTTTC-SEEEEEEEECCSSTH------------------------HHHHHHHHHH
T ss_pred             CCeEEEEeCCcHHHHHHHHHHHHHHHhcCC-CcEEEEEeecccccc------------------------hhhhhhHHHH
Confidence            468999999999999888888777766542 479999986553221                        1222344566


Q ss_pred             HHHhcCCeEEEEEec--------C-Ch--------hhHHHHHHHhcCCCEEEEecCC
Q 031713           83 ICAKHGVVAETMTEM--------G-DP--------KNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        83 ~~~~~~~~~~~~v~~--------g-~~--------~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      .+++.|+++...-..        + +.        ...+..++++.++|.|++|++.
T Consensus        79 ~~~~l~i~~~i~~~~~~~~~~~~~~~~~~~~R~~Ry~~l~~~a~~~~~~~ia~GH~~  135 (216)
T d1wy5a1          79 FAKERNMKIFVGKEDVRAFAKENRMSLEEAGRFLRYKFLKEILESEGFDCIATAHHL  135 (216)
T ss_dssp             HHHHHTCCEEEEECCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHTTCSEEECCCCH
T ss_pred             HHHhhhhhhhhhccchhhhccCCccchHHHHHHHHHHHhhhhccccccceeEeeeec
Confidence            666678876543321        1 11        2455678889999999999874

>d3clsc1 c.26.2.3 (C:1-262) Small, beta subunit of electron transfer flavoprotein ETFP {Methylophilus methylotrophus [TaxId: 17]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: ETFP subunits
domain: Small, beta subunit of electron transfer flavoprotein ETFP
species: Methylophilus methylotrophus [TaxId: 17]

Probab=96.61  E-value=0.0032  Score=41.56  Aligned_cols=103  Identities=15%  Similarity=0.179  Sum_probs=66.4

Q ss_pred             ecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 031713           10 IDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGV   89 (154)
Q Consensus        10 vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   89 (154)
                      .-.++++..|++.|+++....|...+++++.+=+...                           ++.+.++.    ..|.
T Consensus        33 ~viNp~D~~AlE~Al~lke~~gg~~~Vtvvt~Gp~~a---------------------------~~~Lr~al----AmGa   81 (262)
T d3clsc1          33 YDLNEWDDFSLEEAMKIKESSDTDVEVVVVSVGPDRV---------------------------DESLRKCL----AKGA   81 (262)
T ss_dssp             EEECHHHHHHHHHHHHHHHHCSSCCEEEEEEESCTTH---------------------------HHHHHHHH----HTTC
T ss_pred             cccCcccHHHHHHHHHHHhcCCCceEEEEEeccchhH---------------------------HHHHHHHH----hcCC
Confidence            3357789999999999998866324788888866532                           12222222    3465


Q ss_pred             eEEEEEe----cC-C---hhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEE
Q 031713           90 VAETMTE----MG-D---PKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVL  147 (154)
Q Consensus        90 ~~~~~v~----~g-~---~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvl  147 (154)
                      .--+.+.    .| +   .+..|..+++..++|||+.|..... .   -.|.+.-.+......|.+
T Consensus        82 D~avli~d~~~~~~d~~~tA~~lA~~i~~~~~DLIl~G~~s~D-~---~~gqvg~~lAe~Lg~P~v  143 (262)
T d3clsc1          82 DRAVRVWDDAAEGSDAIVVGRILTEVIKKEAPDMVFAGVQSSD-Q---AYASTGISVASYLNWPHA  143 (262)
T ss_dssp             SEEEEECCGGGTTCCHHHHHHHHHHHHHHHCCSEEEEESCCTT-T---CCCCHHHHHHHHHTCCEE
T ss_pred             CeeEEEeccccccchHHHHHHHHHHHhhccCCcEEEEeeeccC-C---CcchHHHHHHHHcCCceE
Confidence            5434442    23 3   4667778888999999999987432 2   245566666666666644

>d1u11a_ c.23.8.1 (A:) N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) {Acetobacter aceti [TaxId: 435]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
family: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
domain: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
species: Acetobacter aceti [TaxId: 435]

Probab=95.94  E-value=0.039  Score=33.27  Aligned_cols=69  Identities=16%  Similarity=0.288  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHH---hcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcC
Q 031713           76 LLGRAKEICAKHGVVAETMTEMG-DPKNVICEAAE---KHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRK  151 (154)
Q Consensus        76 ~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~---~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~  151 (154)
                      ..+++...+++.|++++..+..+ ...+.+.++++   +.+++.+|.++...+.+        ..-+.-.+..||+-||.
T Consensus        17 v~~~a~~~L~~~gI~~e~~v~SAHR~p~~l~~~~~~~e~~~~~viIa~AG~aaaL--------pgvva~~t~~PVIgvP~   88 (159)
T d1u11a_          17 TMRHADALLTELEIPHETLIVSAHRTPDRLADYARTAAERGLNVIIAGAGGAAHL--------PGMCAAWTRLPVLGVPV   88 (159)
T ss_dssp             HHHHHHHHHHHTTCCEEEEECCTTTCHHHHHHHHHHTTTTTCCEEEEEEESSCCH--------HHHHHHHCSSCEEEEEE
T ss_pred             HHHHHHHHHHHhCCceEEEEehHhhChHHHHHHHHHHHhcCCeEEEEEecCCCCC--------ccceeeecceeEEEecc
Confidence            34566777788899999999887 45666666665   46889999998644433        34566788899999985


Q ss_pred             C
Q 031713          152 P  152 (154)
Q Consensus       152 ~  152 (154)
                      .
T Consensus        89 ~   89 (159)
T d1u11a_          89 E   89 (159)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d1efpb_ c.26.2.3 (B:) Small, beta subunit of electron transfer flavoprotein ETFP {Paracoccus denitrificans [TaxId: 266]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: ETFP subunits
domain: Small, beta subunit of electron transfer flavoprotein ETFP
species: Paracoccus denitrificans [TaxId: 266]

Probab=95.93  E-value=0.1  Score=33.77  Aligned_cols=100  Identities=10%  Similarity=0.101  Sum_probs=63.3

Q ss_pred             CCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCeE
Q 031713           12 ESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVA   91 (154)
Q Consensus        12 ~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~   91 (154)
                      .++++..|++.|+++....+- .+++++.+=+....                           +.+.+..    ..|..-
T Consensus        35 iNp~D~~AlE~Al~lke~~~g-~~Vtvls~Gp~~a~---------------------------~~lr~al----AmGaD~   82 (246)
T d1efpb_          35 MNPFDEIAVEEAIRLKEKGQA-EEIIAVSIGVKQAA---------------------------ETLRTAL----AMGADR   82 (246)
T ss_dssp             ECHHHHHHHHHHHHHHTTTSC-SEEEEEEEESGGGH---------------------------HHHHHHH----HHTCSE
T ss_pred             cCccCHHHHHHHHHHhhcCCC-eEEEEEEecCcchH---------------------------HHHHHHH----hhcCCh
Confidence            567899999999999998651 38999988666322                           2222222    235553


Q ss_pred             EEEEe------cC-C---hhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEE
Q 031713           92 ETMTE------MG-D---PKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVL  147 (154)
Q Consensus        92 ~~~v~------~g-~---~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvl  147 (154)
                      -..+.      .| +   .+..+..+++..++|||+.|...... .   .|.+.-.+......|.+
T Consensus        83 avli~~~~~~~~~~d~~ata~~la~~~~~~~~DLIl~G~~s~D~-~---tgqvg~~lAe~Lg~P~v  144 (246)
T d1efpb_          83 AILVVAADDVQQDIEPLAVAKILAAVARAEGTELIIAGKQAIDN-D---MNATGQMLAAILGWAQA  144 (246)
T ss_dssp             EEEEECCSSTTCCCCHHHHHHHHHHHHHHHTCSEEEEESCCTTT-C---CCCHHHHHHHHHTCEEE
T ss_pred             heEEeeccccccccCHHHHHHHHHHHHhhcCCCEEEEEeeeccc-c---ccchhHHHHHHhhccce
Confidence            34332      22 2   34567788888999999999875332 2   34555556666665543

>d1xmpa_ c.23.8.1 (A:) N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) {Bacillus anthracis [TaxId: 1392]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
family: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
domain: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
species: Bacillus anthracis [TaxId: 1392]

Probab=95.87  E-value=0.054  Score=32.44  Aligned_cols=70  Identities=16%  Similarity=0.211  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHH---hcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           75 ALLGRAKEICAKHGVVAETMTEMG-DPKNVICEAAE---KHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        75 ~~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~---~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      ...+++...+++.|++++..+..+ ...+.+.++++   +.+++++|.++...+.+.        .-+...++.||+-||
T Consensus        15 ~~~~~a~~~L~~~gi~~~~~v~SAHrtp~rl~~~~~~~~~~~~~viIa~AG~aa~Lp--------gvva~~t~~PVIgVP   86 (155)
T d1xmpa_          15 ETMKYACDILDELNIPYEKKVVSAHRTPDYMFEYAETARERGLKVIIAGAGGAAHLP--------GMVAAKTNLPVIGVP   86 (155)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEECCTTTSHHHHHHHHHHTTTTTCCEEEEEEESSCCHH--------HHHHTTCCSCEEEEE
T ss_pred             HHHHHHHHHHHHcCCcEEEEEechhcChHHHHHHHHHHHhhcceEEEeecccCCCch--------hHHHHhccceEEEEE
Confidence            345677788888999999999887 45666666666   456789998887544443        445667889999998


Q ss_pred             CC
Q 031713          151 KP  152 (154)
Q Consensus       151 ~~  152 (154)
                      ..
T Consensus        87 ~~   88 (155)
T d1xmpa_          87 VQ   88 (155)
T ss_dssp             EC
T ss_pred             ee
Confidence            65

>d1qcza_ c.23.8.1 (A:) N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
family: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
domain: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
species: Escherichia coli [TaxId: 562]

Probab=95.85  E-value=0.072  Score=32.19  Aligned_cols=71  Identities=20%  Similarity=0.171  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHH---hcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           75 ALLGRAKEICAKHGVVAETMTEMG-DPKNVICEAAE---KHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        75 ~~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~---~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      ...+++...++..|++++..+... ...+.+.++++   +.+++.+|.++...+.+.        .-+.-+++.||+-||
T Consensus        15 ~~~~~a~~~L~~~gI~~e~~v~SAHRtp~~l~~~~~~~~~~~~~ViIa~AG~aa~Lp--------gvvA~~t~~PVIgVP   86 (163)
T d1qcza_          15 ATMQFAAEIFEILNVPHHVEVVSAHRTPDKLFSFAESAEENGYQVIIAGAGGAAHLP--------GMIAAKTLVPVLGVP   86 (163)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEECCTTTCHHHHHHHHHHTTTTTCSEEEEEECSSCCHH--------HHHHHSCSSCEEEEE
T ss_pred             HHHHHHHHHHHHcCCCeEEEEeccccCHHHHHHHHHHHHHcCCeEEEEeccCCCccc--------chhhHhccceeeecc
Confidence            345677777888899999999887 45555656554   467899999986544443        335667889999998


Q ss_pred             CCC
Q 031713          151 KPV  153 (154)
Q Consensus       151 ~~~  153 (154)
                      ...
T Consensus        87 ~~~   89 (163)
T d1qcza_          87 VQS   89 (163)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            653

>d1np7a2 c.28.1.1 (A:1-204) Cryptochrome {Synechocystis sp., pcc 6803 [TaxId: 1143]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: Cryptochrome
species: Synechocystis sp., pcc 6803 [TaxId: 1143]

Probab=95.64  E-value=0.08  Score=33.04  Aligned_cols=103  Identities=16%  Similarity=0.075  Sum_probs=66.0

Q ss_pred             CcEEEEEe--cCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 031713            3 KKKVMVAI--DESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRA   80 (154)
Q Consensus         3 ~~~iLv~v--d~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   80 (154)
                      ..++||=.  |..-....||..|+.    .+  ..|..++|.++........++...+        ........+-+..+
T Consensus         5 p~~~lvWfr~DLRl~DN~aL~~A~~----~~--~~vi~vyi~dp~~~~~~~~~~~~~~--------~~r~~fl~~sL~~L   70 (204)
T d1np7a2           5 PPTVLVWFRNDLRLHDHEPLHRALK----SG--LAITAVYCYDPRQFAQTHQGFAKTG--------PWRSNFLQQSVQNL   70 (204)
T ss_dssp             CCEEEEEESSCCCSTTCHHHHHHHH----TT--SEEEEEEEECGGGGSBCTTSCBSSC--------HHHHHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCccccHHHHHHHHh----cC--CcEEEEEEECchHhcCccccccccc--------HHHHHHHHHHHHHH
Confidence            34555544  444556667777763    23  5899999988654322101111111        12334455667777


Q ss_pred             HHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecC
Q 031713           81 KEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        81 ~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      .+.+++.|+..  .+..|++.+.|.+++++.+++-|+....
T Consensus        71 ~~~L~~~g~~L--~v~~G~~~~~l~~l~~~~~i~~V~~n~~  109 (204)
T d1np7a2          71 AESLQKVGNKL--LVTTGLPEQVIPQIAKQINAKTIYYHRE  109 (204)
T ss_dssp             HHHHHHTTCCE--EEEESCHHHHHHHHHHHTTEEEEEEECC
T ss_pred             HHHHHhccchh--hhhhhhhHHHHHHHHHHhhhhheeeecc
Confidence            78888778664  4568999999999999999999988754

>d1o4va_ c.23.8.1 (A:) N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
family: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
domain: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
species: Thermotoga maritima [TaxId: 2336]

Probab=95.51  E-value=0.08  Score=32.15  Aligned_cols=70  Identities=19%  Similarity=0.262  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHHh---cCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           75 ALLGRAKEICAKHGVVAETMTEMG-DPKNVICEAAEK---HKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        75 ~~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~~---~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      ...+++...++..|++++..+..+ ...+.+.+++++   .+++.+|.++.+.+.+.        .-+...++.||+-||
T Consensus        14 ~~~~~a~~~L~~~gi~~~~~v~saHr~p~rl~~~~~~~~~~~~~viIa~AG~aa~Lp--------gvvA~~t~~PVIgvP   85 (169)
T d1o4va_          14 PVMKQAAEILEEFGIDYEITIVSAHRTPDRMFEYAKNAEERGIEVIIAGAGGAAHLP--------GMVASITHLPVIGVP   85 (169)
T ss_dssp             HHHHHHHHHHHHTTCEEEEEECCTTTCHHHHHHHHHHTTTTTCCEEEEEEESSCCHH--------HHHHHHCSSCEEEEE
T ss_pred             HHHHHHHHHHHHcCCcEEEEEeeeecCHHHHHHHHHHHHhcCCeEEEEeecCCcCch--------HHHHHhcceeEEecc
Confidence            345677778888999999999887 456666666654   57889999987654433        345567789999998


Q ss_pred             CC
Q 031713          151 KP  152 (154)
Q Consensus       151 ~~  152 (154)
                      ..
T Consensus        86 ~~   87 (169)
T d1o4va_          86 VK   87 (169)
T ss_dssp             EC
T ss_pred             cc
Confidence            54

>d1ni5a1 c.26.2.5 (A:0-226) tRNA-Ile-lysidine synthetase, TilS, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: PP-loop ATPase
domain: tRNA-Ile-lysidine synthetase, TilS, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.01  E-value=0.14  Score=32.45  Aligned_cols=96  Identities=11%  Similarity=0.052  Sum_probs=60.9

Q ss_pred             CCcEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 031713            2 DKKKVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAK   81 (154)
Q Consensus         2 ~~~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   81 (154)
                      ..++|+|++.|...|..++..+..+.... ...++.++||........                        ....+.+.
T Consensus        12 ~~kkvlva~SGG~DS~~Ll~ll~~~~~~~-~~~~l~~~~vdh~~r~~s------------------------~~~~~~~~   66 (227)
T d1ni5a1          12 TSRQILVAFSGGLDSTVLLHQLVQWRTEN-PGVALRAIHVHHGLSANA------------------------DAWVTHCE   66 (227)
T ss_dssp             TCSEEEEECCSBHHHHHHHHHHHHHHTTS-TTCEEEEEEECCSCCSSH------------------------HHHHHHHH
T ss_pred             CCCcEEEEecCcHHHHHHHHHHHHHHHhC-CCceEEEEEeCCCCCcch------------------------hhhHHHHH
Confidence            45899999999999998888777775542 227999999976532221                        23345567


Q ss_pred             HHHHhcCCeEEEEEec----C-Chhh------HHHHHHHhcCCCEEEEecCC
Q 031713           82 EICAKHGVVAETMTEM----G-DPKN------VICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        82 ~~~~~~~~~~~~~v~~----g-~~~~------~i~~~a~~~~~dlivlg~~~  122 (154)
                      ..+.+.|++....-..    . +...      .........+++.|++|++.
T Consensus        67 ~~~~~~~i~~~i~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~i~~gH~~  118 (227)
T d1ni5a1          67 NVCQQWQVPLVVERVQLAQEGLGIEAQARQARYQAFARTLLPGEVLVTAQHL  118 (227)
T ss_dssp             HHHHHTTCCEEEECCCCCCSSSTTTTHHHHHHHHHHHHTCCTTEEEECCCCH
T ss_pred             HHHhhccCcceeeeccccccccchhhHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence            7777778875543222    1 1111      11123446788888888753

>d2j07a2 c.28.1.1 (A:2-171) DNA photolyase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: DNA photolyase
species: Thermus thermophilus [TaxId: 274]

Probab=94.78  E-value=0.16  Score=30.71  Aligned_cols=82  Identities=17%  Similarity=0.085  Sum_probs=55.9

Q ss_pred             hHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCeEEEE
Q 031713           15 CRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETM   94 (154)
Q Consensus        15 ~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~   94 (154)
                      ....|+..|+    ..   +++..+++.++.....        +        ........+-+..+.+.+++.|+..  .
T Consensus        14 ~Dn~aL~~A~----~~---~~vi~vfi~d~~~~~~--------~--------~~r~~fl~~sL~~L~~~L~~~g~~L--~   68 (170)
T d2j07a2          14 HDHPALLEAL----AR---GPVVGLVVLDPNNLKT--------T--------PRRRAWFLENVRALREAYRARGGAL--W   68 (170)
T ss_dssp             TTCHHHHHHH----TT---SCEEEEEEECHHHHSS--------C--------HHHHHHHHHHHHHHHHHHHHTTCCE--E
T ss_pred             cchHHHHHHH----hc---CCEEEEEEEecccchh--------h--------HHHHHHHHHHHHHHHHhhhccccch--h
Confidence            3445676665    22   3788888887643321        0        1123344455677777777777554  5


Q ss_pred             EecCChhhHHHHHHHhcCCCEEEEecC
Q 031713           95 TEMGDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        95 v~~g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      +..|++.+.|.+++++.+++-|.....
T Consensus        69 v~~G~~~~~l~~l~~~~~i~~V~~n~~   95 (170)
T d2j07a2          69 VLEGLPWEKVPEAARRLKAKAVYALTS   95 (170)
T ss_dssp             EEESCHHHHHHHHHHHTTCSEEEEECC
T ss_pred             hhhhhHHHHHHHHHHHhhhhHHHhhcc
Confidence            778999999999999999999998764

>d1owla2 c.28.1.1 (A:3-204) DNA photolyase {Synechococcus elongatus [TaxId: 32046]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: DNA photolyase
species: Synechococcus elongatus [TaxId: 32046]

Probab=94.70  E-value=0.046  Score=34.21  Aligned_cols=112  Identities=13%  Similarity=0.102  Sum_probs=69.0

Q ss_pred             hHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCeEEEE
Q 031713           15 CRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETM   94 (154)
Q Consensus        15 ~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~   94 (154)
                      ....++..|+.    .+  .+|..++|+++......     .        ..........+-+.++.+.+++.|+..  .
T Consensus        14 ~DN~aL~~A~~----~~--~~v~~vyi~dp~~~~~~-----~--------~~~~r~~fl~~sL~~L~~~L~~~g~~L--~   72 (202)
T d1owla2          14 SDNIGLAAARA----QS--AQLIGLFCLDPQILQSA-----D--------MAPARVAYLQGCLQELQQRYQQAGSRL--L   72 (202)
T ss_dssp             SSCHHHHHHHH----HC--SCEEEEEEECHHHHTCT-----T--------CCHHHHHHHHHHHHHHHHHHHHHTSCE--E
T ss_pred             chHHHHHHHHh----cC--CcEEEEEEEcchHhcch-----h--------hhHHHHHHHHHHHHHHHHhhhccccce--E
Confidence            34446665553    22  58999999876432210     0        002334455566777777777777664  5


Q ss_pred             EecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEE
Q 031713           95 TEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVV  149 (154)
Q Consensus        95 v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv  149 (154)
                      +..|++.+.+.+.+++.+++.|.....- +...+ -.-....+.+....+.+..+
T Consensus        73 i~~G~~~~~l~~l~~~~~i~~v~~~~~~-~~~~~-~rd~~i~~~~~~~~i~~~~~  125 (202)
T d1owla2          73 LLQGDPQHLIPQLAQQLQAEAVYWNQDI-EPYGR-DRDGQVAAALKTAGIRAVQL  125 (202)
T ss_dssp             EEESCHHHHHHHHHHHTTCSEEEEECCC-SHHHH-HHHHHHHHHHHHTTCEEEEE
T ss_pred             EEEeeeeccchhhccccccceeEEeeec-cchhh-hHHHHHhhhhhhcccccccc
Confidence            6779999999999999999999988653 32222 12223344555556665544

>d1efvb_ c.26.2.3 (B:) Small, beta subunit of electron transfer flavoprotein ETFP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: ETFP subunits
domain: Small, beta subunit of electron transfer flavoprotein ETFP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.70  E-value=0.74  Score=29.65  Aligned_cols=99  Identities=15%  Similarity=0.160  Sum_probs=58.8

Q ss_pred             CCchHHHHHHHHHHHcccCCCCC-eEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCe
Q 031713           12 ESECRHYALQWALENLGDAISKS-DLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVV   90 (154)
Q Consensus        12 ~~~~~~~~l~~a~~la~~~~~~~-~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~   90 (154)
                      .++++..|++.|+++....+  . .++++..-+...                           ++.+.+...    .|..
T Consensus        35 iNp~D~~AlE~Al~lke~~g--g~~v~v~~~gp~~a---------------------------~~~lr~ala----~Gad   81 (252)
T d1efvb_          35 MNPFCEIAVEEAVRLKEKKL--VKEVIAVSCGPAQC---------------------------QETIRTALA----MGAD   81 (252)
T ss_dssp             ECHHHHHHHHHHHHHHHTTS--CSEEEEEEEESTTH---------------------------HHHHHHHHH----HTCS
T ss_pred             cCcccHHHHHHHHHHhhhcC--CceEEEEEecchhH---------------------------HHHHHHHHh----cCCc
Confidence            46779999999999998765  4 455555544421                           222333322    3444


Q ss_pred             EEEEEec------C-C---hhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEE
Q 031713           91 AETMTEM------G-D---PKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVL  147 (154)
Q Consensus        91 ~~~~v~~------g-~---~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvl  147 (154)
                      --..+..      + +   .+..+....+..++|||+.|.......    .|.+.-.+......|.+
T Consensus        82 ~avli~~~~~~~~~~~~~~~a~~~a~~~~~~~~DLIl~G~~s~D~~----tgqVg~~lAe~Lg~P~v  144 (252)
T d1efvb_          82 RGIHVEVPPAEAERLGPLQVARVLAKLAEKEKVDLVLLGKQAIDDD----CNQTGQMTAGFLDWPQG  144 (252)
T ss_dssp             EEEEEECCHHHHTTCCHHHHHHHHHHHHHHHTCSEEEEESCCTTTC----CCCHHHHHHHHHTCCEE
T ss_pred             ceEEEEecccccccccHHHHHHHHHHHHhccCCCEEEEeccchhcc----CCcHHHHHHHhcCCCce
Confidence            3333321      1 2   234555667778999999998753322    35566666666666654

>d1u3da2 c.28.1.1 (A:13-197) Cryptochrome {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: Cryptochrome
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=92.45  E-value=0.48  Score=28.85  Aligned_cols=111  Identities=11%  Similarity=-0.008  Sum_probs=65.5

Q ss_pred             HHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCeEEEEE
Q 031713           16 RHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMT   95 (154)
Q Consensus        16 ~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~v   95 (154)
                      ...|+..|++    .   +++..++++++......     ..+        ........+.+.++.+.++..|..... .
T Consensus        14 DN~aL~~A~~----~---~~vi~vfi~dp~~~~~~-----~~~--------~~~~~fl~~sL~~L~~~L~~~g~~L~v-~   72 (185)
T d1u3da2          14 DNPALAAAVR----A---GPVIALFVWAPEEEGHY-----HPG--------RVSRWWLKNSLAQLDSSLRSLGTCLIT-K   72 (185)
T ss_dssp             TCHHHHHHHH----H---SCEEEEEEECGGGGTTC-----CCC--------HHHHHHHHHHHHHHHHHHHHTTCCEEE-E
T ss_pred             cHHHHHHHHh----C---CCEEEEEEEcchHhccc-----ChH--------HHHHHHHHHHHHHHHHHHHhcCCcceE-e
Confidence            3456766653    2   37888999877543210     000        122334455667777778777866532 2


Q ss_pred             ecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEE
Q 031713           96 EMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVV  149 (154)
Q Consensus        96 ~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv  149 (154)
                      ..|++.+.|.+.+++.+++-|...... +.... -......+.+...++.+..+
T Consensus        73 ~~g~~~~~l~~l~~~~~i~~v~~n~~~-~~~e~-~rd~~v~~~l~~~gi~~~~~  124 (185)
T d1u3da2          73 RSTDSVASLLDVVKSTGASQIFFNHLY-DPLSL-VRDHRAKDVLTAQGIAVRSF  124 (185)
T ss_dssp             ECSCHHHHHHHHHHHHTCCEEEEECCC-SHHHH-HHHHHHHHHHHTTTCEEEEE
T ss_pred             eccchHHHHHHHHHhcCCceEEEeccc-cHHHH-HHHHHHHHHHHHcCCceeec
Confidence            358999999999999999999988753 22222 22223334455555555444

>d1vbka1 c.26.2.6 (A:176-307) Hypothetical protein PH1313, C-terminal domain {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: ThiI-like
domain: Hypothetical protein PH1313, C-terminal domain
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=92.36  E-value=0.13  Score=29.90  Aligned_cols=82  Identities=6%  Similarity=0.039  Sum_probs=48.7

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEIC   84 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   84 (154)
                      ++|+-+++.- |.-    |.+++...|  .++..+|.....                      ...+...+    +.+.+
T Consensus         6 k~l~LlSGGi-SpV----Aa~lmmkRG--~~V~~v~f~~~~----------------------~~~ekv~~----l~~~L   52 (132)
T d1vbka1           6 RMIGILHDEL-SAL----AIFLMMKRG--VEVIPVYIGKDD----------------------KNLEKVRS----LWNLL   52 (132)
T ss_dssp             EEEEECSSHH-HHH----HHHHHHHBT--CEEEEEEESCSS----------------------HHHHHHHH----HHHHH
T ss_pred             eEEEeecCCc-hHH----HHHHHHHCC--CEEEEEEEcCCH----------------------HHHHHHHH----HHHHH
Confidence            5667777666 543    345555677  799999984331                      11222222    22333


Q ss_pred             Hhc--CCeEEEEEecCChhhHHHHHHHhcCCCEEEEecC
Q 031713           85 AKH--GVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        85 ~~~--~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      .++  +.+....+.  ...+...+.|++.+++-++.|-.
T Consensus        53 ~~y~~~~~~~~~v~--~~~~~~~riA~~~~a~~ivtG~~   89 (132)
T d1vbka1          53 KRYSYGSKGFLVVA--ESFDRVLKLIRDFGVKGVIKGLR   89 (132)
T ss_dssp             HTTCTTSCCCCEEE--SSHHHHHHHHHHHTCCEEECCCC
T ss_pred             HHhCCCCCcEEEEe--eHHHHHHHHHHHhhhhceEEEEe
Confidence            333  444444333  34667788999999999998853

>d1ycga1 c.23.5.1 (A:251-399) Nitric oxide reductase C-terminal domain {Moorella thermoacetica [TaxId: 1525]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Flavoproteins
family: Flavodoxin-related
domain: Nitric oxide reductase C-terminal domain
species: Moorella thermoacetica [TaxId: 1525]

Probab=90.18  E-value=0.97  Score=26.14  Aligned_cols=47  Identities=11%  Similarity=0.058  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCC
Q 031713           74 LALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHS  122 (154)
Q Consensus        74 ~~~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~  122 (154)
                      +++.+.+.+.+.+.|+.++..-........+.....  ++|+||+|+..
T Consensus        17 ~~vA~~Ia~~l~~~g~~v~~~~~~~~~~~~~~~~~~--~~d~ii~Gspt   63 (149)
T d1ycga1          17 EKMAHALMDGLVAGGCEVKLFKLSVSDRNDVIKEIL--DARAVLVGSPT   63 (149)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEEGGGSCHHHHHHHHH--HCSEEEEECCC
T ss_pred             HHHHHHHHHHHHhcCCeeEEEEccccchHHHhhhhh--hCCeEEEEeec
Confidence            455666666777778887765555544555555555  69999999974

>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=89.17  E-value=1.6  Score=27.13  Aligned_cols=110  Identities=18%  Similarity=0.175  Sum_probs=62.5

Q ss_pred             EecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 031713            9 AIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHG   88 (154)
Q Consensus         9 ~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~   88 (154)
                      ...+.-=...+...|..+.+. |  .++.++.+..-...                            ..+++....+..+
T Consensus        17 Gp~GvGKTTTiaKLA~~~~~~-g--~kV~lit~Dt~R~g----------------------------A~eQL~~~a~~l~   65 (207)
T d1ls1a2          17 GLQGSGKTTTAAKLALYYKGK-G--RRPLLVAADTQRPA----------------------------AREQLRLLGEKVG   65 (207)
T ss_dssp             CCTTTTHHHHHHHHHHHHHHT-T--CCEEEEECCSSCHH----------------------------HHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHHHHC-C--CcEEEEecccccch----------------------------HHHHHHHHHHhcC
Confidence            334444445677777777654 4  57776665333221                            1245555555557


Q ss_pred             CeEEEEEecCChhhH---HHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcC-CCcEEEEc
Q 031713           89 VVAETMTEMGDPKNV---ICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNA-KCPVLVVR  150 (154)
Q Consensus        89 ~~~~~~v~~g~~~~~---i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~-~~pvliv~  150 (154)
                      +++.......++.+.   ....++..++|+|++.+-|++........... .+.+.. +..+++|.
T Consensus        66 v~~~~~~~~~~~~~~~~~~~~~~~~~~~d~vlIDTaGr~~~d~~~~~el~-~~~~~~~~~~~llv~  130 (207)
T d1ls1a2          66 VPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELA-RLKEVLGPDEVLLVL  130 (207)
T ss_dssp             CCEEECCTTCCHHHHHHHHHHHHHHHTCCEEEEECCCCSSCCHHHHHHHH-HHHHHHCCSEEEEEE
T ss_pred             CccccccccchhhHHHHHHHHHHhhccCcceeecccccchhhhhhHHHHH-HHHhhcCCceEEEEe
Confidence            776553322344333   33456778999999999998887765554443 333333 34555553

>d2c5sa1 c.26.2.6 (A:174-391) Thiamine biosynthesis protein ThiI, C-terminal domain {Bacillus anthracis [TaxId: 1392]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: ThiI-like
domain: Thiamine biosynthesis protein ThiI, C-terminal domain
species: Bacillus anthracis [TaxId: 1392]

Probab=88.49  E-value=1.7  Score=26.62  Aligned_cols=34  Identities=15%  Similarity=0.019  Sum_probs=25.5

Q ss_pred             EEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccC
Q 031713            5 KVMVAIDESECRHYALQWALENLGDAISKSDLIIFTARPT   44 (154)
Q Consensus         5 ~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~   44 (154)
                      |++|++.|...|..++..+.    ..|  .+++++|+...
T Consensus         6 Kvvv~~SGG~DS~vla~ll~----k~g--~~v~av~~~~~   39 (218)
T d2c5sa1           6 KVMVLLSGGIDSPVAAYLTM----KRG--VSVEAVHFHSP   39 (218)
T ss_dssp             EEEEECCSSSHHHHHHHHHH----HBT--EEEEEEEEECT
T ss_pred             EEEEEecCcHHHHHHHHHHH----HcC--CeEEEEEEeCC
Confidence            79999999988876554433    345  69999999654

>d1e5da1 c.23.5.1 (A:251-402) Rubredoxin oxygen:oxidoreductase (ROO), C-terminal domain {Desulfovibrio gigas [TaxId: 879]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Flavoproteins
family: Flavodoxin-related
domain: Rubredoxin oxygen:oxidoreductase (ROO), C-terminal domain
species: Desulfovibrio gigas [TaxId: 879]

Probab=88.23  E-value=1.4  Score=25.47  Aligned_cols=48  Identities=17%  Similarity=0.096  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCC
Q 031713           74 LALLGRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSR  123 (154)
Q Consensus        74 ~~~l~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~  123 (154)
                      +++.+.+.+.+.+.|++++..-......+.+.....  ++|++|+|+...
T Consensus        17 e~~A~~Ia~~l~~~g~ev~~~~~~~~~~~~~~~~l~--~~d~vi~Gspt~   64 (152)
T d1e5da1          17 EKMARVLAESFRDEGCTVKLMWCKACHHSQIMSEIS--DAGAVIVGSPTH   64 (152)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEETTTSCHHHHHHHHH--TCSEEEEECCCB
T ss_pred             HHHHHHHHHHHhhCCCEEEEeecccCChhhhccchh--hCCEEEEecccc
Confidence            455666677777778877665544444455555566  899999999753

>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=87.35  E-value=2.1  Score=26.70  Aligned_cols=94  Identities=12%  Similarity=0.092  Sum_probs=57.0

Q ss_pred             EEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 031713            8 VAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKH   87 (154)
Q Consensus         8 v~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   87 (154)
                      |...+.-=...+...|.++. ..|  .++.++....-...                            ..+++....+..
T Consensus        15 vGptGvGKTTTiAKLA~~~~-~~g--~kV~lit~Dt~R~g----------------------------A~eQL~~~a~~l   63 (211)
T d2qy9a2          15 VGVNGVGKTTTIGKLARQFE-QQG--KSVMLAAGDTFRAA----------------------------AVEQLQVWGQRN   63 (211)
T ss_dssp             ECCTTSCHHHHHHHHHHHHH-TTT--CCEEEECCCTTCHH----------------------------HHHHHHHHHHHT
T ss_pred             ECCCCCCHHHHHHHHHHHHH-HCC--CcEEEEeccccccc----------------------------chhhhhhhhhhc
Confidence            44444444556677776665 445  67777766433221                            235566666666


Q ss_pred             CCeEEEEEecCChhhHHHH---HHHhcCCCEEEEecCCCCCccccccc
Q 031713           88 GVVAETMTEMGDPKNVICE---AAEKHKIQLLIVGSHSRGPIQRAFLG  132 (154)
Q Consensus        88 ~~~~~~~v~~g~~~~~i~~---~a~~~~~dlivlg~~~~~~~~~~~~g  132 (154)
                      |+++...-...++...+.+   .++..++|+|++.+-|++........
T Consensus        64 ~v~~~~~~~~~d~~~~l~~~~~~a~~~~~d~ilIDTaGr~~~d~~~~~  111 (211)
T d2qy9a2          64 NIPVIAQHTGADSASVIFDAIQAAKARNIDVLIADTAGRLQNKSHLME  111 (211)
T ss_dssp             TCCEECCSTTCCHHHHHHHHHHHHHHTTCSEEEECCCCCGGGHHHHHH
T ss_pred             CCcccccccCCCHHHHHHHHHHHHHHcCCCEEEeccCCCccccHHHHH
Confidence            8777543322356555544   45567999999999998776654443

>d3clsd1 c.26.2.3 (D:1-192) Large, alpha subunit of electron transfer flavoprotein ETFP, N-terminal domain {Methylophilus methylotrophus [TaxId: 17]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: ETFP subunits
domain: Large, alpha subunit of electron transfer flavoprotein ETFP, N-terminal domain
species: Methylophilus methylotrophus [TaxId: 17]

Probab=86.45  E-value=2.2  Score=25.87  Aligned_cols=83  Identities=7%  Similarity=0.030  Sum_probs=54.5

Q ss_pred             EEEEEecC-----CchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHH
Q 031713            5 KVMVAIDE-----SECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGR   79 (154)
Q Consensus         5 ~iLv~vd~-----~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~   79 (154)
                      +|||-++.     .+.+..++..|.+++...|  .+++++-+=+..                                +.
T Consensus         2 kIlV~~E~~~g~l~~~slEll~~A~~la~~~g--~~v~avv~G~~~--------------------------------~~   47 (192)
T d3clsd1           2 KILVIAEHRRNDLRPVSLELIGAANGLKKSGE--DKVVVAVIGSQA--------------------------------DA   47 (192)
T ss_dssp             EEEEECCEETTEECTHHHHHHHHHHHHCSSTT--CEEEEEEESTTG--------------------------------GG
T ss_pred             eEEEEEEccCCEECHHHHHHHHHHHHHHHhcC--CcEEEEEeCCch--------------------------------HH
Confidence            67777764     4568899999999999987  788888764331                                12


Q ss_pred             HHHHHHhcCCeEEEEEecCC-------hhhHHHHHHHhcCCCEEEEecC
Q 031713           80 AKEICAKHGVVAETMTEMGD-------PKNVICEAAEKHKIQLLIVGSH  121 (154)
Q Consensus        80 ~~~~~~~~~~~~~~~v~~g~-------~~~~i~~~a~~~~~dlivlg~~  121 (154)
                      ..+.+..+|...-..+....       ....|.+.+++.++++|++++.
T Consensus        48 ~~~~l~~~Ga~~v~~~~~~~~~~~~~~~~~al~~~~~~~~p~~Vl~~~t   96 (192)
T d3clsd1          48 FVPALSVNGVDELVVVKGSSIDFDPDVFEASVSALIAAHNPSVVLLPHS   96 (192)
T ss_dssp             GHHHHCBTTCSEEEEEECSCSSCCHHHHHHHHHHHHHHHCCSEEEEESS
T ss_pred             HHhhhhhcCceEEEEecCcccccCHHHHHHHHHHHHhhcccceEEecCC
Confidence            23344455665433332211       2456777788888888888853

>d1dnpa2 c.28.1.1 (A:1-200) DNA photolyase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: DNA photolyase
species: Escherichia coli [TaxId: 562]

Probab=85.86  E-value=2.5  Score=25.81  Aligned_cols=73  Identities=10%  Similarity=0.085  Sum_probs=47.0

Q ss_pred             CeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEecCC----hhhHHHHHHH
Q 031713           34 SDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKHGVVAETMTEMGD----PKNVICEAAE  109 (154)
Q Consensus        34 ~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~v~~g~----~~~~i~~~a~  109 (154)
                      .+|..+++.++......             ...........+-+..+.+.+++.|+...  +..|+    +.+.|.++++
T Consensus        28 ~~v~~vyi~dp~~~~~~-------------~~~~~r~~fl~~sL~~L~~~L~~~g~~L~--v~~g~~~~~~~~~l~~l~~   92 (200)
T d1dnpa2          28 ARVLALYIATPRQWATH-------------NMSPRQAELINAQLNGLQIALAEKGIPLL--FREVDDFVASVEIVKQVCA   92 (200)
T ss_dssp             SEEEEEEEECHHHHHHT-------------TCCHHHHHHHHHHHHHHHHHHHHTTCCEE--EEECSSHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEcchhhccc-------------CcchhhhhhHHHHHHHHHhhhhhccceeE--EEEecccccchhHHHHHHH
Confidence            47999999876432210             00112344455667777777777776654  44554    5666778889


Q ss_pred             hcCCCEEEEecC
Q 031713          110 KHKIQLLIVGSH  121 (154)
Q Consensus       110 ~~~~dlivlg~~  121 (154)
                      +.+++-|.....
T Consensus        93 ~~~i~~v~~n~~  104 (200)
T d1dnpa2          93 ENSVTHLFYNYQ  104 (200)
T ss_dssp             HHTCCEEEEECC
T ss_pred             hcCCcEEEEecc
Confidence            999998888865

>d2bona1 e.52.1.2 (A:5-299) Lipid kinase YegS {Escherichia coli [TaxId: 562]}

class: Multi-domain proteins (alpha and beta)
fold: NAD kinase/diacylglycerol kinase-like
superfamily: NAD kinase/diacylglycerol kinase-like
family: Diacylglycerol kinase-like
domain: Lipid kinase YegS
species: Escherichia coli [TaxId: 562]

Probab=85.69  E-value=1.3  Score=28.73  Aligned_cols=69  Identities=14%  Similarity=0.158  Sum_probs=45.2

Q ss_pred             HHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCC--C-cEEEEcCC
Q 031713           78 GRAKEICAKHGVVAETMTEMG-DPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAK--C-PVLVVRKP  152 (154)
Q Consensus        78 ~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~--~-pvliv~~~  152 (154)
                      .++...+++.|+++++..... ..+..+.+.+.+.++|.||+.-. .+.     +..+++.++....  . |+-++|-.
T Consensus        18 ~~~~~~l~~~g~~~~v~~T~~~g~a~~~~~~~~~~~~d~Ivv~GG-DGT-----v~ev~~gl~~~~~~~~p~lgilP~G   90 (295)
T d2bona1          18 REAIMLLREEGMTIHVRVTWEKGDAARYVEEARKFGVATVIAGGG-DGT-----INEVSTALIQCEGDDIPALGILPLG   90 (295)
T ss_dssp             HHHHHHHHTTTCCEEEEECCSTTHHHHHHHHHHHHTCSEEEEEES-HHH-----HHHHHHHHHHCCSSCCCEEEEEECS
T ss_pred             HHHHHHHHHCCCEEEEEEcCCcchHHHHHHHHHhcCCCEEEEECC-CcH-----HHHHHHHHHhccCCCCceEEEEECC
Confidence            456666778899998888765 46778888877788998888643 222     3335555554332  3 46677754

>d2qv7a1 e.52.1.2 (A:1-312) Diacylglycerol kinase DgkB {Staphylococcus aureus [TaxId: 1280]}

class: Multi-domain proteins (alpha and beta)
fold: NAD kinase/diacylglycerol kinase-like
superfamily: NAD kinase/diacylglycerol kinase-like
family: Diacylglycerol kinase-like
domain: Diacylglycerol kinase DgkB
species: Staphylococcus aureus [TaxId: 1280]

Probab=85.18  E-value=1.6  Score=28.60  Aligned_cols=73  Identities=16%  Similarity=0.104  Sum_probs=45.2

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEEecC-ChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcC-CCcEEEEcC
Q 031713           74 LALLGRAKEICAKHGVVAETMTEMG-DPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNA-KCPVLVVRK  151 (154)
Q Consensus        74 ~~~l~~~~~~~~~~~~~~~~~v~~g-~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~-~~pvliv~~  151 (154)
                      .+.+.++...+.+.+.+++.....+ .-...+++.+...++|.||+.- |.+.+     ..+++.++..- ..|+.++|-
T Consensus        19 ~~~~~~~~~~l~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~d~ivv~G-GDGTv-----~~v~~~l~~~~~~~~l~iiP~   92 (312)
T d2qv7a1          19 KRELPDALIKLEKAGYETSAYATEKIGDATLEAERAMHENYDVLIAAG-GDGTL-----NEVVNGIAEKPNRPKLGVIPM   92 (312)
T ss_dssp             HHHHHHHHHHHHHTTEEEEEEECCSTTHHHHHHHHHTTTTCSEEEEEE-CHHHH-----HHHHHHHTTCSSCCEEEEEEC
T ss_pred             HHHHHHHHHHHHHCCCeEEEEEcCCccHHHHHHHHHHHcCCCEEEEEc-CCcHH-----HHHHHHHHhhccccceEEeec
Confidence            3445566667777788877766554 4566666666667889887763 33322     23445555333 378999886


Q ss_pred             C
Q 031713          152 P  152 (154)
Q Consensus       152 ~  152 (154)
                      .
T Consensus        93 G   93 (312)
T d2qv7a1          93 G   93 (312)
T ss_dssp             S
T ss_pred             C
Confidence            5

>d1p3y1_ c.34.1.1 (1:) MrsD {Bacillus sp. hil-y85/54728 [TaxId: 69002]}

class: Alpha and beta proteins (a/b)
fold: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD
superfamily: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD
family: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD
domain: MrsD
species: Bacillus sp. hil-y85/54728 [TaxId: 69002]

Probab=85.16  E-value=0.48  Score=29.01  Aligned_cols=34  Identities=15%  Similarity=0.092  Sum_probs=25.1

Q ss_pred             cEEEEEecCCchHHHHHHHHHHHcccCCCCCeEEEEE
Q 031713            4 KKVMVAIDESECRHYALQWALENLGDAISKSDLIIFT   40 (154)
Q Consensus         4 ~~iLv~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~   40 (154)
                      ||||+++.+|-.+-++.++...+-+ .|  .++.++-
T Consensus         7 KkIllgvTGsiaa~k~~~l~~~L~~-~g--~eV~vv~   40 (183)
T d1p3y1_           7 KKLLIGICGSISSVGISSYLLYFKS-FF--KEIRVVM   40 (183)
T ss_dssp             CEEEEEECSCGGGGGTHHHHHHHTT-TS--SEEEEEE
T ss_pred             CEEEEEEeCHHHHHHHHHHHHHHHH-CC--CeEEEEE
Confidence            8999999999887777777655544 45  6776653

>d1nu0a_ c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein YqgF (RuvX)
species: Escherichia coli [TaxId: 562]

Probab=84.21  E-value=0.55  Score=27.30  Aligned_cols=51  Identities=16%  Similarity=-0.003  Sum_probs=35.7

Q ss_pred             hhhHHHHHHHhcCCCEEEEecCC----CCCcccccccchhHHHhhcCCCcEEEEc
Q 031713          100 PKNVICEAAEKHKIQLLIVGSHS----RGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus       100 ~~~~i~~~a~~~~~dlivlg~~~----~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      ..+.|.+.+++.+++.||+|-.-    .........-.++..|-+..++||..+-
T Consensus        41 ~~~~l~~i~~e~~~~~iVvG~P~~~~g~~~~~~~~v~~f~~~L~~~~~i~V~~~D   95 (138)
T d1nu0a_          41 DWNIIERLLKEWQPDEIIVGLPLNMDGTEQPLTARARKFANRIHGRFGVEVKLHD   95 (138)
T ss_dssp             CHHHHHHHHHHHCCSEEEEEEEECTTSCBCHHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             hHHHHHHHhhccCccEEEeecccccccchHHHHHHHHHHHHHHhhccCCCeEEEe
Confidence            57889999999999999999642    1111112344456677777889998874

>d2a9pa1 c.23.1.1 (A:2-118) DNA-binding response regulator MicA, N-terminal domain {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: DNA-binding response regulator MicA, N-terminal domain
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=83.04  E-value=2.4  Score=23.35  Aligned_cols=67  Identities=16%  Similarity=0.129  Sum_probs=40.3

Q ss_pred             HHHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEcCC
Q 031713           78 GRAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVRKP  152 (154)
Q Consensus        78 ~~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~~~  152 (154)
                      +.+...++..|.++..   ..+..++ ++.+++..+|+|++...- ....+   -.....+-+..++||+++-..
T Consensus        14 ~~l~~~L~~~g~~v~~---a~~~~ea-l~~~~~~~~dlillD~~m-p~~~G---~~~~~~i~~~~~~pvI~lt~~   80 (117)
T d2a9pa1          14 DIIKFNMTKEGYEVVT---AFNGREA-LEQFEAEQPDIIILDLML-PEIDG---LEVAKTIRKTSSVPILMLSAK   80 (117)
T ss_dssp             HHHHHHHHHTTCEEEE---ESSHHHH-HHHHHHHCCSEEEECSSC-SSSCH---HHHHHHHHTTCCCCEEEEESC
T ss_pred             HHHHHHHHHCCCEEEE---ECCHHHH-HHHHHhcCCCEEEecccc-CCCCc---cHHHHHHHhCCCCCEEEEecC
Confidence            4455566666765532   2344444 455667899999999752 22332   135566656666999888543

>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=81.78  E-value=4.1  Score=25.15  Aligned_cols=92  Identities=11%  Similarity=0.029  Sum_probs=55.1

Q ss_pred             EEecCCchHHHHHHHHHHHcccCCCCCeEEEEEeccCCchhhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 031713            8 VAIDESECRHYALQWALENLGDAISKSDLIIFTARPTEFIYVQASMFGAAPPDLLMSIQENQKKAALALLGRAKEICAKH   87 (154)
Q Consensus         8 v~vd~~~~~~~~l~~a~~la~~~~~~~~l~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   87 (154)
                      |...++-=...+...|.++.+ .|  .++.++.+..-....                            .+++....+..
T Consensus        12 vGptGvGKTTTiaKLA~~~~~-~g--~kV~lit~Dt~R~gA----------------------------~eQL~~~a~~l   60 (207)
T d1okkd2          12 VGVNGVGKTTTIAKLGRYYQN-LG--KKVMFCAGDTFRAAG----------------------------GTQLSEWGKRL   60 (207)
T ss_dssp             ECSTTSSHHHHHHHHHHHHHT-TT--CCEEEECCCCSSTTH----------------------------HHHHHHHHHHH
T ss_pred             ECCCCCCHHHHHHHHHHHHHH-CC--CcEEEEEeccccccc----------------------------hhhHhhccccc
Confidence            444444445556667766654 45  577766664433222                            24445555555


Q ss_pred             CCeEEEEEecCChhhHHHH---HHHhcCCCEEEEecCCCCCccccc
Q 031713           88 GVVAETMTEMGDPKNVICE---AAEKHKIQLLIVGSHSRGPIQRAF  130 (154)
Q Consensus        88 ~~~~~~~v~~g~~~~~i~~---~a~~~~~dlivlg~~~~~~~~~~~  130 (154)
                      ++++.......++...+.+   +++..++|+|++.+-|++....-.
T Consensus        61 ~i~~~~~~~~~d~~~~~~~~~~~~~~~~~d~ilIDTaGr~~~d~~l  106 (207)
T d1okkd2          61 SIPVIQGPEGTDPAALAYDAVQAMKARGYDLLFVDTAGRLHTKHNL  106 (207)
T ss_dssp             TCCEECCCTTCCHHHHHHHHHHHHHHHTCSEEEECCCCCCTTCHHH
T ss_pred             CceEEeccCCccHHHHHHHHHHHHHHCCCCEEEcCccccchhhHHH
Confidence            7776443333466666654   355679999999999988766543

>d3bzka5 c.55.3.13 (A:325-473) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Tex RuvX-like domain-like
domain: Transcriptional accessory factor Tex
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=80.26  E-value=0.79  Score=27.02  Aligned_cols=45  Identities=16%  Similarity=0.335  Sum_probs=25.3

Q ss_pred             HHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhc---CCCcEEEEcC
Q 031713          103 VICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHN---AKCPVLVVRK  151 (154)
Q Consensus       103 ~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~---~~~pvliv~~  151 (154)
                      .+.++.+++++++|++|....+.-    .-.....+++.   .++++.+|.+
T Consensus        50 ~l~~li~k~~p~vIaIGNgTasre----~~~~v~~l~~~~~~~~i~~~iV~e   97 (149)
T d3bzka5          50 VLAALCAKHQVELIAIGNGTASRE----TDKLAGELIKKYPGMKLTKIMVSE   97 (149)
T ss_dssp             HHHHHHHHTTCCEEEEESSTTHHH----HHHHHHHHHHHCGGGCCEEEEECC
T ss_pred             HHHHHHHHcCCeEEEECCCccHHH----HHHHHHHHHHhCCCCCcEEEEEec
Confidence            466677788888888886432211    12223334433   2477777754

>d1s8na_ c.23.1.1 (A:) Probable two-component system transcriptional regulator Rv1626 {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Probable two-component system transcriptional regulator Rv1626
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=80.08  E-value=4.3  Score=24.30  Aligned_cols=65  Identities=22%  Similarity=0.262  Sum_probs=38.6

Q ss_pred             HHHHHHHhcCCeEEEEEecCChhhHHHHHHHhcCCCEEEEecCCCCCcccccccchhHHHhhcCCCcEEEEc
Q 031713           79 RAKEICAKHGVVAETMTEMGDPKNVICEAAEKHKIQLLIVGSHSRGPIQRAFLGSVSNYCVHNAKCPVLVVR  150 (154)
Q Consensus        79 ~~~~~~~~~~~~~~~~v~~g~~~~~i~~~a~~~~~dlivlg~~~~~~~~~~~~gs~~~~l~~~~~~pvliv~  150 (154)
                      -+...++..|..+.  -..++..++ ++.+++.++|++++.-. .....++   .+..++-...++||+++-
T Consensus        18 ~l~~~L~~~g~~vv--~~a~~g~ea-l~~~~~~~pDlvllDi~-mP~~dG~---e~~~~ir~~~~~pIi~lT   82 (190)
T d1s8na_          18 DLAEMLREEGYEIV--GEAGDGQEA-VELAELHKPDLVIMDVK-MPRRDGI---DAASEIASKRIAPIVVLT   82 (190)
T ss_dssp             HHHHHHHHTTCEEE--EEESSHHHH-HHHHHHHCCSEEEEESS-CSSSCHH---HHHHHHHHTTCSCEEEEE
T ss_pred             HHHHHHHHCCCEEE--EEECCHHHH-HHHHhcCCCCEEEEecc-ccCcchH---HHHHHHHhcCCCCEEEEe
Confidence            33444455575432  122333343 46777789999999986 2223331   355666666779999874