Citrus Sinensis ID: 033949

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------
Protein Sequence
MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL
Secondary Structure (PSIPRED)
cEEEEEccccccEEEEEEEccEEEcccccccEEEEEcEEEEEEEEEcccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEEccHHHHHHHHHHHcccccccccccccHHHHHHHEEEEEEEEEEccccccEEEccccccccccccccccccccccHHHHccccccccccccccEcccccccc
Coil and Loop (DISEMBL)
MFFFFVGGVNQQVSRVLKSgagrcincgstADLVEYEKVLKAFFvpvwkwpakepalfcnncnllfpsslpppppppplvsdvskcrfcdrlvepdfsfcpycgsal
Flexible Loop (DISEMBL)
MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVepdfsfcpycgsal
Low Complexity Region (SEG)
MffffvggvNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFpsslpppppppplVSDVSKCRFCDRLVEPDFSFCPYCGSAL
Disordered region (IsUnstruct)
*FFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLF*****************************************
Disordered Region (DISOPRED)
MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLL*******************KCRFCDRLVEPDFSFCPYCGSA*
Disordered Region (DISEMBL)
MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL
Disordered Region (DISPRO)
MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPP***********SKCRFCDRLVEPDFSFCPYCGS**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL
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

No hits with e-value below 0.001 by BLAST

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	107
255545392	112	conserved hypothetical protein [Ricinus	1.0	0.955	0.687	2e-38
224063078	113	predicted protein [Populus trichocarpa]	1.0	0.946	0.663	2e-37
297846816	101	hypothetical protein ARALYDRAFT_891393 [	0.943	1.0	0.654	2e-34
15219391	101	uncharacterized protein [Arabidopsis tha	0.943	1.0	0.654	2e-34
225459571	102	PREDICTED: uncharacterized protein LOC10	0.953	1.0	0.654	6e-30
226531153	106	uncharacterized protein LOC100275135 [Ze	0.990	1.0	0.598	1e-29
242090657	110	hypothetical protein SORBIDRAFT_09g02146	1.0	0.972	0.581	6e-29
357133537	106	PREDICTED: uncharacterized protein LOC10	0.990	1.0	0.598	1e-28
356552679	114	PREDICTED: uncharacterized protein LOC10	1.0	0.938	0.552	3e-28
326487958	104	predicted protein [Hordeum vulgare subsp	0.971	1.0	0.579	1e-27

>gi|255545392|ref|XP_002513756.1| conserved hypothetical protein [Ricinus communis] gi|223546842|gb|EEF48339.1| conserved hypothetical protein [Ricinus communis]

 Score =  162 bits (410), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 77/112 (68%), Positives = 89/112 (79%), Gaps = 5/112 (4%)

Query: 1   MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCN 60
           MFFFF GGV QQVSRVLKSG GRC+NCGS ADLVEYEKVLK FF+PV+KWP KEPA++CN
Sbjct: 1   MFFFFAGGVEQQVSRVLKSGVGRCVNCGSMADLVEYEKVLKLFFIPVYKWPGKEPAMYCN 60

Query: 61  NCNLLFPSSLPPPPP-----PPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL 107
           NCNL+FP S   PPP      P  VSD  +C FCDR+ EP+F FCP+CG++L
Sbjct: 61  NCNLMFPRSFSFPPPRTDSVSPSAVSDGLRCHFCDRVAEPEFRFCPFCGNSL 112

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224063078|ref|XP_002300985.1| predicted protein [Populus trichocarpa] gi|222842711|gb|EEE80258.1| predicted protein [Populus trichocarpa]

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 75/113 (66%), Positives = 87/113 (76%), Gaps = 6/113 (5%)

Query: 1   MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCN 60
           MFFFFVGGV QQV +VLKSGAGRCI C S ADLVEYEKVLK FF+PVWKWP KEPA+ CN
Sbjct: 1   MFFFFVGGVEQQVRQVLKSGAGRCIRCASKADLVEYEKVLKLFFIPVWKWPGKEPAMHCN 60

Query: 61  NCNLLFPSSLPPPPP------PPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL 107
           NCNL+FP S    PP      P  +V++  +C FCDR+VE +F FCP+CGS+L
Sbjct: 61  NCNLIFPQSFSHTPPKSDYSLPRSVVTESLRCHFCDRVVESEFKFCPFCGSSL 113

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297846816|ref|XP_002891289.1| hypothetical protein ARALYDRAFT_891393 [Arabidopsis lyrata subsp. lyrata] gi|297337131|gb|EFH67548.1| hypothetical protein ARALYDRAFT_891393 [Arabidopsis lyrata subsp. lyrata]

 Score =  149 bits (376), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 70/107 (65%), Positives = 84/107 (78%), Gaps = 6/107 (5%)

Query: 1   MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCN 60
           MFFFFVGGV QQV +VLKSGAG CI CGS ADLV+Y+KVLK FF+PVW+WP K+P L C 
Sbjct: 1   MFFFFVGGVGQQVRQVLKSGAGTCIRCGSEADLVDYDKVLKLFFIPVWRWPGKDPLLHCR 60

Query: 61  NCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL 107
           +C+L FP SL PPP        ++ CRFCDR+VEP+F FCP+CGS+L
Sbjct: 61  DCDLFFPQSLSPPP------VSLATCRFCDRVVEPEFRFCPFCGSSL 101

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15219391|ref|NP_175087.1| uncharacterized protein [Arabidopsis thaliana] gi|13876513|gb|AAK43489.1|AC084807_14 hypothetical protein [Arabidopsis thaliana] gi|44917499|gb|AAS49074.1| At1g44414 [Arabidopsis thaliana] gi|332193912|gb|AEE32033.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  149 bits (375), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 70/107 (65%), Positives = 84/107 (78%), Gaps = 6/107 (5%)

Query: 1   MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCN 60
           MFFFFVGG+ QQV +VLKSGAG CI CGS ADLVEY+KV+K FFVPVW+WP K+P L C 
Sbjct: 1   MFFFFVGGLGQQVRQVLKSGAGTCIRCGSQADLVEYDKVIKLFFVPVWRWPGKDPLLHCR 60

Query: 61  NCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL 107
           +C+L FP SL PPP        ++ CRFCDR+VEP+F FCP+CGS+L
Sbjct: 61  DCDLFFPQSLSPPP------VSLATCRFCDRVVEPEFRFCPFCGSSL 101

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225459571|ref|XP_002285858.1| PREDICTED: uncharacterized protein LOC100262547 [Vitis vinifera]

 Score =  134 bits (337), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 70/107 (65%), Positives = 81/107 (75%), Gaps = 5/107 (4%)

Query: 1   MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCN 60
           MFFFFVGG+ QQV +VLKSGAG+CINCGS ADLV+YEKVLK FFVPVW+WP KEP + C 
Sbjct: 1   MFFFFVGGLEQQVLQVLKSGAGKCINCGSRADLVDYEKVLKLFFVPVWRWPGKEPLMHCP 60

Query: 61  NCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL 107
           +C L F    PPP    PL+ DV +C  C R VE +F FCP+CGSAL
Sbjct: 61  DCFLFF----PPPTRTGPLL-DVLRCASCGRPVESNFRFCPFCGSAL 102

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226531153|ref|NP_001142776.1| uncharacterized protein LOC100275135 [Zea mays] gi|195609474|gb|ACG26567.1| hypothetical protein [Zea mays] gi|195641802|gb|ACG40369.1| hypothetical protein [Zea mays] gi|413949185|gb|AFW81834.1| hypothetical protein ZEAMMB73_807317 [Zea mays]

 Score =  133 bits (335), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 64/107 (59%), Positives = 73/107 (68%), Gaps = 1/107 (0%)

Query: 1   MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCN 60
           MFFFFVGGV Q   RVLK  AGRC+ CG  ADLVE EKVLK FFVPVW+WP K+PA  C 
Sbjct: 1   MFFFFVGGVEQGAGRVLKEAAGRCLRCGGAADLVETEKVLKLFFVPVWRWPGKDPAYLCR 60

Query: 61  NCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL 107
            C LL P SL     P  L+ + ++C  C R V+P F FCP+CGSAL
Sbjct: 61  ECGLLAPGSLGAESGPSLLLRE-ARCGACSRAVDPQFRFCPFCGSAL 106

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242090657|ref|XP_002441161.1| hypothetical protein SORBIDRAFT_09g021460 [Sorghum bicolor] gi|241946446|gb|EES19591.1| hypothetical protein SORBIDRAFT_09g021460 [Sorghum bicolor]

 Score =  131 bits (329), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 64/110 (58%), Positives = 74/110 (67%), Gaps = 3/110 (2%)

Query: 1   MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCN 60
           MFFFFVGGV Q   RVLK  AGRC+ CG  ADLVE EKVLK FFVPVW+WP K+PA  C 
Sbjct: 1   MFFFFVGGVEQGAGRVLKEAAGRCLRCGGAADLVETEKVLKLFFVPVWRWPGKDPAYLCR 60

Query: 61  NCNLLFPSSLPPPPPPPP---LVSDVSKCRFCDRLVEPDFSFCPYCGSAL 107
           +C LL P SL   P P     L+   ++C  C R V+P F FCP+CGS+L
Sbjct: 61  DCGLLAPGSLGAEPGPGRSSLLLPREARCGACSRAVDPQFRFCPFCGSSL 110

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357133537|ref|XP_003568381.1| PREDICTED: uncharacterized protein LOC100838692 [Brachypodium distachyon]

 Score =  130 bits (327), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 64/107 (59%), Positives = 71/107 (66%), Gaps = 1/107 (0%)

Query: 1   MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCN 60
           MFFFFVGGV Q   RVLK  AGRC+ CG TADLVE EKVLK FFVP W+W  K+PA  C 
Sbjct: 1   MFFFFVGGVEQGAGRVLKEAAGRCLRCGGTADLVETEKVLKLFFVPAWRWQGKDPAYVCR 60

Query: 61  NCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL 107
            C LL P SL    P  PL+    +C  C R V+P F FCP+CGSAL
Sbjct: 61  ECGLLAPESL-GSEPAGPLLPRGERCGACSRAVDPQFRFCPFCGSAL 106

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356552679|ref|XP_003544690.1| PREDICTED: uncharacterized protein LOC100820054 [Glycine max]

 Score =  129 bits (323), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 63/114 (55%), Positives = 77/114 (67%), Gaps = 7/114 (6%)

Query: 1   MFFFFVGGVNQQVSRVLKSGAGRCINCGST-ADLVEYEKVLKAFFVPVWKWPAKEPALFC 59
           MFFFFVGG+ Q++ +VLKSG G+C  C +   DLV Y+KVLK FFVPVW+WPAK+P L+C
Sbjct: 1   MFFFFVGGLQQEIRQVLKSGVGKCTFCANNRVDLVNYDKVLKLFFVPVWRWPAKDPLLYC 60

Query: 60  NNCNLLFPSSLPPPP------PPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL 107
             C   FP +   PP        P  V+D  +CRFCDR VE DF FCP+CGS L
Sbjct: 61  GGCKNFFPYNYSLPPGGDGESASPTAVTDALRCRFCDRSVEADFRFCPFCGSEL 114

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326487958|dbj|BAJ89818.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  126 bits (317), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 62/107 (57%), Positives = 70/107 (65%), Gaps = 3/107 (2%)

Query: 1   MFFFFVGGVNQQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCN 60
           MFFFFVGGV Q   RVLK  AGRC+ CG  ADLVE EKVLK FFVP W+WP K+PA  C 
Sbjct: 1   MFFFFVGGVEQGAGRVLKEAAGRCLRCGGAADLVETEKVLKLFFVPAWRWPGKDPAYLCR 60

Query: 61  NCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL 107
            C LL P SL       PL+   ++C  C R V+P F FCP+CGS L
Sbjct: 61  GCGLLAPRSL---GGGEPLLPRAAQCGACSRAVDPQFRFCPFCGSPL 104

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	107
TAIR|locus:2823681	101	AT1G44414 "AT1G44414" [Arabido	0.850	0.900	0.597	3.9e-28

TAIR|locus:2823681 AT1G44414 "AT1G44414" [Arabidopsis thaliana (taxid:3702)]

 Score = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 58/97 (59%), Positives = 71/97 (73%)

Query:    11 QQVSRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFXXXX 70
             QQV +VLKSGAG CI CGS ADLVEY+KV+K FFVPVW+WP K+P L C +C+L F    
Sbjct:    11 QQVRQVLKSGAGTCIRCGSQADLVEYDKVIKLFFVPVWRWPGKDPLLHCRDCDLFFPQSL 70

Query:    71 XXXXXXXXXVSDVSKCRFCDRLVEPDFSFCPYCGSAL 107
                      VS ++ CRFCDR+VEP+F FCP+CGS+L
Sbjct:    71 SPPP-----VS-LATCRFCDRVVEPEFRFCPFCGSSL 101


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.327   0.140   0.481    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      107        86   0.00091  102 3  11 22  0.39    29
                                                     29  0.47    30


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  554 (59 KB)
  Total size of DFA:  121 KB (2078 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  8.24u 0.14s 8.38t   Elapsed:  00:00:01
  Total cpu time:  8.24u 0.14s 8.38t   Elapsed:  00:00:01
  Start:  Fri May 10 09:17:33 2013   End:  Fri May 10 09:17:34 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0006457 "protein folding" evidence=RCA

GO:0009408 "response to heat" evidence=RCA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0042542 "response to hydrogen peroxide" evidence=RCA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: grail3.0003070401 hypothetical protein (113 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	107
PF12773	50	DZR: Double zinc ribbon	99.23
PF13248	26	zf-ribbon_3: zinc-ribbon domain	99.11
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	99.08
PRK14559	645	putative protein serine/threonine phosphatase; Pro	98.95
PRK14714	1337	DNA polymerase II large subunit; Provisional	98.61
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	98.47
PF12773	50	DZR: Double zinc ribbon	98.26
PF13248	26	zf-ribbon_3: zinc-ribbon domain	97.85
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	97.82
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	97.77
PRK04023	1121	DNA polymerase II large subunit; Validated	97.57
PF03833	900	PolC_DP2: DNA polymerase II large subunit DP2; Int	97.5
PRK14559	645	putative protein serine/threonine phosphatase; Pro	97.4
COG1198	730	PriA Primosomal protein N' (replication factor Y)	97.37
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	97.33
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	97.3
PRK14873	665	primosome assembly protein PriA; Provisional	97.14
TIGR00595	505	priA primosomal protein N'. All proteins in this f	97.13
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	97.06
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	96.88
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	96.76
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	96.75
PRK05580	679	primosome assembly protein PriA; Validated	96.7
PRK14714	1337	DNA polymerase II large subunit; Provisional	96.57
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	96.56
PRK04023	1121	DNA polymerase II large subunit; Validated	96.52
PF09889	59	DUF2116: Uncharacterized protein containing a Zn-r	96.51
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	96.41
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	96.4
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	96.39
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	96.34
TIGR00595	505	priA primosomal protein N'. All proteins in this f	96.32
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	96.32
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	96.18
COG1198	730	PriA Primosomal protein N' (replication factor Y)	96.13
PRK00420	112	hypothetical protein; Validated	95.99
COG2093	64	DNA-directed RNA polymerase, subunit E'' [Transcri	95.98
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	95.96
PRK12496	164	hypothetical protein; Provisional	95.96
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	95.95
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	95.92
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	95.9
PF15616	131	TerY-C: TerY-C metal binding domain	95.84
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	95.82
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	95.79
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	95.74
PRK13130	56	H/ACA RNA-protein complex component Nop10p; Review	95.74
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	95.73
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	95.71
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	95.69
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	95.53
PRK14892	99	putative transcription elongation factor Elf1; Pro	95.45
COG1439	177	Predicted nucleic acid-binding protein, consists o	95.44
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	95.4
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	95.37
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	95.32
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	95.3
PRK05580	679	primosome assembly protein PriA; Validated	95.24
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	95.23
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	95.22
PRK14873	665	primosome assembly protein PriA; Provisional	95.22
cd00729	34	rubredoxin_SM Rubredoxin, Small Modular nonheme ir	95.11
PRK02935	110	hypothetical protein; Provisional	95.02
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	95.01
PF10601	73	zf-LITAF-like: LITAF-like zinc ribbon domain; Inte	95.01
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	95.0
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	94.95
PF10083	158	DUF2321: Uncharacterized protein conserved in bact	94.89
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	94.83
COG4260	345	Membrane protease subunit, stomatin/prohibitin fam	94.69
smart00661	52	RPOL9 RNA polymerase subunit 9.	94.65
PF14353	128	CpXC: CpXC protein	94.62
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	94.62
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	94.57
PRK03564	309	formate dehydrogenase accessory protein FdhE; Prov	94.56
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	94.53
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	94.43
cd00729	34	rubredoxin_SM Rubredoxin, Small Modular nonheme ir	94.42
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	94.4
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	94.36
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	94.36
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	94.26
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	94.16
TIGR02300	129	FYDLN_acid conserved hypothetical protein TIGR0230	94.16
smart00714	67	LITAF Possible membrane-associated motif in LPS-in	94.09
PF12172	37	DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35	94.07
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	94.04
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	94.02
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	93.92
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	93.7
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	93.58
smart00661	52	RPOL9 RNA polymerase subunit 9.	93.58
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	93.52
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	93.46
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	93.39
COG1545	140	Predicted nucleic-acid-binding protein containing	93.37
PRK00420	112	hypothetical protein; Validated	93.29
PF09855	64	DUF2082: Nucleic-acid-binding protein containing Z	93.29
PF01155	113	HypA: Hydrogenase expression/synthesis hypA family	93.12
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	92.99
PF11781	36	RRN7: RNA polymerase I-specific transcription init	92.93
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	92.88
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	92.88
PF05191	36	ADK_lid: Adenylate kinase, active site lid; InterP	92.78
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	92.71
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	92.65
PRK04136	48	rpl40e 50S ribosomal protein L40e; Provisional	92.61
PHA00626	59	hypothetical protein	92.55
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	92.52
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	92.49
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	92.32
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	92.31
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	92.24
PF15616	131	TerY-C: TerY-C metal binding domain	92.13
smart00531	147	TFIIE Transcription initiation factor IIE.	92.05
PF14319	111	Zn_Tnp_IS91: Transposase zinc-binding domain	91.96
smart00531	147	TFIIE Transcription initiation factor IIE.	91.92
PRK00432	50	30S ribosomal protein S27ae; Validated	91.81
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	91.7
PRK08351	61	DNA-directed RNA polymerase subunit E''; Validated	91.52
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	91.51
PLN03086	567	PRLI-interacting factor K; Provisional	91.39
PRK14892	99	putative transcription elongation factor Elf1; Pro	91.32
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	91.28
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	91.19
PRK06393	64	rpoE DNA-directed RNA polymerase subunit E''; Vali	91.17
PHA02942	383	putative transposase; Provisional	91.15
PF13453	41	zf-TFIIB: Transcription factor zinc-finger	91.15
PRK12286	57	rpmF 50S ribosomal protein L32; Reviewed	91.12
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	91.11
TIGR01562	305	FdhE formate dehydrogenase accessory protein FdhE.	90.85
PF08772	73	NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon lik	90.83
PF01155	113	HypA: Hydrogenase expression/synthesis hypA family	90.54
PRK02935	110	hypothetical protein; Provisional	90.4
TIGR02300	129	FYDLN_acid conserved hypothetical protein TIGR0230	90.35
TIGR00515	285	accD acetyl-CoA carboxylase, carboxyl transferase,	90.35
PF10058	54	DUF2296: Predicted integral membrane metal-binding	90.32
CHL00174	296	accD acetyl-CoA carboxylase beta subunit; Reviewed	90.3
COG2093	64	DNA-directed RNA polymerase, subunit E'' [Transcri	90.3
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	90.3
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	90.17
PRK06266	178	transcription initiation factor E subunit alpha; V	90.14
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	90.12
PRK12495	226	hypothetical protein; Provisional	90.11
TIGR03831	46	YgiT_finger YgiT-type zinc finger domain. This dom	89.89
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	89.67
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	89.58
PF01783	56	Ribosomal_L32p: Ribosomal L32p protein family; Int	89.55
PRK05978	148	hypothetical protein; Provisional	89.47
PF03833	900	PolC_DP2: DNA polymerase II large subunit DP2; Int	89.39
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	89.33
KOG2906	105	consensus RNA polymerase III subunit C11 [Transcri	89.12
PF14369	35	zf-RING_3: zinc-finger	88.89
PRK12496	164	hypothetical protein; Provisional	88.86
COG0375	115	HybF Zn finger protein HypA/HybF (possibly regulat	88.63
TIGR01031	55	rpmF_bact ribosomal protein L32. This protein desc	88.55
COG4306	160	Uncharacterized protein conserved in bacteria [Fun	88.54
PRK00762	124	hypA hydrogenase nickel incorporation protein; Pro	88.54
PRK05654	292	acetyl-CoA carboxylase subunit beta; Validated	88.51
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	88.48
PRK12775	1006	putative trifunctional 2-polyprenylphenol hydroxyl	88.43
COG4888	104	Uncharacterized Zn ribbon-containing protein [Gene	88.33
PF14205	55	Cys_rich_KTR: Cysteine-rich KTR	88.17
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	88.11
PF05129	81	Elf1: Transcription elongation factor Elf1 like; I	87.99
smart00647	64	IBR In Between Ring fingers. the domains occurs be	87.78
TIGR03826	137	YvyF flagellar operon protein TIGR03826. This gene	87.78
PRK14973	936	DNA topoisomerase I; Provisional	87.74
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	87.67
smart00547	26	ZnF_RBZ Zinc finger domain. Zinc finger domain in	87.6
PRK08579	625	anaerobic ribonucleoside triphosphate reductase; P	87.34
COG2260	59	Predicted Zn-ribbon RNA-binding protein [Translati	87.34
PLN00209	86	ribosomal protein S27; Provisional	87.32
PF04981	236	NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 p	87.27
COG1592	166	Rubrerythrin [Energy production and conversion]	87.13
PRK15103	419	paraquat-inducible membrane protein A; Provisional	87.09
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	87.05
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	87.03
PF00641	30	zf-RanBP: Zn-finger in Ran binding protein and oth	86.98
COG0675	364	Transposase and inactivated derivatives [DNA repli	86.79
TIGR01562	305	FdhE formate dehydrogenase accessory protein FdhE.	86.55
COG1552	50	RPL40A Ribosomal protein L40E [Translation, riboso	86.51
PRK03564	309	formate dehydrogenase accessory protein FdhE; Prov	86.34
PF07295	146	DUF1451: Protein of unknown function (DUF1451); In	86.29
PF02591	56	DUF164: Putative zinc ribbon domain; InterPro: IPR	86.26
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	86.21
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	86.17
PTZ00083	85	40S ribosomal protein S27; Provisional	86.15
PF06827	30	zf-FPG_IleRS: Zinc finger found in FPG and IleRS;	86.03
PRK05978	148	hypothetical protein; Provisional	86.0
PRK06266	178	transcription initiation factor E subunit alpha; V	85.95
PRK07418	616	acetolactate synthase 3 catalytic subunit; Reviewe	85.9
PF09567	314	RE_MamI: MamI restriction endonuclease; InterPro:	85.79
PF01396	39	zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc	85.73
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	85.69
PF09986	214	DUF2225: Uncharacterized protein conserved in bact	85.66
PRK08270	656	anaerobic ribonucleoside triphosphate reductase; P	85.58
PRK08271	623	anaerobic ribonucleoside triphosphate reductase; P	85.35
PRK07219	822	DNA topoisomerase I; Validated	85.28
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	85.16
PF06044	254	DRP: Dam-replacing family; InterPro: IPR010324 Dam	85.15
PRK06260	397	threonine synthase; Validated	85.13
PRK11595	227	DNA utilization protein GntX; Provisional	85.06
PF13597	546	NRDD: Anaerobic ribonucleoside-triphosphate reduct	85.04
COG0068	750	HypF Hydrogenase maturation factor [Posttranslatio	84.95
COG4640	465	Predicted membrane protein [Function unknown]	84.8
COG0777	294	AccD Acetyl-CoA carboxylase beta subunit [Lipid me	84.35
PRK11032	160	hypothetical protein; Provisional	84.34
PRK10445	263	endonuclease VIII; Provisional	84.28
PRK14810	272	formamidopyrimidine-DNA glycosylase; Provisional	84.08
PRK03922	113	hypothetical protein; Provisional	84.06
PRK01103	274	formamidopyrimidine/5-formyluracil/ 5-hydroxymethy	83.77
PF14353	128	CpXC: CpXC protein	83.75
PF06221	57	zf-C2HC5: Putative zinc finger motif, C2HC5-type;	83.7
COG1592	166	Rubrerythrin [Energy production and conversion]	83.66
TIGR00577	272	fpg formamidopyrimidine-DNA glycosylase (fpg). All	83.46
cd01675	555	RNR_III Class III ribonucleotide reductase. Ribonu	83.2
COG1545	140	Predicted nucleic-acid-binding protein containing	83.18
PRK03988	138	translation initiation factor IF-2 subunit beta; V	83.06
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	83.04
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	83.0
TIGR00311	133	aIF-2beta translation initiation factor aIF-2, bet	82.86
PF04475	102	DUF555: Protein of unknown function (DUF555); Inte	82.84
COG1997	89	RPL43A Ribosomal protein L37AE/L43A [Translation,	82.66
COG4391	62	Uncharacterized protein conserved in bacteria [Fun	82.6
smart00653	110	eIF2B_5 domain present in translation initiation f	82.44
COG1885	115	Uncharacterized protein conserved in archaea [Func	82.36
TIGR00155	403	pqiA_fam integral membrane protein, PqiA family. T	82.31
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	82.21
PRK14811	269	formamidopyrimidine-DNA glycosylase; Provisional	82.02
TIGR00354	1095	polC DNA polymerase, archaeal type II, large subun	81.97
COG2816	279	NPY1 NTP pyrophosphohydrolases containing a Zn-fin	81.97
PF09986	214	DUF2225: Uncharacterized protein conserved in bact	81.95
TIGR00155	403	pqiA_fam integral membrane protein, PqiA family. T	81.89
PF14569	80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	81.73
PF01363	69	FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc f	81.61
PRK09678	72	DNA-binding transcriptional regulator; Provisional	81.6
PRK00481	242	NAD-dependent deacetylase; Provisional	81.59
PRK07591	421	threonine synthase; Validated	81.52
TIGR02487	579	NrdD anaerobic ribonucleoside-triphosphate reducta	81.32
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	81.09
PF07295	146	DUF1451: Protein of unknown function (DUF1451); In	81.06
PRK09710	64	lar restriction alleviation and modification prote	81.05
TIGR00310	192	ZPR1_znf ZPR1 zinc finger domain.	80.75
COG2995	418	PqiA Uncharacterized paraquat-inducible protein A	80.72
COG0333	57	RpmF Ribosomal protein L32 [Translation, ribosomal	80.56
PF09334	391	tRNA-synt_1g: tRNA synthetases class I (M); InterP	80.55
PF04502	324	DUF572: Family of unknown function (DUF572) ; Inte	80.47
PF13005	47	zf-IS66: zinc-finger binding domain of transposase	80.32
PF04606	47	Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I	80.19
PRK11827	60	hypothetical protein; Provisional	80.06

>PF12773 DZR: Double zinc ribbon

Probab=99.23  E-value=7.3e-12  Score=71.41  Aligned_cols=42  Identities=31%  Similarity=0.755  Sum_probs=34.8

Q ss_pred             CCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCC
Q 033949           53 KEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCG  104 (107)
Q Consensus        53 ~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG  104 (107)
                      .....+|++||..+.....          ....|++||++++.+++||++||
T Consensus         9 ~~~~~fC~~CG~~l~~~~~----------~~~~C~~Cg~~~~~~~~fC~~CG   50 (50)
T PF12773_consen    9 PDDAKFCPHCGTPLPPPDQ----------SKKICPNCGAENPPNAKFCPNCG   50 (50)
T ss_pred             CccccCChhhcCChhhccC----------CCCCCcCCcCCCcCCcCccCccc
Confidence            3579999999999872111          25789999999999999999998

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=99.11  E-value=2.5e-11  Score=60.84  Aligned_cols=24  Identities=42%  Similarity=1.032  Sum_probs=22.8

Q ss_pred             cccccCCceecCCCccCcCCCCCC
Q 033949           84 SKCRFCDRLVEPDFSFCPYCGSAL  107 (107)
Q Consensus        84 ~~C~~CG~~i~~~~~fCP~CG~~l  107 (107)
                      +.||+||++++++++|||+||++|
T Consensus         3 ~~Cp~Cg~~~~~~~~fC~~CG~~L   26 (26)
T PF13248_consen    3 MFCPNCGAEIDPDAKFCPNCGAKL   26 (26)
T ss_pred             CCCcccCCcCCcccccChhhCCCC
Confidence            579999999999999999999987

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=99.08  E-value=3.9e-11  Score=58.50  Aligned_cols=23  Identities=43%  Similarity=1.024  Sum_probs=21.8

Q ss_pred             ccccCCceecCCCccCcCCCCCC
Q 033949           85 KCRFCDRLVEPDFSFCPYCGSAL  107 (107)
Q Consensus        85 ~C~~CG~~i~~~~~fCP~CG~~l  107 (107)
                      +||+||++|+.+++|||+||++|
T Consensus         1 ~Cp~CG~~~~~~~~fC~~CG~~l   23 (23)
T PF13240_consen    1 YCPNCGAEIEDDAKFCPNCGTPL   23 (23)
T ss_pred             CCcccCCCCCCcCcchhhhCCcC
Confidence            49999999999999999999986

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=98.95  E-value=4.6e-10  Score=92.56  Aligned_cols=50  Identities=26%  Similarity=0.602  Sum_probs=42.9

Q ss_pred             EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCc
Q 033949           22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCP  101 (107)
Q Consensus        22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP  101 (107)
                      .+||+||...                     .....+|+.||..+.               ...||+||++++.+++|||
T Consensus         2 ~~Cp~Cg~~n---------------------~~~akFC~~CG~~l~---------------~~~Cp~CG~~~~~~~~fC~   45 (645)
T PRK14559          2 LICPQCQFEN---------------------PNNNRFCQKCGTSLT---------------HKPCPQCGTEVPVDEAHCP   45 (645)
T ss_pred             CcCCCCCCcC---------------------CCCCccccccCCCCC---------------CCcCCCCCCCCCccccccc
Confidence            4799999943                     347999999999973               2479999999999999999


Q ss_pred             CCCCCC
Q 033949          102 YCGSAL  107 (107)
Q Consensus       102 ~CG~~l  107 (107)
                      +||+++
T Consensus        46 ~CG~~~   51 (645)
T PRK14559         46 NCGAET   51 (645)
T ss_pred             ccCCcc
Confidence            999875

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=98.61  E-value=3.7e-08  Score=85.44  Aligned_cols=51  Identities=33%  Similarity=0.671  Sum_probs=41.2

Q ss_pred             CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCC---
Q 033949           20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPD---   96 (107)
Q Consensus        20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~---   96 (107)
                      ...+||+||...                       +..+||.||+..+.              .+.||+||++++++   
T Consensus       666 ~~rkCPkCG~~t-----------------------~~~fCP~CGs~te~--------------vy~CPsCGaev~~des~  708 (1337)
T PRK14714        666 GRRRCPSCGTET-----------------------YENRCPDCGTHTEP--------------VYVCPDCGAEVPPDESG  708 (1337)
T ss_pred             EEEECCCCCCcc-----------------------ccccCcccCCcCCC--------------ceeCccCCCccCCCccc
Confidence            357899999942                       33499999999743              35899999999876   


Q ss_pred             CccCcCCCCCC
Q 033949           97 FSFCPYCGSAL  107 (107)
Q Consensus        97 ~~fCP~CG~~l  107 (107)
                      +.+||+||+++
T Consensus       709 a~~CP~CGtpl  719 (1337)
T PRK14714        709 RVECPRCDVEL  719 (1337)
T ss_pred             cccCCCCCCcc
Confidence            88999999875

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=98.47  E-value=7.4e-08  Score=48.15  Aligned_cols=23  Identities=35%  Similarity=0.805  Sum_probs=21.1

Q ss_pred             cccccCCceecCCCccCcCCCCC
Q 033949           84 SKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        84 ~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      +.||+|+++|+.++++||.||..
T Consensus         1 K~CP~C~~~V~~~~~~Cp~CG~~   23 (26)
T PF10571_consen    1 KTCPECGAEVPESAKFCPHCGYD   23 (26)
T ss_pred             CcCCCCcCCchhhcCcCCCCCCC
Confidence            46999999999999999999975

Several members are annotated as putative helicases.

>PF12773 DZR: Double zinc ribbon

Probab=98.26  E-value=7.5e-07  Score=50.46  Aligned_cols=36  Identities=25%  Similarity=0.698  Sum_probs=29.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCccCccccccCCceec---CCCccCcCCCCCC
Q 033949           59 CNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE---PDFSFCPYCGSAL  107 (107)
Q Consensus        59 C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~---~~~~fCP~CG~~l  107 (107)
                      ||+||+.++.+             ...|++||+.+.   ....+||.||+.+
T Consensus         1 Cp~Cg~~~~~~-------------~~fC~~CG~~l~~~~~~~~~C~~Cg~~~   39 (50)
T PF12773_consen    1 CPHCGTPNPDD-------------AKFCPHCGTPLPPPDQSKKICPNCGAEN   39 (50)
T ss_pred             CCCcCCcCCcc-------------ccCChhhcCChhhccCCCCCCcCCcCCC
Confidence            78999997653             368999999998   3578999999864

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=97.85  E-value=7.2e-06  Score=40.77  Aligned_cols=25  Identities=24%  Similarity=0.646  Sum_probs=16.4

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV   93 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i   93 (107)
                      .+.||+||+.++.+             .+.|++||+.+
T Consensus         2 ~~~Cp~Cg~~~~~~-------------~~fC~~CG~~L   26 (26)
T PF13248_consen    2 EMFCPNCGAEIDPD-------------AKFCPNCGAKL   26 (26)
T ss_pred             cCCCcccCCcCCcc-------------cccChhhCCCC
Confidence            35688888865432             35788888764

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=97.82  E-value=8.7e-06  Score=39.45  Aligned_cols=23  Identities=22%  Similarity=0.641  Sum_probs=15.6

Q ss_pred             eCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949           58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV   93 (107)
Q Consensus        58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i   93 (107)
                      +||+||+.++.+             .+.|++||++|
T Consensus         1 ~Cp~CG~~~~~~-------------~~fC~~CG~~l   23 (23)
T PF13240_consen    1 YCPNCGAEIEDD-------------AKFCPNCGTPL   23 (23)
T ss_pred             CCcccCCCCCCc-------------CcchhhhCCcC
Confidence            477888877542             35688888764

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=97.77  E-value=9.9e-06  Score=45.32  Aligned_cols=23  Identities=48%  Similarity=0.873  Sum_probs=11.2

Q ss_pred             cccccCCceecC----CCccCcCCCCC
Q 033949           84 SKCRFCDRLVEP----DFSFCPYCGSA  106 (107)
Q Consensus        84 ~~C~~CG~~i~~----~~~fCP~CG~~  106 (107)
                      ++|++||++++.    ....||+||++
T Consensus         4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~   30 (46)
T PRK00398          4 YKCARCGREVELDEYGTGVRCPYCGYR   30 (46)
T ss_pred             EECCCCCCEEEECCCCCceECCCCCCe
Confidence            445555555422    23455555554

>PRK04023 DNA polymerase II large subunit; Validated

Probab=97.57  E-value=7.4e-05  Score=64.36  Aligned_cols=50  Identities=28%  Similarity=0.539  Sum_probs=37.6

Q ss_pred             CCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCc
Q 033949           19 SGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFS   98 (107)
Q Consensus        19 ~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~   98 (107)
                      .....||.||..                       .....||+||+.-+              ..+.||.||.....  .
T Consensus       624 Vg~RfCpsCG~~-----------------------t~~frCP~CG~~Te--------------~i~fCP~CG~~~~~--y  664 (1121)
T PRK04023        624 IGRRKCPSCGKE-----------------------TFYRRCPFCGTHTE--------------PVYRCPRCGIEVEE--D  664 (1121)
T ss_pred             ccCccCCCCCCc-----------------------CCcccCCCCCCCCC--------------cceeCccccCcCCC--C
Confidence            345679999994                       15578999999832              24689999998654  5


Q ss_pred             cCcCCCCCC
Q 033949           99 FCPYCGSAL  107 (107)
Q Consensus        99 fCP~CG~~l  107 (107)
                      .||+||.++
T Consensus       665 ~CPKCG~El  673 (1121)
T PRK04023        665 ECEKCGREP  673 (1121)
T ss_pred             cCCCCCCCC
Confidence            599999864

>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus

Probab=97.50  E-value=2.2e-05  Score=66.42  Aligned_cols=49  Identities=35%  Similarity=0.647  Sum_probs=0.0

Q ss_pred             CCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCc
Q 033949           19 SGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFS   98 (107)
Q Consensus        19 ~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~   98 (107)
                      .....||.||..                       ++...||.||+.-+.              .+.||.||.++..+  
T Consensus       653 i~~r~Cp~Cg~~-----------------------t~~~~Cp~CG~~T~~--------------~~~Cp~C~~~~~~~--  693 (900)
T PF03833_consen  653 IGRRRCPKCGKE-----------------------TFYNRCPECGSHTEP--------------VYVCPDCGIEVEED--  693 (900)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             eecccCcccCCc-----------------------chhhcCcccCCcccc--------------ceeccccccccCcc--
Confidence            345679999993                       367889999998643              57899999998877  


Q ss_pred             cCcCCCCC
Q 033949           99 FCPYCGSA  106 (107)
Q Consensus        99 fCP~CG~~  106 (107)
                      .||.||.+
T Consensus       694 ~C~~C~~~  701 (900)
T PF03833_consen  694 ECPKCGRE  701 (900)
T ss_dssp             --------
T ss_pred             cccccccc
Confidence            99999975

The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=97.40  E-value=0.00012  Score=60.95  Aligned_cols=36  Identities=28%  Similarity=0.768  Sum_probs=28.1

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCCC
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL  107 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~l  107 (107)
                      +.||.||+....+             .+.|++||+.+..  +.||.||+.+
T Consensus         2 ~~Cp~Cg~~n~~~-------------akFC~~CG~~l~~--~~Cp~CG~~~   37 (645)
T PRK14559          2 LICPQCQFENPNN-------------NRFCQKCGTSLTH--KPCPQCGTEV   37 (645)
T ss_pred             CcCCCCCCcCCCC-------------CccccccCCCCCC--CcCCCCCCCC
Confidence            5799999987543             3689999998753  6899999864

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

Probab=97.37  E-value=0.00024  Score=59.92  Aligned_cols=50  Identities=26%  Similarity=0.591  Sum_probs=30.8

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCC
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      .+.|..||+..+-.+-...+..+.......|+.||.. ..-...||.||+.
T Consensus       435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~-~~~p~~Cp~Cgs~  484 (730)
T COG1198         435 LLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQ-EPIPQSCPECGSE  484 (730)
T ss_pred             eeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCC-CCCCCCCCCCCCC
Confidence            3445555544433322222222222346789999999 8889999999986

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=97.33  E-value=0.00015  Score=42.72  Aligned_cols=10  Identities=30%  Similarity=0.770  Sum_probs=5.0

Q ss_pred             ceeCCCCCCC
Q 033949           56 ALFCNNCNLL   65 (107)
Q Consensus        56 ~~~C~~CG~~   65 (107)
                      .-.||+||+.
T Consensus        27 ~F~CPnCGe~   36 (61)
T COG2888          27 KFPCPNCGEV   36 (61)
T ss_pred             EeeCCCCCce
Confidence            3345555543

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=97.30  E-value=0.00025  Score=41.79  Aligned_cols=10  Identities=30%  Similarity=0.962  Sum_probs=5.8

Q ss_pred             ceeCCCCCCC
Q 033949           56 ALFCNNCNLL   65 (107)
Q Consensus        56 ~~~C~~CG~~   65 (107)
                      .-.||+||+.
T Consensus        25 ~F~CPnCG~~   34 (59)
T PRK14890         25 KFLCPNCGEV   34 (59)
T ss_pred             EeeCCCCCCe
Confidence            4456666654

>PRK14873 primosome assembly protein PriA; Provisional

Probab=97.14  E-value=0.00043  Score=57.86  Aligned_cols=23  Identities=39%  Similarity=0.924  Sum_probs=19.0

Q ss_pred             CccccccCCceecCCCccCcCCCCC
Q 033949           82 DVSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        82 ~~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      ....|+.||...  ....||+||+.
T Consensus       409 ~~l~Ch~CG~~~--~p~~Cp~Cgs~  431 (665)
T PRK14873        409 GTPRCRWCGRAA--PDWRCPRCGSD  431 (665)
T ss_pred             CeeECCCCcCCC--cCccCCCCcCC
Confidence            357899999974  37899999985

>TIGR00595 priA primosomal protein N'

Probab=97.13  E-value=0.00058  Score=55.31  Aligned_cols=50  Identities=24%  Similarity=0.520  Sum_probs=32.0

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCC
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      .+.|..||+...-.+-..++..+.......|+.||.. .+-...||.||+.
T Consensus       213 ~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~-~~~~~~Cp~C~s~  262 (505)
T TIGR00595       213 NLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQ-EPIPKTCPQCGSE  262 (505)
T ss_pred             eeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCc-CCCCCCCCCCCCC
Confidence            5667777776644333333333333346789999988 4445799999985

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

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=97.06  E-value=0.00027  Score=39.38  Aligned_cols=26  Identities=27%  Similarity=0.584  Sum_probs=13.6

Q ss_pred             eCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949           58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV   93 (107)
Q Consensus        58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i   93 (107)
                      .|..||..++++..          ....||+||..|
T Consensus         4 ~C~~Cg~~~~~~~~----------~~irC~~CG~rI   29 (44)
T smart00659        4 ICGECGRENEIKSK----------DVVRCRECGYRI   29 (44)
T ss_pred             ECCCCCCEeecCCC----------CceECCCCCceE
Confidence            46666666555321          134566666555

present in RNA polymerase I, II and III

>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Probab=96.88  E-value=0.00058  Score=35.57  Aligned_cols=10  Identities=20%  Similarity=0.607  Sum_probs=4.6

Q ss_pred             CCCCCCCCCC
Q 033949           59 CNNCNLLFPS   68 (107)
Q Consensus        59 C~~CG~~~~~   68 (107)
                      |..||+..++
T Consensus         3 C~~Cg~~~~~   12 (32)
T PF03604_consen    3 CGECGAEVEL   12 (32)
T ss_dssp             ESSSSSSE-B
T ss_pred             CCcCCCeeEc
Confidence            4555555543

Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=96.76  E-value=0.00048  Score=36.70  Aligned_cols=34  Identities=18%  Similarity=0.351  Sum_probs=17.5

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE   94 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~   94 (107)
                      +.||+||+.+.++.+.....    .....|++||+.+.
T Consensus         3 ~~CP~C~~~~~v~~~~~~~~----~~~v~C~~C~~~~~   36 (38)
T TIGR02098         3 IQCPNCKTSFRVVDSQLGAN----GGKVRCGKCGHVWY   36 (38)
T ss_pred             EECCCCCCEEEeCHHHcCCC----CCEEECCCCCCEEE
Confidence            46777777666544321000    01356777776654

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=96.75  E-value=0.00088  Score=33.28  Aligned_cols=10  Identities=30%  Similarity=0.830  Sum_probs=5.0

Q ss_pred             eCCCCCCCCC
Q 033949           58 FCNNCNLLFP   67 (107)
Q Consensus        58 ~C~~CG~~~~   67 (107)
                      .||.|++.+.
T Consensus         2 ~CP~C~~~V~   11 (26)
T PF10571_consen    2 TCPECGAEVP   11 (26)
T ss_pred             cCCCCcCCch
Confidence            3555555543

Several members are annotated as putative helicases.

>PRK05580 primosome assembly protein PriA; Validated

Probab=96.70  E-value=0.002  Score=53.89  Aligned_cols=50  Identities=20%  Similarity=0.398  Sum_probs=29.3

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCC
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      ++.|..||+...-.+-..++..+.......|+.||.... -...||.||+.
T Consensus       381 ~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~-~~~~Cp~Cg~~  430 (679)
T PRK05580        381 FLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEP-IPKACPECGST  430 (679)
T ss_pred             ceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCC-CCCCCCCCcCC
Confidence            555666666553322222222222224678999998844 44679999975

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=96.57  E-value=0.0017  Score=57.42  Aligned_cols=36  Identities=28%  Similarity=0.705  Sum_probs=28.1

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCCC
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL  107 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~l  107 (107)
                      ...||.||+...               ...||+||+.+.+.+ .||.||.++
T Consensus       667 ~rkCPkCG~~t~---------------~~fCP~CGs~te~vy-~CPsCGaev  702 (1337)
T PRK14714        667 RRRCPSCGTETY---------------ENRCPDCGTHTEPVY-VCPDCGAEV  702 (1337)
T ss_pred             EEECCCCCCccc---------------cccCcccCCcCCCce-eCccCCCcc
Confidence            368999999642               247999999987655 899999853

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=96.56  E-value=0.0016  Score=36.22  Aligned_cols=13  Identities=15%  Similarity=0.358  Sum_probs=8.3

Q ss_pred             ceeCCCCCCCCCC
Q 033949           56 ALFCNNCNLLFPS   68 (107)
Q Consensus        56 ~~~C~~CG~~~~~   68 (107)
                      .+.||.||+.+..
T Consensus        21 ~~~Cp~CG~~~~~   33 (46)
T PRK00398         21 GVRCPYCGYRILF   33 (46)
T ss_pred             ceECCCCCCeEEE
Confidence            5677777766544

>PRK04023 DNA polymerase II large subunit; Validated

Probab=96.52  E-value=0.0018  Score=56.16  Aligned_cols=36  Identities=25%  Similarity=0.562  Sum_probs=29.2

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCC
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      ...+|+.||....               ...||+||+. .....+||.||..
T Consensus       625 g~RfCpsCG~~t~---------------~frCP~CG~~-Te~i~fCP~CG~~  660 (1121)
T PRK04023        625 GRRKCPSCGKETF---------------YRRCPFCGTH-TEPVYRCPRCGIE  660 (1121)
T ss_pred             cCccCCCCCCcCC---------------cccCCCCCCC-CCcceeCccccCc
Confidence            4568999999851               3689999999 5677899999975

>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown

Probab=96.51  E-value=0.00035  Score=41.30  Aligned_cols=23  Identities=39%  Similarity=1.003  Sum_probs=19.7

Q ss_pred             ccccccCCceecCCCccC-cCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFC-PYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fC-P~CG~  105 (107)
                      .++|++||++|+++-.|| +.|++
T Consensus         3 HkHC~~CG~~Ip~~~~fCS~~C~~   26 (59)
T PF09889_consen    3 HKHCPVCGKPIPPDESFCSPKCRE   26 (59)
T ss_pred             CCcCCcCCCcCCcchhhhCHHHHH
Confidence            368999999999999999 57764

They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length

Probab=96.41  E-value=0.0005  Score=41.93  Aligned_cols=27  Identities=19%  Similarity=0.454  Sum_probs=13.9

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      ....|..|+..+..              ...||.||.+++.
T Consensus        16 ~~~~C~~C~~~~~~--------------~a~CPdC~~~Le~   42 (70)
T PF07191_consen   16 GHYHCEACQKDYKK--------------EAFCPDCGQPLEV   42 (70)
T ss_dssp             TEEEETTT--EEEE--------------EEE-TTT-SB-EE
T ss_pred             CEEECcccccccee--------------cccCCCcccHHHH
Confidence            56777777776643              3467777776654

Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=96.40  E-value=0.0027  Score=33.73  Aligned_cols=35  Identities=20%  Similarity=0.368  Sum_probs=22.7

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP   67 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~   67 (107)
                      .+.||+|+..+.            ||-=+....+..+.|++||+.+.
T Consensus         2 ~~~CP~C~~~~~------------v~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         2 RIQCPNCKTSFR------------VVDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             EEECCCCCCEEE------------eCHHHcCCCCCEEECCCCCCEEE
Confidence            368999999542            22222223345799999998763

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=96.39  E-value=0.0018  Score=34.41  Aligned_cols=32  Identities=22%  Similarity=0.586  Sum_probs=20.6

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      +.||+|++.|+++++..+-.    ....+|++||..
T Consensus         3 i~Cp~C~~~y~i~d~~ip~~----g~~v~C~~C~~~   34 (36)
T PF13717_consen    3 ITCPNCQAKYEIDDEKIPPK----GRKVRCSKCGHV   34 (36)
T ss_pred             EECCCCCCEEeCCHHHCCCC----CcEEECCCCCCE
Confidence            57888888887766533211    125678888865

>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]

Probab=96.34  E-value=0.0013  Score=37.39  Aligned_cols=10  Identities=20%  Similarity=0.491  Sum_probs=4.9

Q ss_pred             eCCCCCCCCC
Q 033949           58 FCNNCNLLFP   67 (107)
Q Consensus        58 ~C~~CG~~~~   67 (107)
                      .|..||..++
T Consensus         8 ~C~~Cg~~~~   17 (49)
T COG1996           8 KCARCGREVE   17 (49)
T ss_pred             EhhhcCCeee
Confidence            3555555543

>TIGR00595 priA primosomal protein N'

Probab=96.32  E-value=0.004  Score=50.46  Aligned_cols=29  Identities=28%  Similarity=0.563  Sum_probs=22.7

Q ss_pred             cCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           50 WPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        50 ~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      ++++...+.|.+||...++.              ..||+||..
T Consensus       234 ~h~~~~~l~Ch~Cg~~~~~~--------------~~Cp~C~s~  262 (505)
T TIGR00595       234 YHKKEGKLRCHYCGYQEPIP--------------KTCPQCGSE  262 (505)
T ss_pred             EecCCCeEEcCCCcCcCCCC--------------CCCCCCCCC
Confidence            34456799999999998653              379999985

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

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=96.32  E-value=0.004  Score=36.72  Aligned_cols=41  Identities=20%  Similarity=0.455  Sum_probs=28.0

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce-ecC--------CCccCcCCCC
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL-VEP--------DFSFCPYCGS  105 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~-i~~--------~~~fCP~CG~  105 (107)
                      ...|++||..+...+..         ....|||||++ |..        +.-.||+||-
T Consensus         7 ~~~CtSCg~~i~~~~~~---------~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF   56 (59)
T PRK14890          7 PPKCTSCGIEIAPREKA---------VKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGF   56 (59)
T ss_pred             CccccCCCCcccCCCcc---------CEeeCCCCCCeeEeechhHHhcCCceECCCCCC
Confidence            45799999988543311         24679999998 432        5667999984

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=96.18  E-value=0.0026  Score=33.95  Aligned_cols=33  Identities=21%  Similarity=0.500  Sum_probs=17.1

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV   93 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i   93 (107)
                      +.||+|++.+.++.+..+..    ....+|++||...
T Consensus         3 i~CP~C~~~f~v~~~~l~~~----~~~vrC~~C~~~f   35 (37)
T PF13719_consen    3 ITCPNCQTRFRVPDDKLPAG----GRKVRCPKCGHVF   35 (37)
T ss_pred             EECCCCCceEEcCHHHcccC----CcEEECCCCCcEe
Confidence            45777777766655421100    0245677776543

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

Probab=96.13  E-value=0.0064  Score=51.48  Aligned_cols=29  Identities=21%  Similarity=0.387  Sum_probs=23.0

Q ss_pred             cCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           50 WPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        50 ~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      +++....+.|.+||+...+              ...||+||.+
T Consensus       456 ~H~~~~~L~CH~Cg~~~~~--------------p~~Cp~Cgs~  484 (730)
T COG1198         456 LHKATGQLRCHYCGYQEPI--------------PQSCPECGSE  484 (730)
T ss_pred             EecCCCeeEeCCCCCCCCC--------------CCCCCCCCCC
Confidence            4445689999999999654              2479999998

>PRK00420 hypothetical protein; Validated

Probab=95.99  E-value=0.0037  Score=41.44  Aligned_cols=24  Identities=21%  Similarity=0.466  Sum_probs=14.9

Q ss_pred             ccccccCCceec---CCCccCcCCCCC
Q 033949           83 VSKCRFCDRLVE---PDFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~---~~~~fCP~CG~~  106 (107)
                      ..+||.||+++-   .+..+||.||+.
T Consensus        23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~   49 (112)
T PRK00420         23 SKHCPVCGLPLFELKDGEVVCPVHGKV   49 (112)
T ss_pred             cCCCCCCCCcceecCCCceECCCCCCe
Confidence            356777776654   366677777654

>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]

Probab=95.98  E-value=0.0036  Score=37.32  Aligned_cols=23  Identities=43%  Similarity=1.058  Sum_probs=16.7

Q ss_pred             cccccCCceecCCCccCcCCCCC
Q 033949           84 SKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        84 ~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      +-|.+|+..++.+.+.||.||+.
T Consensus         5 kAC~~Ck~l~~~d~e~CP~Cgs~   27 (64)
T COG2093           5 KACKNCKRLTPEDTEICPVCGST   27 (64)
T ss_pred             HHHhhccccCCCCCccCCCCCCc
Confidence            45777777777777777777764

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length

Probab=95.96  E-value=0.0011  Score=40.35  Aligned_cols=39  Identities=26%  Similarity=0.582  Sum_probs=21.7

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCCC
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL  107 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~l  107 (107)
                      +.||.|+..++...           ..++|..|+..... -.+||.||++|
T Consensus         2 ~~CP~C~~~L~~~~-----------~~~~C~~C~~~~~~-~a~CPdC~~~L   40 (70)
T PF07191_consen    2 NTCPKCQQELEWQG-----------GHYHCEACQKDYKK-EAFCPDCGQPL   40 (70)
T ss_dssp             -B-SSS-SBEEEET-----------TEEEETTT--EEEE-EEE-TTT-SB-
T ss_pred             CcCCCCCCccEEeC-----------CEEECcccccccee-cccCCCcccHH
Confidence            46888888865533           25789999887554 34799998876

Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.

>PRK12496 hypothetical protein; Provisional

Probab=95.96  E-value=0.0039  Score=43.70  Aligned_cols=24  Identities=25%  Similarity=0.639  Sum_probs=17.7

Q ss_pred             cccccCCceecC--CCccCcCCCCCC
Q 033949           84 SKCRFCDRLVEP--DFSFCPYCGSAL  107 (107)
Q Consensus        84 ~~C~~CG~~i~~--~~~fCP~CG~~l  107 (107)
                      +.|+.||...+.  ...+||-||++|
T Consensus       128 ~~C~gC~~~~~~~~~~~~C~~CG~~~  153 (164)
T PRK12496        128 KVCKGCKKKYPEDYPDDVCEICGSPV  153 (164)
T ss_pred             EECCCCCccccCCCCCCcCCCCCChh
Confidence            568888888764  446788888875

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=95.95  E-value=0.008  Score=35.50  Aligned_cols=42  Identities=19%  Similarity=0.383  Sum_probs=29.2

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC---------CCccCcCCCC
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP---------DFSFCPYCGS  105 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~---------~~~fCP~CG~  105 (107)
                      +...|++||..+.+.+.-         ....|||||+++..         +--.||+||-
T Consensus         8 ~~~~CtSCg~~i~p~e~~---------v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF   58 (61)
T COG2888           8 DPPVCTSCGREIAPGETA---------VKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGF   58 (61)
T ss_pred             CCceeccCCCEeccCCce---------eEeeCCCCCceeeehhhhHHHcCCceECCCcCc
Confidence            356899999998664421         24679999954433         5667999984

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=95.92  E-value=0.0033  Score=33.62  Aligned_cols=33  Identities=18%  Similarity=0.353  Sum_probs=16.0

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV   93 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i   93 (107)
                      |...|+.||+.++......+      .....||+||+++
T Consensus         4 Y~y~C~~Cg~~fe~~~~~~~------~~~~~CP~Cg~~~   36 (41)
T smart00834        4 YEYRCEDCGHTFEVLQKISD------DPLATCPECGGDV   36 (41)
T ss_pred             EEEEcCCCCCEEEEEEecCC------CCCCCCCCCCCcc
Confidence            34466666666654221110      0134577777654

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=95.90  E-value=0.0034  Score=34.39  Aligned_cols=16  Identities=31%  Similarity=0.789  Sum_probs=9.8

Q ss_pred             CCCceeCCCCCCCCCC
Q 033949           53 KEPALFCNNCNLLFPS   68 (107)
Q Consensus        53 ~~~~~~C~~CG~~~~~   68 (107)
                      ....+.|+.||..++.
T Consensus        16 ~~g~~vC~~CG~Vl~e   31 (43)
T PF08271_consen   16 ERGELVCPNCGLVLEE   31 (43)
T ss_dssp             TTTEEEETTT-BBEE-
T ss_pred             CCCeEECCCCCCEeec
Confidence            3467788888877654

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.

>PF15616 TerY-C: TerY-C metal binding domain

Probab=95.84  E-value=0.0068  Score=41.20  Aligned_cols=31  Identities=19%  Similarity=0.368  Sum_probs=23.0

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCC
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPD   96 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~   96 (107)
                      .++.| .||..+-++.+          ....||.||.....+
T Consensus        88 ~fa~C-~CGkl~Ci~g~----------~~~~CPwCg~~g~~~  118 (131)
T PF15616_consen   88 AFAVC-GCGKLFCIDGE----------GEVTCPWCGNEGSFG  118 (131)
T ss_pred             cEEEe-cCCCEEEeCCC----------CCEECCCCCCeeeec
Confidence            56777 79999876553          257899999987654

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=95.82  E-value=0.0069  Score=32.36  Aligned_cols=25  Identities=28%  Similarity=0.743  Sum_probs=19.2

Q ss_pred             ccccccCCceecC-------CCccCcCCCCCC
Q 033949           83 VSKCRFCDRLVEP-------DFSFCPYCGSAL  107 (107)
Q Consensus        83 ~~~C~~CG~~i~~-------~~~fCP~CG~~l  107 (107)
                      .+.|++||...+.       ....||.||.++
T Consensus         5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~   36 (41)
T smart00834        5 EYRCEDCGHTFEVLQKISDDPLATCPECGGDV   36 (41)
T ss_pred             EEEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence            4789999996643       456899999853

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins

Probab=95.79  E-value=0.0091  Score=35.55  Aligned_cols=42  Identities=17%  Similarity=0.223  Sum_probs=25.5

Q ss_pred             eeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCC
Q 033949           46 PVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPD   96 (107)
Q Consensus        46 P~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~   96 (107)
                      +++..+.......||.||...+....         .....|++||...+.|
T Consensus        18 ~v~~v~~~~TSq~C~~CG~~~~~~~~---------~r~~~C~~Cg~~~~rD   59 (69)
T PF07282_consen   18 QVVEVDEAYTSQTCPRCGHRNKKRRS---------GRVFTCPNCGFEMDRD   59 (69)
T ss_pred             EEEEECCCCCccCccCcccccccccc---------cceEEcCCCCCEECcH
Confidence            34444554446678888887755111         1256788888887664

More information about these proteins can be found at Protein of the Month: Transposase [].

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=95.74  E-value=0.019  Score=36.87  Aligned_cols=15  Identities=13%  Similarity=0.366  Sum_probs=11.2

Q ss_pred             CCceeCCCCCCCCCC
Q 033949           54 EPALFCNNCNLLFPS   68 (107)
Q Consensus        54 ~~~~~C~~CG~~~~~   68 (107)
                      +..+.|+.||...+.
T Consensus        14 ~~~~~C~~C~~~~~~   28 (104)
T TIGR01384        14 NGVYVCPSCGYEKEK   28 (104)
T ss_pred             CCeEECcCCCCcccc
Confidence            367888888877665

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed

Probab=95.74  E-value=0.0087  Score=34.97  Aligned_cols=12  Identities=17%  Similarity=0.490  Sum_probs=6.2

Q ss_pred             cccccCCceecC
Q 033949           84 SKCRFCDRLVEP   95 (107)
Q Consensus        84 ~~C~~CG~~i~~   95 (107)
                      ..||.||+.+..
T Consensus        18 ~~CP~CG~~t~~   29 (56)
T PRK13130         18 EICPVCGGKTKN   29 (56)
T ss_pred             ccCcCCCCCCCC
Confidence            346666655433

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=95.73  E-value=0.0081  Score=32.01  Aligned_cols=35  Identities=31%  Similarity=0.539  Sum_probs=23.4

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP   67 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~   67 (107)
                      .++||+|+..+.            ||-=++..++..+.|+.|++.+.
T Consensus         2 ~i~CP~C~~~f~------------v~~~~l~~~~~~vrC~~C~~~f~   36 (37)
T PF13719_consen    2 IITCPNCQTRFR------------VPDDKLPAGGRKVRCPKCGHVFR   36 (37)
T ss_pred             EEECCCCCceEE------------cCHHHcccCCcEEECCCCCcEee
Confidence            468999999543            22122334456999999998763

>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues

Probab=95.71  E-value=0.0075  Score=39.70  Aligned_cols=31  Identities=26%  Similarity=0.787  Sum_probs=23.9

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCC
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSS   69 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~   69 (107)
                      ..+||+||.++                +-+++. + +.||+||+.+.+.
T Consensus         9 KR~Cp~CG~kF----------------YDLnk~-P-ivCP~CG~~~~~~   39 (108)
T PF09538_consen    9 KRTCPSCGAKF----------------YDLNKD-P-IVCPKCGTEFPPE   39 (108)
T ss_pred             cccCCCCcchh----------------ccCCCC-C-ccCCCCCCccCcc
Confidence            45799999965                345653 4 6799999999887

The function of members of this family is unknown.

>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins

Probab=95.69  E-value=0.0042  Score=41.11  Aligned_cols=12  Identities=25%  Similarity=0.454  Sum_probs=6.5

Q ss_pred             CceeCCCCCCCC
Q 033949           55 PALFCNNCNLLF   66 (107)
Q Consensus        55 ~~~~C~~CG~~~   66 (107)
                      ..+.||+||+..
T Consensus        68 v~V~CP~C~K~T   79 (114)
T PF11023_consen   68 VQVECPNCGKQT   79 (114)
T ss_pred             eeeECCCCCChH
Confidence            455555555554

; GO: 0005887 integral to plasma membrane

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=95.53  E-value=0.01  Score=32.92  Aligned_cols=12  Identities=17%  Similarity=0.595  Sum_probs=8.2

Q ss_pred             CceeCCCCCCCC
Q 033949           55 PALFCNNCNLLF   66 (107)
Q Consensus        55 ~~~~C~~CG~~~   66 (107)
                      +.+.||+||+.+
T Consensus        18 ~~irC~~CG~rI   29 (44)
T smart00659       18 DVVRCRECGYRI   29 (44)
T ss_pred             CceECCCCCceE
Confidence            567777777665

present in RNA polymerase I, II and III

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=95.45  E-value=0.027  Score=36.55  Aligned_cols=36  Identities=22%  Similarity=0.393  Sum_probs=26.0

Q ss_pred             CCCcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           18 KSGAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        18 ~~~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      ....+.||+||+ ++.               +++++....+.|++||..+..
T Consensus        18 lpt~f~CP~Cge~~v~---------------v~~~k~~~h~~C~~CG~y~~~   54 (99)
T PRK14892         18 LPKIFECPRCGKVSIS---------------VKIKKNIAIITCGNCGLYTEF   54 (99)
T ss_pred             CCcEeECCCCCCeEee---------------eecCCCcceEECCCCCCccCE
Confidence            356778999997 332               334444579999999998865

>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]

Probab=95.44  E-value=0.0077  Score=42.83  Aligned_cols=25  Identities=40%  Similarity=0.940  Sum_probs=21.4

Q ss_pred             ccccccCCceecCCCccCcCCCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGSAL  107 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~~l  107 (107)
                      .+.|..|+...+....+||.||+++
T Consensus       139 ~~rC~GC~~~f~~~~~~Cp~CG~~~  163 (177)
T COG1439         139 RLRCHGCKRIFPEPKDFCPICGSPL  163 (177)
T ss_pred             eEEEecCceecCCCCCcCCCCCCce
Confidence            5679999999888999999999874

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=95.40  E-value=0.0049  Score=40.88  Aligned_cols=31  Identities=23%  Similarity=0.464  Sum_probs=22.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcC
Q 033949           59 CNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPY  102 (107)
Q Consensus        59 C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~  102 (107)
                      ||.||..+.++.             ..|++||+.|...+..+..
T Consensus         1 CPvCg~~l~vt~-------------l~C~~C~t~i~G~F~l~~~   31 (113)
T PF09862_consen    1 CPVCGGELVVTR-------------LKCPSCGTEIEGEFELPWF   31 (113)
T ss_pred             CCCCCCceEEEE-------------EEcCCCCCEEEeeeccchh
Confidence            788888876543             6788888888877766654

>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species

Probab=95.37  E-value=0.0099  Score=28.97  Aligned_cols=24  Identities=17%  Similarity=0.375  Sum_probs=13.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCccCccccccCCc
Q 033949           59 CNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDR   91 (107)
Q Consensus        59 C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~   91 (107)
                      |.+||..+...+..         ..+.|||||.
T Consensus         1 C~sC~~~i~~r~~~---------v~f~CPnCG~   24 (24)
T PF07754_consen    1 CTSCGRPIAPREQA---------VPFPCPNCGF   24 (24)
T ss_pred             CccCCCcccCcccC---------ceEeCCCCCC
Confidence            56677766543211         2467888874

It is likely to bind zinc via its four well-conserved cysteine residues.

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=95.32  E-value=0.012  Score=31.16  Aligned_cols=34  Identities=26%  Similarity=0.576  Sum_probs=22.6

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCC
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLF   66 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~   66 (107)
                      .+.||+|+..+++-.            =++..++..+.|+.||+.+
T Consensus         2 ~i~Cp~C~~~y~i~d------------~~ip~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    2 IITCPNCQAKYEIDD------------EKIPPKGRKVRCSKCGHVF   35 (36)
T ss_pred             EEECCCCCCEEeCCH------------HHCCCCCcEEECCCCCCEe
Confidence            468999999543221            1233445689999999875

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=95.30  E-value=0.01  Score=39.18  Aligned_cols=24  Identities=25%  Similarity=0.519  Sum_probs=14.6

Q ss_pred             ccccccCCceecCCC---ccCcCCCCC
Q 033949           83 VSKCRFCDRLVEPDF---SFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~---~fCP~CG~~  106 (107)
                      ..+|++||...+...   ..||.||+.
T Consensus        70 ~~~C~~Cg~~~~~~~~~~~~CP~Cgs~   96 (114)
T PRK03681         70 ECWCETCQQYVTLLTQRVRRCPQCHGD   96 (114)
T ss_pred             EEEcccCCCeeecCCccCCcCcCcCCC
Confidence            456777777665532   337777753

>PRK05580 primosome assembly protein PriA; Validated

Probab=95.24  E-value=0.02  Score=48.04  Aligned_cols=28  Identities=21%  Similarity=0.444  Sum_probs=21.7

Q ss_pred             CCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949           52 AKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV   93 (107)
Q Consensus        52 ~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i   93 (107)
                      +....+.|..||......              ..||+||...
T Consensus       404 ~~~~~l~Ch~Cg~~~~~~--------------~~Cp~Cg~~~  431 (679)
T PRK05580        404 RFQRRLRCHHCGYQEPIP--------------KACPECGSTD  431 (679)
T ss_pred             CCCCeEECCCCcCCCCCC--------------CCCCCCcCCe
Confidence            445789999999987653              3799998863

>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center

Probab=95.23  E-value=0.016  Score=30.01  Aligned_cols=25  Identities=16%  Similarity=0.511  Sum_probs=15.4

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      ..|+.||..++....           ...||.||+.
T Consensus         2 ~~C~~CGy~y~~~~~-----------~~~CP~Cg~~   26 (33)
T cd00350           2 YVCPVCGYIYDGEEA-----------PWVCPVCGAP   26 (33)
T ss_pred             EECCCCCCEECCCcC-----------CCcCcCCCCc
Confidence            357777777655331           2467777764

The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=95.22  E-value=0.012  Score=38.84  Aligned_cols=23  Identities=30%  Similarity=0.632  Sum_probs=12.8

Q ss_pred             ccccccCCceecCCCc--cCcCCCC
Q 033949           83 VSKCRFCDRLVEPDFS--FCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~--fCP~CG~  105 (107)
                      ..+|++||.+.+....  .||.||+
T Consensus        70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs   94 (113)
T PRK12380         70 QAWCWDCSQVVEIHQHDAQCPHCHG   94 (113)
T ss_pred             EEEcccCCCEEecCCcCccCcCCCC
Confidence            4556666665554322  2777765

>PRK14873 primosome assembly protein PriA; Provisional

Probab=95.22  E-value=0.028  Score=47.25  Aligned_cols=40  Identities=20%  Similarity=0.434  Sum_probs=28.0

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      ...||+|+....                 ++++...+.|.+||... .              ...||+||..
T Consensus       392 ~~~C~~C~~~L~-----------------~h~~~~~l~Ch~CG~~~-~--------------p~~Cp~Cgs~  431 (665)
T PRK14873        392 PARCRHCTGPLG-----------------LPSAGGTPRCRWCGRAA-P--------------DWRCPRCGSD  431 (665)
T ss_pred             eeECCCCCCcee-----------------EecCCCeeECCCCcCCC-c--------------CccCCCCcCC
Confidence            456777777433                 33445789999999864 2              2479999986

>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase

Probab=95.11  E-value=0.019  Score=30.11  Aligned_cols=12  Identities=17%  Similarity=0.620  Sum_probs=7.3

Q ss_pred             eeCCCCCCCCCC
Q 033949           57 LFCNNCNLLFPS   68 (107)
Q Consensus        57 ~~C~~CG~~~~~   68 (107)
                      ..|+.||..++.
T Consensus         3 ~~C~~CG~i~~g   14 (34)
T cd00729           3 WVCPVCGYIHEG   14 (34)
T ss_pred             EECCCCCCEeEC
Confidence            456777766543

In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PRK02935 hypothetical protein; Provisional

Probab=95.02  E-value=0.011  Score=38.71  Aligned_cols=24  Identities=21%  Similarity=0.548  Sum_probs=11.5

Q ss_pred             cccccCCceecC--CCccCcCCCCCC
Q 033949           84 SKCRFCDRLVEP--DFSFCPYCGSAL  107 (107)
Q Consensus        84 ~~C~~CG~~i~~--~~~fCP~CG~~l  107 (107)
                      ..||+|++++.-  ....|.+|+++|
T Consensus        71 V~CP~C~K~TKmLGrvD~CM~C~~PL   96 (110)
T PRK02935         71 VICPSCEKPTKMLGRVDACMHCNQPL   96 (110)
T ss_pred             eECCCCCchhhhccceeecCcCCCcC
Confidence            345555554433  344555555543

>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Probab=95.01  E-value=0.014  Score=30.37  Aligned_cols=22  Identities=41%  Similarity=0.712  Sum_probs=12.7

Q ss_pred             ccccCCceecC---CCccCcCCCCC
Q 033949           85 KCRFCDRLVEP---DFSFCPYCGSA  106 (107)
Q Consensus        85 ~C~~CG~~i~~---~~~fCP~CG~~  106 (107)
                      .|..||++++.   +...||+||.+
T Consensus         2 ~C~~Cg~~~~~~~~~~irC~~CG~R   26 (32)
T PF03604_consen    2 ICGECGAEVELKPGDPIRCPECGHR   26 (32)
T ss_dssp             BESSSSSSE-BSTSSTSSBSSSS-S
T ss_pred             CCCcCCCeeEcCCCCcEECCcCCCe
Confidence            46667766654   45567777654

Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....

>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues

Probab=95.01  E-value=0.013  Score=35.44  Aligned_cols=49  Identities=20%  Similarity=0.399  Sum_probs=29.4

Q ss_pred             CCcEECCCCCC-CcEEEEEee-EE--------------EEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949           19 SGAGRCINCGS-TADLVEYEK-VL--------------KAFFVPVWKWPAKEPALFCNNCNLLFP   67 (107)
Q Consensus        19 ~~~~~C~~Cg~-~~~~~~~~~-~f--------------~lFFIP~~~~~~~~~~~~C~~CG~~~~   67 (107)
                      +..+.||+|++ ....+++.. +.              -++|||++==.-++-...||+|+..+.
T Consensus         5 p~~~~CP~C~~~~~T~v~~~~g~~t~~~~~~l~~~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg   69 (73)
T PF10601_consen    5 PVRIYCPYCQQQVQTRVEYKSGTMTYICAALLCLFGCWPCCCIPFCCDSCKDVYHYCPNCGAFLG   69 (73)
T ss_pred             ceeeECCCCCCEEEEEEEEEeChHHHHHHHHHHHHHHHHHhhHhhccccccCceEECCCCCCEeE
Confidence            45688999999 555555433 21              135666433333435777777777654

Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=95.00  E-value=0.016  Score=33.58  Aligned_cols=14  Identities=14%  Similarity=0.574  Sum_probs=6.7

Q ss_pred             CceeCCCCCCCCCC
Q 033949           55 PALFCNNCNLLFPS   68 (107)
Q Consensus        55 ~~~~C~~CG~~~~~   68 (107)
                      ..+.|+.||+.+++
T Consensus        21 eiV~Cp~CGaeleV   34 (54)
T TIGR01206        21 ELVICDECGAELEV   34 (54)
T ss_pred             CEEeCCCCCCEEEE
Confidence            34455555554443

This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=94.95  E-value=0.016  Score=38.30  Aligned_cols=24  Identities=29%  Similarity=0.748  Sum_probs=12.8

Q ss_pred             ccccccCCceecCC--CccCcCCCCC
Q 033949           83 VSKCRFCDRLVEPD--FSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~~--~~fCP~CG~~  106 (107)
                      ..+|++||...+..  ..-||.||+.
T Consensus        70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs~   95 (115)
T TIGR00100        70 ECECEDCSEEVSPEIDLYRCPKCHGI   95 (115)
T ss_pred             EEEcccCCCEEecCCcCccCcCCcCC
Confidence            34566666655553  2236666653

In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.

>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454

Probab=94.89  E-value=0.0032  Score=43.89  Aligned_cols=10  Identities=40%  Similarity=1.032  Sum_probs=5.6

Q ss_pred             CccCcCCCCC
Q 033949           97 FSFCPYCGSA  106 (107)
Q Consensus        97 ~~fCP~CG~~  106 (107)
                      .+||-+||++
T Consensus        68 PsYC~~CGkp   77 (158)
T PF10083_consen   68 PSYCHNCGKP   77 (158)
T ss_pred             ChhHHhCCCC
Confidence            3556666654

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.

>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains

Probab=94.83  E-value=0.012  Score=30.25  Aligned_cols=11  Identities=27%  Similarity=0.763  Sum_probs=4.0

Q ss_pred             eCCCCCCCCCC
Q 033949           58 FCNNCNLLFPS   68 (107)
Q Consensus        58 ~C~~CG~~~~~   68 (107)
                      +|+.||.....
T Consensus         5 fC~~CG~~t~~   15 (32)
T PF09297_consen    5 FCGRCGAPTKP   15 (32)
T ss_dssp             B-TTT--BEEE
T ss_pred             ccCcCCccccC
Confidence            45555555433

; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.

>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]

Probab=94.69  E-value=0.015  Score=44.44  Aligned_cols=24  Identities=29%  Similarity=0.715  Sum_probs=17.2

Q ss_pred             cccccCCceecC-----CCccCcCCCCCC
Q 033949           84 SKCRFCDRLVEP-----DFSFCPYCGSAL  107 (107)
Q Consensus        84 ~~C~~CG~~i~~-----~~~fCP~CG~~l  107 (107)
                      +.|++||--..+     .++|||.||.++
T Consensus       316 nfc~ncG~~~t~~~~ng~a~fcp~cgq~~  344 (345)
T COG4260         316 NFCLNCGCGTTADFDNGKAKFCPECGQGF  344 (345)
T ss_pred             ccccccCcccccCCccchhhhChhhcCCC
Confidence            478888822222     789999999874

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=94.65  E-value=0.038  Score=30.92  Aligned_cols=15  Identities=20%  Similarity=0.527  Sum_probs=9.6

Q ss_pred             ceeCCCCCCCCCCCC
Q 033949           56 ALFCNNCNLLFPSSL   70 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~   70 (107)
                      ...|+.||....++.
T Consensus        20 ~~vC~~Cg~~~~~~~   34 (52)
T smart00661       20 RFVCRKCGYEEPIEQ   34 (52)
T ss_pred             EEECCcCCCeEECCC
Confidence            566777777665543

>PF14353 CpXC: CpXC protein

Probab=94.62  E-value=0.0098  Score=39.57  Aligned_cols=13  Identities=15%  Similarity=0.319  Sum_probs=8.3

Q ss_pred             ccccccCCceecC
Q 033949           83 VSKCRFCDRLVEP   95 (107)
Q Consensus        83 ~~~C~~CG~~i~~   95 (107)
                      ...||+||+....
T Consensus        38 ~~~CP~Cg~~~~~   50 (128)
T PF14353_consen   38 SFTCPSCGHKFRL   50 (128)
T ss_pred             EEECCCCCCceec
Confidence            5667777776544

>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria

Probab=94.62  E-value=0.022  Score=31.10  Aligned_cols=31  Identities=19%  Similarity=0.350  Sum_probs=19.3

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCc
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDR   91 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~   91 (107)
                      |.-.|+.||+.++.-....+ .     ....||.||.
T Consensus         4 Yey~C~~Cg~~fe~~~~~~~-~-----~~~~CP~Cg~   34 (42)
T PF09723_consen    4 YEYRCEECGHEFEVLQSISE-D-----DPVPCPECGS   34 (42)
T ss_pred             EEEEeCCCCCEEEEEEEcCC-C-----CCCcCCCCCC
Confidence            55678888888765332211 0     2457888887

The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=94.57  E-value=0.02  Score=33.19  Aligned_cols=32  Identities=19%  Similarity=0.419  Sum_probs=22.6

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      ..||.||+.+++.....       .....|+.||++++.
T Consensus         3 ~~CP~CG~~iev~~~~~-------GeiV~Cp~CGaeleV   34 (54)
T TIGR01206         3 FECPDCGAEIELENPEL-------GELVICDECGAELEV   34 (54)
T ss_pred             cCCCCCCCEEecCCCcc-------CCEEeCCCCCCEEEE
Confidence            37999999887754311       124689999999864

This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.

>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional

Probab=94.56  E-value=0.049  Score=41.89  Aligned_cols=48  Identities=25%  Similarity=0.441  Sum_probs=27.4

Q ss_pred             CcEECCCCCC-C-cEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           20 GAGRCINCGS-T-ADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        20 ~~~~C~~Cg~-~-~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      ....||-||+ . ..+++.            .=....-++.|+-|++......             ..|++||..
T Consensus       186 ~~~~CPvCGs~P~~s~v~~------------~~~~G~RyL~CslC~teW~~~R-------------~~C~~Cg~~  235 (309)
T PRK03564        186 QRQFCPVCGSMPVSSVVQI------------GTTQGLRYLHCNLCESEWHVVR-------------VKCSNCEQS  235 (309)
T ss_pred             CCCCCCCCCCcchhheeec------------cCCCCceEEEcCCCCCcccccC-------------ccCCCCCCC
Confidence            4568999999 3 222210            0011113788888888775432             467777753

>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center

Probab=94.53  E-value=0.036  Score=28.67  Aligned_cols=23  Identities=26%  Similarity=0.723  Sum_probs=19.2

Q ss_pred             cccccCCceecC--CCccCcCCCCC
Q 033949           84 SKCRFCDRLVEP--DFSFCPYCGSA  106 (107)
Q Consensus        84 ~~C~~CG~~i~~--~~~fCP~CG~~  106 (107)
                      ..|..||...+.  ....||.||.+
T Consensus         2 ~~C~~CGy~y~~~~~~~~CP~Cg~~   26 (33)
T cd00350           2 YVCPVCGYIYDGEEAPWVCPVCGAP   26 (33)
T ss_pred             EECCCCCCEECCCcCCCcCcCCCCc
Confidence            579999999776  47799999974

The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=94.43  E-value=0.02  Score=33.18  Aligned_cols=28  Identities=21%  Similarity=0.416  Sum_probs=15.6

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE   94 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~   94 (107)
                      ...|+.||..+....           +...||.||++--
T Consensus         5 ~~~C~~Cg~~~~~~d-----------DiVvCp~CgapyH   32 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGD-----------DIVVCPECGAPYH   32 (54)
T ss_pred             CccChhhCCcccCCC-----------CEEECCCCCCccc
Confidence            345666666664322           2456666666543

>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase

Probab=94.42  E-value=0.032  Score=29.19  Aligned_cols=23  Identities=30%  Similarity=0.753  Sum_probs=15.5

Q ss_pred             cccccCCceecCC--CccCcCCCCC
Q 033949           84 SKCRFCDRLVEPD--FSFCPYCGSA  106 (107)
Q Consensus        84 ~~C~~CG~~i~~~--~~fCP~CG~~  106 (107)
                      ..|..||...+.+  ...||.||.+
T Consensus         3 ~~C~~CG~i~~g~~~p~~CP~Cg~~   27 (34)
T cd00729           3 WVCPVCGYIHEGEEAPEKCPICGAP   27 (34)
T ss_pred             EECCCCCCEeECCcCCCcCcCCCCc
Confidence            5677788775543  4678888764

In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues

Probab=94.40  E-value=0.027  Score=37.03  Aligned_cols=30  Identities=23%  Similarity=0.484  Sum_probs=17.7

Q ss_pred             ceeCCCCCCCC-CCCCCCCCCCCCCccCccccccCCceecCC
Q 033949           56 ALFCNNCNLLF-PSSLPPPPPPPPLVSDVSKCRFCDRLVEPD   96 (107)
Q Consensus        56 ~~~C~~CG~~~-~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~   96 (107)
                      .-.||+||+.| .+++           .-.+||+||+.....
T Consensus         9 KR~Cp~CG~kFYDLnk-----------~PivCP~CG~~~~~~   39 (108)
T PF09538_consen    9 KRTCPSCGAKFYDLNK-----------DPIVCPKCGTEFPPE   39 (108)
T ss_pred             cccCCCCcchhccCCC-----------CCccCCCCCCccCcc
Confidence            34678888766 2222           124578887776554

The function of members of this family is unknown.

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=94.36  E-value=0.026  Score=38.37  Aligned_cols=15  Identities=27%  Similarity=0.552  Sum_probs=11.1

Q ss_pred             CceeCCCCCCCCCCC
Q 033949           55 PALFCNNCNLLFPSS   69 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~   69 (107)
                      ....|+.||..+..+
T Consensus        69 ~~~~C~~CG~~~~~~   83 (135)
T PRK03824         69 AVLKCRNCGNEWSLK   83 (135)
T ss_pred             eEEECCCCCCEEecc
Confidence            567788888777664

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=94.36  E-value=0.03  Score=38.03  Aligned_cols=28  Identities=29%  Similarity=0.772  Sum_probs=21.6

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP   67 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~   67 (107)
                      ..+||.||..                ||+   +++.++||.||....
T Consensus        28 ~~hCp~Cg~P----------------LF~---KdG~v~CPvC~~~~~   55 (131)
T COG1645          28 AKHCPKCGTP----------------LFR---KDGEVFCPVCGYREV   55 (131)
T ss_pred             HhhCcccCCc----------------cee---eCCeEECCCCCceEE
Confidence            4579999994                466   458999999996543

>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria

Probab=94.26  E-value=0.018  Score=31.48  Aligned_cols=30  Identities=20%  Similarity=0.554  Sum_probs=17.4

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCC
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNL   64 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~   64 (107)
                      ...|+.||+..++.             .+.+. ...+.||.||.
T Consensus         5 ey~C~~Cg~~fe~~-------------~~~~~-~~~~~CP~Cg~   34 (42)
T PF09723_consen    5 EYRCEECGHEFEVL-------------QSISE-DDPVPCPECGS   34 (42)
T ss_pred             EEEeCCCCCEEEEE-------------EEcCC-CCCCcCCCCCC
Confidence            45677777733322             22333 36777777777

The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []

Probab=94.16  E-value=0.01  Score=44.71  Aligned_cols=14  Identities=21%  Similarity=0.427  Sum_probs=7.8

Q ss_pred             CceeCCCCCCCCCC
Q 033949           55 PALFCNNCNLLFPS   68 (107)
Q Consensus        55 ~~~~C~~CG~~~~~   68 (107)
                      -++.|+.||+....
T Consensus       196 R~L~Cs~C~t~W~~  209 (290)
T PF04216_consen  196 RYLHCSLCGTEWRF  209 (290)
T ss_dssp             EEEEETTT--EEE-
T ss_pred             EEEEcCCCCCeeee
Confidence            37778888877654

The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.

>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300

Probab=94.16  E-value=0.037  Score=37.41  Aligned_cols=31  Identities=19%  Similarity=0.262  Sum_probs=23.5

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCC
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSS   69 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~   69 (107)
                      ..+||+||.++                +-+++  .-+.||+||+.+.+.
T Consensus         9 Kr~Cp~cg~kF----------------YDLnk--~p~vcP~cg~~~~~~   39 (129)
T TIGR02300         9 KRICPNTGSKF----------------YDLNR--RPAVSPYTGEQFPPE   39 (129)
T ss_pred             cccCCCcCccc----------------cccCC--CCccCCCcCCccCcc
Confidence            45799999965                23443  578899999999775

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.

>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins

Probab=94.09  E-value=0.013  Score=34.96  Aligned_cols=48  Identities=23%  Similarity=0.346  Sum_probs=26.1

Q ss_pred             CcEECCCCCC-CcEEEEEee-EEE---------EEEEeeeec---CCCCCceeCCCCCCCCC
Q 033949           20 GAGRCINCGS-TADLVEYEK-VLK---------AFFVPVWKW---PAKEPALFCNNCNLLFP   67 (107)
Q Consensus        20 ~~~~C~~Cg~-~~~~~~~~~-~f~---------lFFIP~~~~---~~~~~~~~C~~CG~~~~   67 (107)
                      ..+.||+|++ ..+.+++.. ..+         +++..++||   +-++-...||+||..+.
T Consensus         2 ~~i~Cp~C~~~~~T~v~~~~g~~t~~~~~ll~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg   63 (67)
T smart00714        2 YQLFCPRCQNNVTTRVETETGVCAWLICCLLFLLCFCCCLPCCLDSFKDVNHYCPNCGAFLG   63 (67)
T ss_pred             cceECCCCCCEEEEEEEEEeChHHHHHHHHHHHHHHHHHHHHhcccccCccEECCCCCCEeE
Confidence            4578999999 555555443 111         112233443   33334666777776553

>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins

Probab=94.07  E-value=0.024  Score=29.89  Aligned_cols=23  Identities=43%  Similarity=0.947  Sum_probs=13.3

Q ss_pred             ccccccCCceecCCCccCcCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~  105 (107)
                      ..+|.+||...-+-...||.||+
T Consensus        11 ~~rC~~Cg~~~~pPr~~Cp~C~s   33 (37)
T PF12172_consen   11 GQRCRDCGRVQFPPRPVCPHCGS   33 (37)
T ss_dssp             EEE-TTT--EEES--SEETTTT-
T ss_pred             EEEcCCCCCEecCCCcCCCCcCc
Confidence            45788888887777788888875

The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C

Probab=94.04  E-value=0.015  Score=30.60  Aligned_cols=30  Identities=20%  Similarity=0.452  Sum_probs=13.1

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCc
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDR   91 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~   91 (107)
                      .+||.||..++..-...+     ......|++||.
T Consensus         1 kfC~~CG~~l~~~ip~gd-----~r~R~vC~~Cg~   30 (34)
T PF14803_consen    1 KFCPQCGGPLERRIPEGD-----DRERLVCPACGF   30 (34)
T ss_dssp             -B-TTT--B-EEE--TT------SS-EEEETTTTE
T ss_pred             CccccccChhhhhcCCCC-----CccceECCCCCC
Confidence            378999998754221100     013567999886

>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]

Probab=94.02  E-value=0.035  Score=33.48  Aligned_cols=33  Identities=15%  Similarity=0.407  Sum_probs=23.6

Q ss_pred             CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      -.++||.|||..                +=|+.....+.|..||..+..
T Consensus        18 l~VkCpdC~N~q----------------~vFshast~V~C~~CG~~l~~   50 (67)
T COG2051          18 LRVKCPDCGNEQ----------------VVFSHASTVVTCLICGTTLAE   50 (67)
T ss_pred             EEEECCCCCCEE----------------EEeccCceEEEecccccEEEe
Confidence            356899999932                225556578999999998743

>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]

Probab=93.92  E-value=0.13  Score=34.04  Aligned_cols=32  Identities=25%  Similarity=0.454  Sum_probs=23.0

Q ss_pred             ECCCCCCCcEEEEEeeEEEEEEEeeeecCC-CCCceeCCCCCCCCCCCC
Q 033949           23 RCINCGSTADLVEYEKVLKAFFVPVWKWPA-KEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        23 ~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~-~~~~~~C~~CG~~~~~~~   70 (107)
                      -||.||+.+                +|-.. .+..+.|+.||..++++.
T Consensus         4 FCp~Cgsll----------------~p~~~~~~~~l~C~kCgye~~~~~   36 (113)
T COG1594           4 FCPKCGSLL----------------YPKKDDEGGKLVCRKCGYEEEASN   36 (113)
T ss_pred             ccCCccCee----------------EEeEcCCCcEEECCCCCcchhccc
Confidence            599999943                22111 235999999999998875

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=93.70  E-value=0.065  Score=31.63  Aligned_cols=34  Identities=15%  Similarity=0.358  Sum_probs=24.5

Q ss_pred             CCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           19 SGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        19 ~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      ...++||.|++..                +=|+.....+.|..||..+..
T Consensus         9 F~~VkCp~C~n~q----------------~vFsha~t~V~C~~Cg~~L~~   42 (59)
T PRK00415          9 FLKVKCPDCGNEQ----------------VVFSHASTVVRCLVCGKTLAE   42 (59)
T ss_pred             EEEEECCCCCCeE----------------EEEecCCcEEECcccCCCccc
Confidence            3467899999922                125556579999999998844

>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues

Probab=93.58  E-value=0.025  Score=28.96  Aligned_cols=11  Identities=18%  Similarity=0.350  Sum_probs=7.1

Q ss_pred             ccccccCCcee
Q 033949           83 VSKCRFCDRLV   93 (107)
Q Consensus        83 ~~~C~~CG~~i   93 (107)
                      ...||.||.++
T Consensus        19 ~~vCp~C~~ew   29 (30)
T PF08274_consen   19 LLVCPECGHEW   29 (30)
T ss_dssp             SEEETTTTEEE
T ss_pred             EEeCCcccccC
Confidence            45677777664

The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=93.58  E-value=0.04  Score=30.84  Aligned_cols=33  Identities=18%  Similarity=0.333  Sum_probs=21.9

Q ss_pred             eCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCC
Q 033949           58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDF   97 (107)
Q Consensus        58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~   97 (107)
                      +||.||..+.......       .....|+.||.....++
T Consensus         2 FCp~Cg~~l~~~~~~~-------~~~~vC~~Cg~~~~~~~   34 (52)
T smart00661        2 FCPKCGNMLIPKEGKE-------KRRFVCRKCGYEEPIEQ   34 (52)
T ss_pred             CCCCCCCccccccCCC-------CCEEECCcCCCeEECCC
Confidence            7999999876543211       02567999998765543

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=93.52  E-value=0.041  Score=36.48  Aligned_cols=23  Identities=26%  Similarity=0.779  Sum_probs=11.4

Q ss_pred             ccccccCCceecCC-C-c-cCcCCCC
Q 033949           83 VSKCRFCDRLVEPD-F-S-FCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~~-~-~-fCP~CG~  105 (107)
                      ..+|.+||...+.+ . . .||.||+
T Consensus        71 ~~~C~~Cg~~~~~~~~~~~~CP~Cgs   96 (117)
T PRK00564         71 ELECKDCSHVFKPNALDYGVCEKCHS   96 (117)
T ss_pred             EEEhhhCCCccccCCccCCcCcCCCC
Confidence            34566666554442 1 1 2666665

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=93.46  E-value=0.032  Score=37.94  Aligned_cols=24  Identities=29%  Similarity=0.647  Sum_probs=18.6

Q ss_pred             CccccccCCceecC--CCccCcCCCC
Q 033949           82 DVSKCRFCDRLVEP--DFSFCPYCGS  105 (107)
Q Consensus        82 ~~~~C~~CG~~i~~--~~~fCP~CG~  105 (107)
                      +..+||.||.++-.  +-.|||.||.
T Consensus        27 L~~hCp~Cg~PLF~KdG~v~CPvC~~   52 (131)
T COG1645          27 LAKHCPKCGTPLFRKDGEVFCPVCGY   52 (131)
T ss_pred             HHhhCcccCCcceeeCCeEECCCCCc
Confidence            46788888888755  7788888884

>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]

Probab=93.39  E-value=0.048  Score=31.03  Aligned_cols=23  Identities=52%  Similarity=0.917  Sum_probs=10.8

Q ss_pred             cccccCCceecC----CCccCcCCCCC
Q 033949           84 SKCRFCDRLVEP----DFSFCPYCGSA  106 (107)
Q Consensus        84 ~~C~~CG~~i~~----~~~fCP~CG~~  106 (107)
                      +.|-.||++++.    ...-||+||++
T Consensus         7 Y~C~~Cg~~~~~~~~~~~irCp~Cg~r   33 (49)
T COG1996           7 YKCARCGREVELDQETRGIRCPYCGSR   33 (49)
T ss_pred             EEhhhcCCeeehhhccCceeCCCCCcE
Confidence            445555555442    34445555543

>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]

Probab=93.37  E-value=0.053  Score=37.05  Aligned_cols=24  Identities=42%  Similarity=1.007  Sum_probs=15.5

Q ss_pred             ccccccCCceecCCCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      ..+|++||+.--+--.+||+||++
T Consensus        29 g~kC~~CG~v~~PPr~~Cp~C~~~   52 (140)
T COG1545          29 GTKCKKCGRVYFPPRAYCPKCGSE   52 (140)
T ss_pred             EEEcCCCCeEEcCCcccCCCCCCC
Confidence            345666666666666666666654

>PRK00420 hypothetical protein; Validated

Probab=93.29  E-value=0.07  Score=35.36  Aligned_cols=32  Identities=16%  Similarity=0.409  Sum_probs=23.4

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~   70 (107)
                      +.+||.||...                |.+  +....+||.||..+....
T Consensus        23 ~~~CP~Cg~pL----------------f~l--k~g~~~Cp~Cg~~~~v~~   54 (112)
T PRK00420         23 SKHCPVCGLPL----------------FEL--KDGEVVCPVHGKVYIVKS   54 (112)
T ss_pred             cCCCCCCCCcc----------------eec--CCCceECCCCCCeeeecc
Confidence            35799999843                444  347999999999876643

>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins

Probab=93.29  E-value=0.14  Score=30.71  Aligned_cols=39  Identities=23%  Similarity=0.497  Sum_probs=24.0

Q ss_pred             ECCCCCC-CcEEEEEe---eEEEEEEEeeeecCCC-CCceeCCCCCCC
Q 033949           23 RCINCGS-TADLVEYE---KVLKAFFVPVWKWPAK-EPALFCNNCNLL   65 (107)
Q Consensus        23 ~C~~Cg~-~~~~~~~~---~~f~lFFIP~~~~~~~-~~~~~C~~CG~~   65 (107)
                      .||.||+ .++.-+.+   .-++-    +|.+..+ -..+.|++||..
T Consensus         2 ~C~KCg~~~~e~~~v~~tgg~~sk----iFdvq~~~f~~v~C~~CGYT   45 (64)
T PF09855_consen    2 KCPKCGNEEYESGEVRATGGGLSK----IFDVQNKKFTTVSCTNCGYT   45 (64)
T ss_pred             CCCCCCCcceecceEEccCCeeEE----EEEecCcEEEEEECCCCCCE
Confidence            5999999 44433322   23442    4666433 337889999986

>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation

Probab=93.12  E-value=0.036  Score=36.48  Aligned_cols=24  Identities=42%  Similarity=0.798  Sum_probs=11.3

Q ss_pred             ccccccCCceecC--CCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEP--DFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~--~~~fCP~CG~~  106 (107)
                      ..+|.+||.+.+.  ....||.||+.
T Consensus        70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs~   95 (113)
T PF01155_consen   70 RARCRDCGHEFEPDEFDFSCPRCGSP   95 (113)
T ss_dssp             EEEETTTS-EEECHHCCHH-SSSSSS
T ss_pred             cEECCCCCCEEecCCCCCCCcCCcCC
Confidence            3456666666544  22336666653

The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.

>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2

Probab=92.99  E-value=0.032  Score=29.40  Aligned_cols=9  Identities=44%  Similarity=1.235  Sum_probs=4.5

Q ss_pred             eCCCCCCCC
Q 033949           58 FCNNCNLLF   66 (107)
Q Consensus        58 ~C~~CG~~~   66 (107)
                      +||.||..+
T Consensus         3 FCp~C~nlL   11 (35)
T PF02150_consen    3 FCPECGNLL   11 (35)
T ss_dssp             BETTTTSBE
T ss_pred             eCCCCCccc
Confidence            455555544

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....

>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[]

Probab=92.93  E-value=0.059  Score=28.62  Aligned_cols=14  Identities=14%  Similarity=0.572  Sum_probs=9.6

Q ss_pred             CCCceeCCCCCCCC
Q 033949           53 KEPALFCNNCNLLF   66 (107)
Q Consensus        53 ~~~~~~C~~CG~~~   66 (107)
                      .++..+|..||+..
T Consensus        22 ~dG~~yC~~cG~~~   35 (36)
T PF11781_consen   22 DDGFYYCDRCGHQS   35 (36)
T ss_pred             cCCEEEhhhCceEc
Confidence            45677777777754

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=92.88  E-value=0.068  Score=30.02  Aligned_cols=31  Identities=16%  Similarity=0.343  Sum_probs=20.0

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCc
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDR   91 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~   91 (107)
                      |...|+.||..+++.....+      .....||.||+
T Consensus         4 Yey~C~~Cg~~fe~~~~~~~------~~~~~CP~Cg~   34 (52)
T TIGR02605         4 YEYRCTACGHRFEVLQKMSD------DPLATCPECGG   34 (52)
T ss_pred             EEEEeCCCCCEeEEEEecCC------CCCCCCCCCCC
Confidence            56689999998876432111      02346999997

This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=92.88  E-value=0.062  Score=31.72  Aligned_cols=30  Identities=20%  Similarity=0.466  Sum_probs=17.3

Q ss_pred             ceeCCCCCCCCCC-CCCCCCCCCCCccCccccccCCceec
Q 033949           56 ALFCNNCNLLFPS-SLPPPPPPPPLVSDVSKCRFCDRLVE   94 (107)
Q Consensus        56 ~~~C~~CG~~~~~-~~~~~~~~~~~~~~~~~C~~CG~~i~   94 (107)
                      .++||.|+...-+ ++..         ....|..||+.+.
T Consensus        11 ~VkCp~C~n~q~vFsha~---------t~V~C~~Cg~~L~   41 (59)
T PRK00415         11 KVKCPDCGNEQVVFSHAS---------TVVRCLVCGKTLA   41 (59)
T ss_pred             EEECCCCCCeEEEEecCC---------cEEECcccCCCcc
Confidence            5667777776533 1111         2456777777763

>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2

Probab=92.78  E-value=0.047  Score=29.00  Aligned_cols=31  Identities=19%  Similarity=0.544  Sum_probs=18.5

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE   94 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~   94 (107)
                      ..|+.||+.|.+......       ....|.+||.++.
T Consensus         2 r~C~~Cg~~Yh~~~~pP~-------~~~~Cd~cg~~L~   32 (36)
T PF05191_consen    2 RICPKCGRIYHIEFNPPK-------VEGVCDNCGGELV   32 (36)
T ss_dssp             EEETTTTEEEETTTB--S-------STTBCTTTTEBEB
T ss_pred             cCcCCCCCccccccCCCC-------CCCccCCCCCeeE
Confidence            357888888765332111       1357888887764

7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....

>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins

Probab=92.71  E-value=0.088  Score=34.89  Aligned_cols=31  Identities=23%  Similarity=0.367  Sum_probs=23.3

Q ss_pred             CcEECCCCCC-C-cEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCC
Q 033949           20 GAGRCINCGS-T-ADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLP   71 (107)
Q Consensus        20 ~~~~C~~Cg~-~-~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~   71 (107)
                      .+++||+||. + .                  .   +..-.|.+|++++.++++
T Consensus        68 v~V~CP~C~K~TKm------------------L---Gr~D~CM~C~~pLTLd~~  100 (114)
T PF11023_consen   68 VQVECPNCGKQTKM------------------L---GRVDACMHCKEPLTLDPS  100 (114)
T ss_pred             eeeECCCCCChHhh------------------h---chhhccCcCCCcCccCch
Confidence            5678999999 2 2                  1   234589999999988765

; GO: 0005887 integral to plasma membrane

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=92.65  E-value=0.077  Score=35.04  Aligned_cols=9  Identities=22%  Similarity=0.796  Sum_probs=4.8

Q ss_pred             cEECCCCCC
Q 033949           21 AGRCINCGS   29 (107)
Q Consensus        21 ~~~C~~Cg~   29 (107)
                      ...|++||.
T Consensus        70 ~~~C~~Cg~   78 (115)
T TIGR00100        70 ECECEDCSE   78 (115)
T ss_pred             EEEcccCCC
Confidence            445555555

In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.

>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional

Probab=92.61  E-value=0.079  Score=29.94  Aligned_cols=25  Identities=20%  Similarity=0.377  Sum_probs=22.3

Q ss_pred             CccccccCCceecCCCccCcCCCCC
Q 033949           82 DVSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        82 ~~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      +.++|-.|+|.+++.|+.|-.||++
T Consensus        13 ~k~ICrkC~ARnp~~A~~CRKCg~~   37 (48)
T PRK04136         13 NKKICMRCNARNPWRATKCRKCGYK   37 (48)
T ss_pred             cccchhcccCCCCccccccccCCCC
Confidence            4678999999999999999999974

>PHA00626 hypothetical protein

Probab=92.55  E-value=0.11  Score=30.38  Aligned_cols=14  Identities=14%  Similarity=0.380  Sum_probs=9.0

Q ss_pred             CceeCCCCCCCCCC
Q 033949           55 PALFCNNCNLLFPS   68 (107)
Q Consensus        55 ~~~~C~~CG~~~~~   68 (107)
                      +.-.|+.||..+..
T Consensus        22 nrYkCkdCGY~ft~   35 (59)
T PHA00626         22 DDYVCCDCGYNDSK   35 (59)
T ss_pred             cceEcCCCCCeech
Confidence            55667777776644

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=92.52  E-value=0.083  Score=34.81  Aligned_cols=13  Identities=15%  Similarity=0.583  Sum_probs=6.0

Q ss_pred             ceeCCCCCCCCCC
Q 033949           56 ALFCNNCNLLFPS   68 (107)
Q Consensus        56 ~~~C~~CG~~~~~   68 (107)
                      ...|+.||..+++
T Consensus        70 ~~~C~~Cg~~~~~   82 (113)
T PRK12380         70 QAWCWDCSQVVEI   82 (113)
T ss_pred             EEEcccCCCEEec
Confidence            4445555544433

>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)

Probab=92.49  E-value=0.07  Score=29.19  Aligned_cols=22  Identities=23%  Similarity=0.576  Sum_probs=16.3

Q ss_pred             ccccccCCceecC---CCccCcCCC
Q 033949           83 VSKCRFCDRLVEP---DFSFCPYCG  104 (107)
Q Consensus        83 ~~~C~~CG~~i~~---~~~fCP~CG  104 (107)
                      ...||.||.++-.   +-.+||.|+
T Consensus        17 ~~~Cp~C~~PL~~~k~g~~~Cv~C~   41 (41)
T PF06677_consen   17 DEHCPDCGTPLMRDKDGKIYCVSCG   41 (41)
T ss_pred             cCccCCCCCeeEEecCCCEECCCCC
Confidence            4578888887754   667888885

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors []

Probab=92.32  E-value=0.13  Score=26.82  Aligned_cols=13  Identities=23%  Similarity=0.447  Sum_probs=9.1

Q ss_pred             CCceeCCCCCCCC
Q 033949           54 EPALFCNNCNLLF   66 (107)
Q Consensus        54 ~~~~~C~~CG~~~   66 (107)
                      ..+..|+.||..+
T Consensus        19 ~~~~~C~~Cg~~~   31 (33)
T PF08792_consen   19 DDYEVCIFCGSSF   31 (33)
T ss_pred             CCeEEcccCCcEe
Confidence            3677777777765

>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []

Probab=92.31  E-value=0.028  Score=42.35  Aligned_cols=40  Identities=15%  Similarity=0.184  Sum_probs=17.5

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE   94 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~   94 (107)
                      ..+.||+||..-..+.......++-......|.+||.-+.
T Consensus       210 ~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK  249 (290)
T PF04216_consen  210 VRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK  249 (290)
T ss_dssp             -TTS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred             cCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence            4668999999865433211111111124578999998764

The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.

>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length

Probab=92.24  E-value=0.071  Score=31.13  Aligned_cols=13  Identities=23%  Similarity=0.603  Sum_probs=7.9

Q ss_pred             eCCCCCCCCCCCC
Q 033949           58 FCNNCNLLFPSSL   70 (107)
Q Consensus        58 ~C~~CG~~~~~~~   70 (107)
                      -|..|+..++.+.
T Consensus         7 nCE~C~~dLp~~s   19 (57)
T PF06906_consen    7 NCECCDKDLPPDS   19 (57)
T ss_pred             CccccCCCCCCCC
Confidence            3666777666544

This family contains a number of conserved cysteine residues and its function is unknown.

>PF15616 TerY-C: TerY-C metal binding domain

Probab=92.13  E-value=0.11  Score=35.33  Aligned_cols=12  Identities=33%  Similarity=0.963  Sum_probs=9.4

Q ss_pred             CCCccCcCCCCC
Q 033949           95 PDFSFCPYCGSA  106 (107)
Q Consensus        95 ~~~~fCP~CG~~  106 (107)
                      ++-..||-||+.
T Consensus       103 ~~~~~CPwCg~~  114 (131)
T PF15616_consen  103 EGEVTCPWCGNE  114 (131)
T ss_pred             CCCEECCCCCCe
Confidence            366889999975

>smart00531 TFIIE Transcription initiation factor IIE

Probab=92.05  E-value=0.06  Score=36.87  Aligned_cols=40  Identities=15%  Similarity=0.262  Sum_probs=23.9

Q ss_pred             CCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949           53 KEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        53 ~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      ......||+||..+...... .+.+  ......||+||+++..
T Consensus        96 ~~~~Y~Cp~C~~~y~~~ea~-~~~d--~~~~f~Cp~Cg~~l~~  135 (147)
T smart00531       96 NNAYYKCPNCQSKYTFLEAN-QLLD--MDGTFTCPRCGEELEE  135 (147)
T ss_pred             CCcEEECcCCCCEeeHHHHH-HhcC--CCCcEECCCCCCEEEE
Confidence            33577899999888642211 0000  0123789999999865

>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain

Probab=91.96  E-value=0.15  Score=33.50  Aligned_cols=7  Identities=43%  Similarity=1.364  Sum_probs=3.1

Q ss_pred             cCcCCCC
Q 033949           99 FCPYCGS  105 (107)
Q Consensus        99 fCP~CG~  105 (107)
                      +||.||.
T Consensus        62 ~CP~C~~   68 (111)
T PF14319_consen   62 HCPSCQA   68 (111)
T ss_pred             CCCCCCC
Confidence            4444443

>smart00531 TFIIE Transcription initiation factor IIE

Probab=91.92  E-value=0.058  Score=36.92  Aligned_cols=12  Identities=17%  Similarity=0.520  Sum_probs=7.2

Q ss_pred             eeCCCCCCCCCC
Q 033949           57 LFCNNCNLLFPS   68 (107)
Q Consensus        57 ~~C~~CG~~~~~   68 (107)
                      ..||.||..+..
T Consensus       124 f~Cp~Cg~~l~~  135 (147)
T smart00531      124 FTCPRCGEELEE  135 (147)
T ss_pred             EECCCCCCEEEE
Confidence            566666666544

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=91.81  E-value=0.12  Score=29.43  Aligned_cols=7  Identities=43%  Similarity=1.317  Sum_probs=3.4

Q ss_pred             eCCCCCC
Q 033949           58 FCNNCNL   64 (107)
Q Consensus        58 ~C~~CG~   64 (107)
                      +||.||+
T Consensus        22 fCP~Cg~   28 (50)
T PRK00432         22 FCPRCGS   28 (50)
T ss_pred             cCcCCCc
Confidence            4444444

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=91.70  E-value=0.11  Score=30.10  Aligned_cols=30  Identities=17%  Similarity=0.533  Sum_probs=21.3

Q ss_pred             CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      ....|+-||..+                   ..+++.+.||.||+++..
T Consensus         4 ~~~~C~~Cg~~~-------------------~~~dDiVvCp~CgapyHR   33 (54)
T PF14446_consen    4 EGCKCPVCGKKF-------------------KDGDDIVVCPECGAPYHR   33 (54)
T ss_pred             cCccChhhCCcc-------------------cCCCCEEECCCCCCcccH
Confidence            345788888853                   224578889999988854

>PRK08351 DNA-directed RNA polymerase subunit E''; Validated

Probab=91.52  E-value=0.11  Score=30.77  Aligned_cols=9  Identities=22%  Similarity=0.888  Sum_probs=5.5

Q ss_pred             eCCCCCCCC
Q 033949           58 FCNNCNLLF   66 (107)
Q Consensus        58 ~C~~CG~~~   66 (107)
                      .|.+|+...
T Consensus         5 AC~~C~~i~   13 (61)
T PRK08351          5 ACRHCHYIT   13 (61)
T ss_pred             hhhhCCccc
Confidence            566666665

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=91.51  E-value=0.11  Score=42.79  Aligned_cols=13  Identities=23%  Similarity=0.455  Sum_probs=7.6

Q ss_pred             ccccccCCceecC
Q 033949           83 VSKCRFCDRLVEP   95 (107)
Q Consensus        83 ~~~C~~CG~~i~~   95 (107)
                      .+.||.||..|+.
T Consensus       229 ~y~C~~Cg~~i~e  241 (557)
T PF05876_consen  229 RYVCPHCGCEIEE  241 (557)
T ss_pred             EEECCCCcCCCCH
Confidence            4556666666553

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>PLN03086 PRLI-interacting factor K; Provisional

Probab=91.39  E-value=0.13  Score=42.59  Aligned_cols=11  Identities=27%  Similarity=0.604  Sum_probs=8.4

Q ss_pred             CCcEECCCCCC
Q 033949           19 SGAGRCINCGS   29 (107)
Q Consensus        19 ~~~~~C~~Cg~   29 (107)
                      ...+.|+||+.
T Consensus       405 ~~~V~C~NC~~  415 (567)
T PLN03086        405 VDTVECRNCKH  415 (567)
T ss_pred             CCeEECCCCCC
Confidence            35667999988

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=91.32  E-value=0.11  Score=33.64  Aligned_cols=10  Identities=20%  Similarity=0.580  Sum_probs=6.5

Q ss_pred             CceeCCCCCC
Q 033949           55 PALFCNNCNL   64 (107)
Q Consensus        55 ~~~~C~~CG~   64 (107)
                      ....||+||+
T Consensus        20 t~f~CP~Cge   29 (99)
T PRK14892         20 KIFECPRCGK   29 (99)
T ss_pred             cEeECCCCCC
Confidence            3566777774

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=91.28  E-value=0.13  Score=34.88  Aligned_cols=12  Identities=33%  Similarity=0.753  Sum_probs=9.0

Q ss_pred             CcEECCCCCCCc
Q 033949           20 GAGRCINCGSTA   31 (107)
Q Consensus        20 ~~~~C~~Cg~~~   31 (107)
                      ....|++||..+
T Consensus        69 ~~~~C~~CG~~~   80 (135)
T PRK03824         69 AVLKCRNCGNEW   80 (135)
T ss_pred             eEEECCCCCCEE
Confidence            566799999844

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=91.19  E-value=0.16  Score=32.54  Aligned_cols=11  Identities=36%  Similarity=1.038  Sum_probs=8.5

Q ss_pred             eCCCCCCCCCC
Q 033949           58 FCNNCNLLFPS   68 (107)
Q Consensus        58 ~C~~CG~~~~~   68 (107)
                      +||.||..+..
T Consensus         2 fC~~Cg~~l~~   12 (104)
T TIGR01384         2 FCPKCGSLMTP   12 (104)
T ss_pred             CCcccCccccc
Confidence            68888888755

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated

Probab=91.17  E-value=0.12  Score=30.95  Aligned_cols=23  Identities=22%  Similarity=0.472  Sum_probs=15.0

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      ..+.|..|+...+.               ..||+||..
T Consensus         4 ~~~AC~~C~~i~~~---------------~~Cp~Cgs~   26 (64)
T PRK06393          4 QYRACKKCKRLTPE---------------KTCPVHGDE   26 (64)
T ss_pred             hhhhHhhCCcccCC---------------CcCCCCCCC
Confidence            56677777777531               357777776

>PHA02942 putative transposase; Provisional

Probab=91.15  E-value=0.23  Score=39.09  Aligned_cols=42  Identities=14%  Similarity=0.169  Sum_probs=27.7

Q ss_pred             EeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCC
Q 033949           45 VPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPD   96 (107)
Q Consensus        45 IP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~   96 (107)
                      |+++..++......||.||+......          .....|++||...+.|
T Consensus       314 ~~Vv~V~p~yTSq~Cs~CG~~~~~l~----------~r~f~C~~CG~~~drD  355 (383)
T PHA02942        314 MIVEFVNPSYSSVSCPKCGHKMVEIA----------HRYFHCPSCGYENDRD  355 (383)
T ss_pred             CEEEEECCCCCCccCCCCCCccCcCC----------CCEEECCCCCCEeCcH
Confidence            55666666644678999998653110          0246899999988764

>PF13453 zf-TFIIB: Transcription factor zinc-finger

Probab=91.15  E-value=0.086  Score=28.44  Aligned_cols=28  Identities=14%  Similarity=0.400  Sum_probs=16.1

Q ss_pred             eCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      .||.|+..+...... ++      ....|++||-.
T Consensus         1 ~CP~C~~~l~~~~~~-~~------~id~C~~C~G~   28 (41)
T PF13453_consen    1 KCPRCGTELEPVRLG-DV------EIDVCPSCGGI   28 (41)
T ss_pred             CcCCCCcccceEEEC-CE------EEEECCCCCeE
Confidence            488888876542211 11      24568888753

>PRK12286 rpmF 50S ribosomal protein L32; Reviewed

Probab=91.12  E-value=0.13  Score=30.08  Aligned_cols=21  Identities=29%  Similarity=0.774  Sum_probs=10.8

Q ss_pred             cccccCCceecCCCccCcCCCC
Q 033949           84 SKCRFCDRLVEPDFSFCPYCGS  105 (107)
Q Consensus        84 ~~C~~CG~~i~~~~~fCP~CG~  105 (107)
                      ..|++||+. ...-..||+||.
T Consensus        28 ~~C~~CG~~-~~~H~vC~~CG~   48 (57)
T PRK12286         28 VECPNCGEP-KLPHRVCPSCGY   48 (57)
T ss_pred             eECCCCCCc-cCCeEECCCCCc
Confidence            345556555 233455555554

>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc

Probab=91.11  E-value=0.28  Score=27.06  Aligned_cols=10  Identities=40%  Similarity=0.793  Sum_probs=6.1

Q ss_pred             CcEECCCCCC
Q 033949           20 GAGRCINCGS   29 (107)
Q Consensus        20 ~~~~C~~Cg~   29 (107)
                      +.+.||+||+
T Consensus        17 ~g~~CP~Cg~   26 (46)
T PF12760_consen   17 DGFVCPHCGS   26 (46)
T ss_pred             CCCCCCCCCC
Confidence            3355777776

It may be a zinc-binding beta ribbon domain that could bind DNA.

>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE

Probab=90.85  E-value=0.24  Score=38.08  Aligned_cols=24  Identities=25%  Similarity=0.539  Sum_probs=16.6

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      ++.|+-|++......             ..|++||..
T Consensus       210 yL~CslC~teW~~~R-------------~~C~~Cg~~  233 (305)
T TIGR01562       210 YLSCSLCATEWHYVR-------------VKCSHCEES  233 (305)
T ss_pred             EEEcCCCCCcccccC-------------ccCCCCCCC
Confidence            788888888775532             467777754

The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).

>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1

Probab=90.83  E-value=0.13  Score=31.54  Aligned_cols=12  Identities=25%  Similarity=0.423  Sum_probs=4.3

Q ss_pred             CceeCCCCCCCC
Q 033949           55 PALFCNNCNLLF   66 (107)
Q Consensus        55 ~~~~C~~CG~~~   66 (107)
                      +.+.|..|-...
T Consensus         8 ~vlrC~aCf~~t   19 (73)
T PF08772_consen    8 WVLRCHACFKIT   19 (73)
T ss_dssp             EEEE-SSS--EE
T ss_pred             eeEEccccccCc
Confidence            445555554443

; PDB: 2CON_A.

>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation

Probab=90.54  E-value=0.05  Score=35.78  Aligned_cols=27  Identities=19%  Similarity=0.349  Sum_probs=13.3

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      ....|..||+.++++..           ...||+||..
T Consensus        69 ~~~~C~~Cg~~~~~~~~-----------~~~CP~Cgs~   95 (113)
T PF01155_consen   69 ARARCRDCGHEFEPDEF-----------DFSCPRCGSP   95 (113)
T ss_dssp             -EEEETTTS-EEECHHC-----------CHH-SSSSSS
T ss_pred             CcEECCCCCCEEecCCC-----------CCCCcCCcCC
Confidence            45566666666655331           2456666664

The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.

>PRK02935 hypothetical protein; Provisional

Probab=90.40  E-value=0.31  Score=31.97  Aligned_cols=31  Identities=16%  Similarity=0.232  Sum_probs=22.9

Q ss_pred             CcEECCCCCC--CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCC
Q 033949           20 GAGRCINCGS--TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLP   71 (107)
Q Consensus        20 ~~~~C~~Cg~--~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~   71 (107)
                      .++.||+|+.  ..                     -+..-.|.+|+.++..+++
T Consensus        69 vqV~CP~C~K~TKm---------------------LGrvD~CM~C~~PLTLd~~  101 (110)
T PRK02935         69 VQVICPSCEKPTKM---------------------LGRVDACMHCNQPLTLDRS  101 (110)
T ss_pred             eeeECCCCCchhhh---------------------ccceeecCcCCCcCCcCcc
Confidence            4678999999  32                     2345689999999877664

>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300

Probab=90.35  E-value=0.23  Score=33.62  Aligned_cols=29  Identities=14%  Similarity=0.216  Sum_probs=16.9

Q ss_pred             ceeCCCCCCCC-CCCCCCCCCCCCCccCccccccCCceecC
Q 033949           56 ALFCNNCNLLF-PSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        56 ~~~C~~CG~~~-~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      .-.||+||+.| .+.+           .-..||+||+....
T Consensus         9 Kr~Cp~cg~kFYDLnk-----------~p~vcP~cg~~~~~   38 (129)
T TIGR02300         9 KRICPNTGSKFYDLNR-----------RPAVSPYTGEQFPP   38 (129)
T ss_pred             cccCCCcCccccccCC-----------CCccCCCcCCccCc
Confidence            34677777765 2222           23467777777554

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.

>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit

Probab=90.35  E-value=0.13  Score=39.09  Aligned_cols=24  Identities=25%  Similarity=0.772  Sum_probs=15.0

Q ss_pred             ccccccCCceecC-----CCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEP-----DFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~-----~~~fCP~CG~~  106 (107)
                      ..+||+||+.+-.     +...||+||..
T Consensus        26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h   54 (285)
T TIGR00515        26 WTKCPKCGQVLYTKELERNLEVCPKCDHH   54 (285)
T ss_pred             eeECCCCcchhhHHHHHhhCCCCCCCCCc
Confidence            4567777765533     56677777754

The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.

>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function []

Probab=90.32  E-value=0.21  Score=28.83  Aligned_cols=33  Identities=21%  Similarity=0.393  Sum_probs=19.9

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      +.+.|++|.........     .+....+++|++||+.
T Consensus        21 ~aLIC~~C~~hNGla~~-----~~~~~i~y~C~~Cg~~   53 (54)
T PF10058_consen   21 YALICSKCFSHNGLAPK-----EEFEEIQYRCPYCGAL   53 (54)
T ss_pred             eeEECcccchhhccccc-----ccCCceEEEcCCCCCc
Confidence            67778888776655321     0111236788888874

>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed

Probab=90.30  E-value=0.13  Score=39.33  Aligned_cols=24  Identities=25%  Similarity=0.578  Sum_probs=16.8

Q ss_pred             ccccccCCceecC-----CCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEP-----DFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~-----~~~fCP~CG~~  106 (107)
                      ..+||+|++.+..     +...||+||..
T Consensus        38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h   66 (296)
T CHL00174         38 WVQCENCYGLNYKKFLKSKMNICEQCGYH   66 (296)
T ss_pred             eeECCCccchhhHHHHHHcCCCCCCCCCC
Confidence            5677777776643     67778888764

>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]

Probab=90.30  E-value=0.12  Score=30.90  Aligned_cols=24  Identities=29%  Similarity=0.688  Sum_probs=14.5

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      ++.|.+|+...+.+.             ..||.||.+
T Consensus         4 ~kAC~~Ck~l~~~d~-------------e~CP~Cgs~   27 (64)
T COG2093           4 EKACKNCKRLTPEDT-------------EICPVCGST   27 (64)
T ss_pred             hHHHhhccccCCCCC-------------ccCCCCCCc
Confidence            456667766664422             457777766

>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=90.30  E-value=0.23  Score=28.39  Aligned_cols=16  Identities=38%  Similarity=0.966  Sum_probs=9.2

Q ss_pred             cccccCCceecCCCccCcCCCC
Q 033949           84 SKCRFCDRLVEPDFSFCPYCGS  105 (107)
Q Consensus        84 ~~C~~CG~~i~~~~~fCP~CG~  105 (107)
                      ..|+.||.+      ||-.|+.
T Consensus        41 ~~C~~C~~~------fC~~C~~   56 (64)
T PF01485_consen   41 VTCPSCGTE------FCFKCGE   56 (64)
T ss_dssp             CCTTSCCSE------ECSSSTS
T ss_pred             eECCCCCCc------CccccCc
Confidence            456666655      5655554

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=90.17  E-value=0.23  Score=32.86  Aligned_cols=13  Identities=31%  Similarity=0.864  Sum_probs=5.8

Q ss_pred             ceeCCCCCCCCCC
Q 033949           56 ALFCNNCNLLFPS   68 (107)
Q Consensus        56 ~~~C~~CG~~~~~   68 (107)
                      ...|..||..+++
T Consensus        71 ~~~C~~Cg~~~~~   83 (117)
T PRK00564         71 ELECKDCSHVFKP   83 (117)
T ss_pred             EEEhhhCCCcccc
Confidence            4445555544433

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=90.14  E-value=0.18  Score=35.77  Aligned_cols=11  Identities=45%  Similarity=1.252  Sum_probs=5.6

Q ss_pred             ceeCCCCCCCC
Q 033949           56 ALFCNNCNLLF   66 (107)
Q Consensus        56 ~~~C~~CG~~~   66 (107)
                      +-.||.||..+
T Consensus       117 ~Y~Cp~C~~ry  127 (178)
T PRK06266        117 FFFCPNCHIRF  127 (178)
T ss_pred             EEECCCCCcEE
Confidence            44455555544

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=90.12  E-value=0.2  Score=33.00  Aligned_cols=12  Identities=17%  Similarity=0.717  Sum_probs=5.4

Q ss_pred             ceeCCCCCCCCC
Q 033949           56 ALFCNNCNLLFP   67 (107)
Q Consensus        56 ~~~C~~CG~~~~   67 (107)
                      ...|+.||..++
T Consensus        70 ~~~C~~Cg~~~~   81 (114)
T PRK03681         70 ECWCETCQQYVT   81 (114)
T ss_pred             EEEcccCCCeee
Confidence            444444444443

>PRK12495 hypothetical protein; Provisional

Probab=90.11  E-value=0.16  Score=37.32  Aligned_cols=25  Identities=24%  Similarity=0.627  Sum_probs=18.9

Q ss_pred             CccccccCCceecC--CCccCcCCCCC
Q 033949           82 DVSKCRFCDRLVEP--DFSFCPYCGSA  106 (107)
Q Consensus        82 ~~~~C~~CG~~i~~--~~~fCP~CG~~  106 (107)
                      ...+|+.||.+|..  +-.+||.|+..
T Consensus        41 sa~hC~~CG~PIpa~pG~~~Cp~CQ~~   67 (226)
T PRK12495         41 TNAHCDECGDPIFRHDGQEFCPTCQQP   67 (226)
T ss_pred             chhhcccccCcccCCCCeeECCCCCCc
Confidence            45678888888876  77788888753

>TIGR03831 YgiT_finger YgiT-type zinc finger domain

Probab=89.89  E-value=0.69  Score=24.77  Aligned_cols=6  Identities=50%  Similarity=1.365  Sum_probs=3.3

Q ss_pred             CCCCCC
Q 033949           24 CINCGS   29 (107)
Q Consensus        24 C~~Cg~   29 (107)
                      ||.||.
T Consensus         1 C~~C~~    6 (46)
T TIGR03831         1 CPICGG    6 (46)
T ss_pred             CCCCCC
Confidence            556654

This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=89.67  E-value=0.29  Score=28.21  Aligned_cols=10  Identities=20%  Similarity=0.584  Sum_probs=8.2

Q ss_pred             CceeCCCCCC
Q 033949           55 PALFCNNCNL   64 (107)
Q Consensus        55 ~~~~C~~CG~   64 (107)
                      +++.|..||.
T Consensus        28 ~~V~C~~Cga   37 (61)
T PF14354_consen   28 YYVECTDCGA   37 (61)
T ss_pred             EEEEcCCCCC
Confidence            5688999988

>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=89.58  E-value=0.24  Score=28.80  Aligned_cols=30  Identities=13%  Similarity=0.453  Sum_probs=17.8

Q ss_pred             cEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949           21 AGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP   67 (107)
Q Consensus        21 ~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~   67 (107)
                      .++||.|++ ..                 =|+.....+.|..||..+.
T Consensus         7 ~VkCp~C~~~q~-----------------vFSha~t~V~C~~Cg~~L~   37 (55)
T PF01667_consen    7 DVKCPGCYNIQT-----------------VFSHAQTVVKCVVCGTVLA   37 (55)
T ss_dssp             EEE-TTT-SEEE-----------------EETT-SS-EE-SSSTSEEE
T ss_pred             EEECCCCCCeeE-----------------EEecCCeEEEcccCCCEec
Confidence            567999999 32                 1666656888999998763

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.

>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=89.55  E-value=0.23  Score=28.74  Aligned_cols=20  Identities=35%  Similarity=0.878  Sum_probs=9.6

Q ss_pred             cccccCCceecCCCccCcCCC
Q 033949           84 SKCRFCDRLVEPDFSFCPYCG  104 (107)
Q Consensus        84 ~~C~~CG~~i~~~~~fCP~CG  104 (107)
                      ..|++||+. ...-..||.||
T Consensus        27 ~~c~~cg~~-~~~H~vc~~cG   46 (56)
T PF01783_consen   27 VKCPNCGEP-KLPHRVCPSCG   46 (56)
T ss_dssp             EESSSSSSE-ESTTSBCTTTB
T ss_pred             eeeccCCCE-ecccEeeCCCC
Confidence            345555533 33344555554

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....

>PRK05978 hypothetical protein; Provisional

Probab=89.47  E-value=0.27  Score=34.04  Aligned_cols=33  Identities=27%  Similarity=0.647  Sum_probs=21.2

Q ss_pred             cEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949           21 AGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        21 ~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~   70 (107)
                      ..+||+||+ +.                |+ +--+-.-.|++||..++...
T Consensus        33 ~grCP~CG~G~L----------------F~-g~Lkv~~~C~~CG~~~~~~~   66 (148)
T PRK05978         33 RGRCPACGEGKL----------------FR-AFLKPVDHCAACGEDFTHHR   66 (148)
T ss_pred             cCcCCCCCCCcc----------------cc-cccccCCCccccCCccccCC
Confidence            457999999 54                11 00113556999999987754

>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus

Probab=89.39  E-value=0.11  Score=44.81  Aligned_cols=39  Identities=31%  Similarity=0.742  Sum_probs=0.0

Q ss_pred             CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949           20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      ....||.||+.-                      .....||.||.....               ..||+||.+...
T Consensus       666 ~~~~Cp~CG~~T----------------------~~~~~Cp~C~~~~~~---------------~~C~~C~~~~~~  704 (900)
T PF03833_consen  666 FYNRCPECGSHT----------------------EPVYVCPDCGIEVEE---------------DECPKCGRETTS  704 (900)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             hhhcCcccCCcc----------------------ccceeccccccccCc---------------cccccccccCcc
Confidence            345799999942                      367889999998753               369999998655

The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=89.33  E-value=0.18  Score=35.04  Aligned_cols=33  Identities=15%  Similarity=0.282  Sum_probs=16.2

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      .+-.||.|+..+.-...        .+....||.||+++..
T Consensus       108 ~~Y~Cp~c~~r~tf~eA--------~~~~F~Cp~Cg~~L~~  140 (158)
T TIGR00373       108 MFFICPNMCVRFTFNEA--------MELNFTCPRCGAMLDY  140 (158)
T ss_pred             CeEECCCCCcEeeHHHH--------HHcCCcCCCCCCEeee
Confidence            45556666665532110        0123456666666544

This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.

>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]

Probab=89.12  E-value=0.42  Score=31.05  Aligned_cols=34  Identities=24%  Similarity=0.490  Sum_probs=23.1

Q ss_pred             ECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCC
Q 033949           23 RCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLP   71 (107)
Q Consensus        23 ~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~   71 (107)
                      .||.|||.+.+..               +..-....|+-|+..++|+.+
T Consensus         3 FCP~Cgn~Live~---------------g~~~~rf~C~tCpY~~~I~~e   36 (105)
T KOG2906|consen    3 FCPTCGNMLIVES---------------GESCNRFSCRTCPYVFPISRE   36 (105)
T ss_pred             ccCCCCCEEEEec---------------CCeEeeEEcCCCCceeeEeee
Confidence            5999999442111               112257889999999988754

>PF14369 zf-RING_3: zinc-finger

Probab=88.89  E-value=0.36  Score=25.37  Aligned_cols=22  Identities=32%  Similarity=0.700  Sum_probs=14.4

Q ss_pred             cccccCCceecC-----CCccCcCCCC
Q 033949           84 SKCRFCDRLVEP-----DFSFCPYCGS  105 (107)
Q Consensus        84 ~~C~~CG~~i~~-----~~~fCP~CG~  105 (107)
                      +.|.+|...+..     +...||+|+.
T Consensus         3 ywCh~C~~~V~~~~~~~~~~~CP~C~~   29 (35)
T PF14369_consen    3 YWCHQCNRFVRIAPSPDSDVACPRCHG   29 (35)
T ss_pred             EeCccCCCEeEeCcCCCCCcCCcCCCC
Confidence            567888866653     3334888875

>PRK12496 hypothetical protein; Provisional

Probab=88.86  E-value=0.36  Score=33.80  Aligned_cols=12  Identities=25%  Similarity=0.880  Sum_probs=6.6

Q ss_pred             eeCCCCCCCCCC
Q 033949           57 LFCNNCNLLFPS   68 (107)
Q Consensus        57 ~~C~~CG~~~~~   68 (107)
                      ..|+-||..++.
T Consensus       128 ~~C~gC~~~~~~  139 (164)
T PRK12496        128 KVCKGCKKKYPE  139 (164)
T ss_pred             EECCCCCccccC
Confidence            346666666543

>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]

Probab=88.63  E-value=0.25  Score=32.85  Aligned_cols=23  Identities=39%  Similarity=0.554  Sum_probs=12.6

Q ss_pred             ccccccCCceecC--CCccCcCCCC
Q 033949           83 VSKCRFCDRLVEP--DFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~--~~~fCP~CG~  105 (107)
                      .-.|.+|+.++..  ..-.||.||+
T Consensus        70 ~~~C~~C~~~~~~e~~~~~CP~C~s   94 (115)
T COG0375          70 ECWCLDCGQEVELEELDYRCPKCGS   94 (115)
T ss_pred             EEEeccCCCeecchhheeECCCCCC
Confidence            3456666666555  2223666665

>TIGR01031 rpmF_bact ribosomal protein L32

Probab=88.55  E-value=0.23  Score=28.72  Aligned_cols=19  Identities=32%  Similarity=0.931  Sum_probs=8.1

Q ss_pred             ccccCCceecCCCccCcCCC
Q 033949           85 KCRFCDRLVEPDFSFCPYCG  104 (107)
Q Consensus        85 ~C~~CG~~i~~~~~fCP~CG  104 (107)
                      .|++||+. ...-..||.||
T Consensus        28 ~C~~cG~~-~~~H~vc~~cG   46 (55)
T TIGR01031        28 VCPNCGEF-KLPHRVCPSCG   46 (55)
T ss_pred             ECCCCCCc-ccCeeECCccC
Confidence            34444443 22334444444

This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.

>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=88.54  E-value=0.12  Score=35.15  Aligned_cols=10  Identities=30%  Similarity=0.574  Sum_probs=6.5

Q ss_pred             cccccCCcee
Q 033949           84 SKCRFCDRLV   93 (107)
Q Consensus        84 ~~C~~CG~~i   93 (107)
                      ..|+|||+..
T Consensus        69 sfchncgs~f   78 (160)
T COG4306          69 SFCHNCGSRF   78 (160)
T ss_pred             chhhcCCCCC
Confidence            4577777654

>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional

Probab=88.54  E-value=0.24  Score=33.08  Aligned_cols=11  Identities=18%  Similarity=0.407  Sum_probs=5.2

Q ss_pred             ceeCCCCCCCCC
Q 033949           56 ALFCNNCNLLFP   67 (107)
Q Consensus        56 ~~~C~~CG~~~~   67 (107)
                      ...| .||..++
T Consensus        70 ~~~C-~Cg~~~~   80 (124)
T PRK00762         70 EIEC-ECGYEGV   80 (124)
T ss_pred             eEEe-eCcCccc
Confidence            4445 5554443

>PRK05654 acetyl-CoA carboxylase subunit beta; Validated

Probab=88.51  E-value=0.21  Score=38.13  Aligned_cols=24  Identities=29%  Similarity=0.865  Sum_probs=15.1

Q ss_pred             ccccccCCceecC-----CCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEP-----DFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~-----~~~fCP~CG~~  106 (107)
                      ..+||+|+..+-.     +...||+||..
T Consensus        27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h   55 (292)
T PRK05654         27 WTKCPSCGQVLYRKELEANLNVCPKCGHH   55 (292)
T ss_pred             eeECCCccchhhHHHHHhcCCCCCCCCCC
Confidence            4567777766533     56677777764

>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]

Probab=88.48  E-value=0.27  Score=35.36  Aligned_cols=13  Identities=15%  Similarity=0.378  Sum_probs=7.2

Q ss_pred             ceeCCCCCCCCCC
Q 033949           56 ALFCNNCNLLFPS   68 (107)
Q Consensus        56 ~~~C~~CG~~~~~   68 (107)
                      +..|+.|++.+..
T Consensus       149 ~A~CsrC~~~L~~  161 (188)
T COG1096         149 YARCSRCRAPLVK  161 (188)
T ss_pred             EEEccCCCcceEE
Confidence            3446666666544

>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional

Probab=88.43  E-value=0.38  Score=42.24  Aligned_cols=51  Identities=20%  Similarity=0.419  Sum_probs=32.0

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC---CCccCcCCCCCC
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP---DFSFCPYCGSAL  107 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~---~~~fCP~CG~~l  107 (107)
                      +...||.|+..++-+++-.  .-.-.+++.+|..||+.-+-   ...-||+||.+|
T Consensus       795 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  848 (1006)
T PRK12775        795 GVATCPKCHRPLEGDEEYV--CCATSELQWRCDDCGKVSEGFAFPYGMCPACGGKL  848 (1006)
T ss_pred             CCccCcccCCCCCCCceeE--EecCcceeeehhhhccccccccCCcCcCcccccch
Confidence            4667888877776554310  00011246889999987655   346799999764

>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]

Probab=88.33  E-value=0.4  Score=31.20  Aligned_cols=40  Identities=23%  Similarity=0.431  Sum_probs=25.5

Q ss_pred             CCcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949           19 SGAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        19 ~~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~   70 (107)
                      ...++||+||. .+..-            ..+-....+.+.|.+||..++-..
T Consensus        20 ~k~FtCp~Cghe~vs~c------------tvkk~~~~g~~~Cg~CGls~e~ev   60 (104)
T COG4888          20 PKTFTCPRCGHEKVSSC------------TVKKTVNIGTAVCGNCGLSFECEV   60 (104)
T ss_pred             CceEecCccCCeeeeEE------------EEEecCceeEEEcccCcceEEEec
Confidence            35788999999 43200            012222346899999999886543

>PF14205 Cys_rich_KTR: Cysteine-rich KTR

Probab=88.17  E-value=0.71  Score=26.78  Aligned_cols=14  Identities=21%  Similarity=0.444  Sum_probs=7.8

Q ss_pred             CceeCCCCCCCCCC
Q 033949           55 PALFCNNCNLLFPS   68 (107)
Q Consensus        55 ~~~~C~~CG~~~~~   68 (107)
                      .-++||.|....-+
T Consensus        27 fPlyCpKCK~EtlI   40 (55)
T PF14205_consen   27 FPLYCPKCKQETLI   40 (55)
T ss_pred             ccccCCCCCceEEE
Confidence            45566666655433

>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]

Probab=88.11  E-value=0.25  Score=32.66  Aligned_cols=33  Identities=24%  Similarity=0.401  Sum_probs=21.5

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      ..+||.||+.+...+....       ....|++||.+.+.
T Consensus         2 m~FCp~Cgsll~p~~~~~~-------~~l~C~kCgye~~~   34 (113)
T COG1594           2 MRFCPKCGSLLYPKKDDEG-------GKLVCRKCGYEEEA   34 (113)
T ss_pred             ccccCCccCeeEEeEcCCC-------cEEECCCCCcchhc
Confidence            4689999999866432110       24678888876544

>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines

Probab=87.99  E-value=0.24  Score=30.87  Aligned_cols=35  Identities=23%  Similarity=0.380  Sum_probs=16.7

Q ss_pred             CCcEECCCCCC--CcEEEEEeeEEEEEEEeeeecCCC--CCceeCCCCCCCCCC
Q 033949           19 SGAGRCINCGS--TADLVEYEKVLKAFFVPVWKWPAK--EPALFCNNCNLLFPS   68 (107)
Q Consensus        19 ~~~~~C~~Cg~--~~~~~~~~~~f~lFFIP~~~~~~~--~~~~~C~~CG~~~~~   68 (107)
                      ...+.||.||+  ++.+               .++++  ...+.|..||..++.
T Consensus        20 ~~~F~CPfC~~~~sV~v---------------~idkk~~~~~~~C~~Cg~~~~~   58 (81)
T PF05129_consen   20 PKVFDCPFCNHEKSVSV---------------KIDKKEGIGILSCRVCGESFQT   58 (81)
T ss_dssp             SS----TTT--SS-EEE---------------EEETTTTEEEEEESSS--EEEE
T ss_pred             CceEcCCcCCCCCeEEE---------------EEEccCCEEEEEecCCCCeEEE
Confidence            46788999996  4432               23333  348999999998754

; PDB: 1WII_A.

>smart00647 IBR In Between Ring fingers

Probab=87.78  E-value=0.56  Score=26.74  Aligned_cols=11  Identities=18%  Similarity=0.646  Sum_probs=5.0

Q ss_pred             CceeCCCCCCC
Q 033949           55 PALFCNNCNLL   65 (107)
Q Consensus        55 ~~~~C~~CG~~   65 (107)
                      ..+.|+.||..
T Consensus        39 ~~v~C~~C~~~   49 (64)
T smart00647       39 NRVTCPKCGFS   49 (64)
T ss_pred             CeeECCCCCCe
Confidence            34445444433

the domains occurs between pairs og RING fingers

>TIGR03826 YvyF flagellar operon protein TIGR03826

Probab=87.78  E-value=0.17  Score=34.57  Aligned_cols=23  Identities=17%  Similarity=0.499  Sum_probs=19.8

Q ss_pred             CccccccCCceecCCCccCcCCCC
Q 033949           82 DVSKCRFCDRLVEPDFSFCPYCGS  105 (107)
Q Consensus        82 ~~~~C~~CG~~i~~~~~fCP~CG~  105 (107)
                      ..+.|..||+.|..+ +||+.|-.
T Consensus        80 l~~~CE~CG~~I~~G-r~C~~C~~  102 (137)
T TIGR03826        80 LGYPCERCGTSIREG-RLCDSCAG  102 (137)
T ss_pred             CcCcccccCCcCCCC-CccHHHHH
Confidence            468899999998887 99999854

This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.

>PRK14973 DNA topoisomerase I; Provisional

Probab=87.74  E-value=0.93  Score=39.75  Aligned_cols=66  Identities=17%  Similarity=0.307  Sum_probs=35.9

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCC---CCCCCCCCCCC-CCCCCCCccCccccccCCcee--c
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNN---CNLLFPSSLPP-PPPPPPLVSDVSKCRFCDRLV--E   94 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~---CG~~~~~~~~~-~~~~~~~~~~~~~C~~CG~~i--~   94 (107)
                      ...||.||....               +++.+.+.++.|+.   |+..+.+..+. .++    ......||.||..+  .
T Consensus       588 ~~~CP~CG~~l~---------------ik~~k~gkFigCS~Yp~Ck~t~~L~~~~~g~~----~~~~~~Cp~CG~p~~~~  648 (936)
T PRK14973        588 IGPCPVCGKDLR---------------IKHIGSSQFIGCSGYPDCTFNIGLPGTTWGWA----IRTDEVCPIHHLNHVRL  648 (936)
T ss_pred             cccCCcccccce---------------eecccCceeEECCCCCCCCccccCCccccccC----CCCCCCCCCCCCCceEE
Confidence            357999998431               23333334677765   88766553221 010    00124799999732  1


Q ss_pred             -C----CCc-cCcCCCC
Q 033949           95 -P----DFS-FCPYCGS  105 (107)
Q Consensus        95 -~----~~~-fCP~CG~  105 (107)
                       .    ++- =||.|..
T Consensus       649 ~r~Gr~g~fl~CP~C~~  665 (936)
T PRK14973        649 IRKGARPWDIGCPLCSH  665 (936)
T ss_pred             eecCCCcccccCccccc
Confidence             1    222 3999864

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=87.67  E-value=0.46  Score=33.07  Aligned_cols=12  Identities=25%  Similarity=0.509  Sum_probs=8.7

Q ss_pred             eeCCCCCCCCCC
Q 033949           57 LFCNNCNLLFPS   68 (107)
Q Consensus        57 ~~C~~CG~~~~~   68 (107)
                      ..|++||..+..
T Consensus        29 ~~c~~c~~~f~~   40 (154)
T PRK00464         29 RECLACGKRFTT   40 (154)
T ss_pred             eeccccCCcceE
Confidence            568888887743

>smart00547 ZnF_RBZ Zinc finger domain

Probab=87.60  E-value=0.36  Score=23.14  Aligned_cols=22  Identities=32%  Similarity=0.564  Sum_probs=17.3

Q ss_pred             ccccCCceecCCCccCcCCCCC
Q 033949           85 KCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        85 ~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      .|+.|+....+....|-.||++
T Consensus         4 ~C~~C~~~N~~~~~~C~~C~~p   25 (26)
T smart00547        4 ECPACTFLNFASRSKCFACGAP   25 (26)
T ss_pred             cCCCCCCcChhhhccccccCCc
Confidence            5788888877888888888875

Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.

>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=87.34  E-value=0.36  Score=40.48  Aligned_cols=24  Identities=33%  Similarity=0.845  Sum_probs=18.2

Q ss_pred             ccccccCCceecCCCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      ..+|+.||..+......||.||+.
T Consensus       568 ~~~C~~CG~~~~g~~~~CP~CGs~  591 (625)
T PRK08579        568 ITVCNKCGRSTTGLYTRCPRCGSE  591 (625)
T ss_pred             CccCCCCCCccCCCCCcCcCCCCc
Confidence            567888888666667788888853

>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]

Probab=87.34  E-value=0.42  Score=28.11  Aligned_cols=9  Identities=33%  Similarity=0.759  Sum_probs=4.5

Q ss_pred             ccccCCcee
Q 033949           85 KCRFCDRLV   93 (107)
Q Consensus        85 ~C~~CG~~i   93 (107)
                      +||.||..+
T Consensus        19 ~Cp~CG~~t   27 (59)
T COG2260          19 KCPVCGGDT   27 (59)
T ss_pred             cCCCCCCcc
Confidence            455555443

>PLN00209 ribosomal protein S27; Provisional

Probab=87.32  E-value=0.48  Score=29.96  Aligned_cols=33  Identities=12%  Similarity=0.398  Sum_probs=23.3

Q ss_pred             CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      ..++||.|++..                +=|+.....+.|..||..+..
T Consensus        35 m~VkCp~C~n~q----------------~VFShA~t~V~C~~Cg~~L~~   67 (86)
T PLN00209         35 MDVKCQGCFNIT----------------TVFSHSQTVVVCGSCQTVLCQ   67 (86)
T ss_pred             EEEECCCCCCee----------------EEEecCceEEEccccCCEeec
Confidence            367899999921                115555568999999998743

>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay

Probab=87.27  E-value=0.43  Score=35.00  Aligned_cols=13  Identities=31%  Similarity=0.516  Sum_probs=9.3

Q ss_pred             ccccccCCceecC
Q 033949           83 VSKCRFCDRLVEP   95 (107)
Q Consensus        83 ~~~C~~CG~~i~~   95 (107)
                      ...|+.||+-...
T Consensus        35 v~~C~~Cg~~~~~   47 (236)
T PF04981_consen   35 VTICPKCGRYRIG   47 (236)
T ss_pred             ceECCCCCCEECC
Confidence            4678888877655

This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].

>COG1592 Rubrerythrin [Energy production and conversion]

Probab=87.13  E-value=0.52  Score=33.25  Aligned_cols=25  Identities=16%  Similarity=0.458  Sum_probs=16.1

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      ...|+.||....-..            -..||.||++
T Consensus       134 ~~vC~vCGy~~~ge~------------P~~CPiCga~  158 (166)
T COG1592         134 VWVCPVCGYTHEGEA------------PEVCPICGAP  158 (166)
T ss_pred             EEEcCCCCCcccCCC------------CCcCCCCCCh
Confidence            677888877765422            2367777765

>PRK15103 paraquat-inducible membrane protein A; Provisional

Probab=87.09  E-value=0.43  Score=38.12  Aligned_cols=21  Identities=29%  Similarity=0.903  Sum_probs=9.8

Q ss_pred             cccCCceecCCCccCcCCCCC
Q 033949           86 CRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        86 C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      |+.||...+.+...||.||+.
T Consensus       224 C~~Cd~l~~~~~a~CpRC~~~  244 (419)
T PRK15103        224 CSCCTAILPADQPVCPRCHTK  244 (419)
T ss_pred             CCCCCCCCCCCCCCCCCCCCc
Confidence            555554443333345555543

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=87.05  E-value=0.19  Score=34.97  Aligned_cols=25  Identities=24%  Similarity=0.246  Sum_probs=12.9

Q ss_pred             ccccccCCceecC-----CCccCcCCCCCC
Q 033949           83 VSKCRFCDRLVEP-----DFSFCPYCGSAL  107 (107)
Q Consensus        83 ~~~C~~CG~~i~~-----~~~fCP~CG~~l  107 (107)
                      .+.||+||.....     .-=-||.||..|
T Consensus       109 ~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L  138 (158)
T TIGR00373       109 FFICPNMCVRFTFNEAMELNFTCPRCGAML  138 (158)
T ss_pred             eEECCCCCcEeeHHHHHHcCCcCCCCCCEe
Confidence            4556666655433     123366666543

This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.

>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]

Probab=87.03  E-value=0.27  Score=35.36  Aligned_cols=23  Identities=26%  Similarity=0.775  Sum_probs=20.2

Q ss_pred             ccccccCCceecC--CCccCcCCCC
Q 033949           83 VSKCRFCDRLVEP--DFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~--~~~fCP~CG~  105 (107)
                      ...|.+||+++..  ....||.||+
T Consensus       149 ~A~CsrC~~~L~~~~~~l~Cp~Cg~  173 (188)
T COG1096         149 YARCSRCRAPLVKKGNMLKCPNCGN  173 (188)
T ss_pred             EEEccCCCcceEEcCcEEECCCCCC
Confidence            5679999999987  6789999996

>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.98  E-value=0.4  Score=23.97  Aligned_cols=22  Identities=32%  Similarity=0.650  Sum_probs=13.5

Q ss_pred             ccccCCceecCCCccCcCCCCC
Q 033949           85 KCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        85 ~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      .|+.|+....+....|-.||++
T Consensus         6 ~C~~C~~~N~~~~~~C~~C~~~   27 (30)
T PF00641_consen    6 KCPSCTFMNPASRSKCVACGAP   27 (30)
T ss_dssp             EETTTTEEEESSSSB-TTT--B
T ss_pred             cCCCCcCCchHHhhhhhCcCCC
Confidence            5777777777777777777753

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....

>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=86.79  E-value=0.63  Score=34.41  Aligned_cols=13  Identities=31%  Similarity=0.577  Sum_probs=8.3

Q ss_pred             cccccCCceecCC
Q 033949           84 SKCRFCDRLVEPD   96 (107)
Q Consensus        84 ~~C~~CG~~i~~~   96 (107)
                      ..||+||...+.|
T Consensus       323 ~~C~~cg~~~~rD  335 (364)
T COG0675         323 FKCPRCGFVHDRD  335 (364)
T ss_pred             EECCCCCCeehhh
Confidence            4677777766553

>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE

Probab=86.55  E-value=0.67  Score=35.67  Aligned_cols=41  Identities=12%  Similarity=0.208  Sum_probs=22.3

Q ss_pred             CceeCCCCCCCCCCCCCCCCCC-CCCccCccccccCCceecC
Q 033949           55 PALFCNNCNLLFPSSLPPPPPP-PPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~-~~~~~~~~~C~~CG~~i~~   95 (107)
                      ..+.|++||..-.+.....+-. ++.......|..|+.-+..
T Consensus       223 ~R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~  264 (305)
T TIGR01562       223 VRVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLKI  264 (305)
T ss_pred             cCccCCCCCCCCceeeEeecCCCCCcceEEeeccccccchhh
Confidence            4789999998633221111110 0111235679999886644

The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).

>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]

Probab=86.51  E-value=0.14  Score=29.10  Aligned_cols=25  Identities=28%  Similarity=0.563  Sum_probs=22.4

Q ss_pred             CccccccCCceecCCCccCcCCCCC
Q 033949           82 DVSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        82 ~~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      +.++|-.|+|..+.+|+-|-.||++
T Consensus        13 ~kkIC~rC~Arnp~~A~kCRkC~~k   37 (50)
T COG1552          13 NKKICRRCYARNPPRATKCRKCGYK   37 (50)
T ss_pred             hHHHHHHhcCCCCcchhHHhhccCC
Confidence            3678999999999999999999975

>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional

Probab=86.34  E-value=0.8  Score=35.32  Aligned_cols=53  Identities=15%  Similarity=0.180  Sum_probs=32.3

Q ss_pred             CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCC-CccCccccccCCceecC
Q 033949           20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPP-LVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~-~~~~~~~C~~CG~~i~~   95 (107)
                      .-..|+-|+..|                     ....+.|++||..-.+.-.  .+.++ .......|..|+.-+..
T Consensus       211 RyL~CslC~teW---------------------~~~R~~C~~Cg~~~~l~y~--~~~~~~~~~r~e~C~~C~~YlK~  264 (309)
T PRK03564        211 RYLHCNLCESEW---------------------HVVRVKCSNCEQSGKLHYW--SLDSEQAAVKAESCGDCGTYLKI  264 (309)
T ss_pred             eEEEcCCCCCcc---------------------cccCccCCCCCCCCceeee--eecCCCcceEeeeccccccccee
Confidence            455799999987                     3357899999974322111  11111 11235679999876644

>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length

Probab=86.29  E-value=0.64  Score=32.07  Aligned_cols=13  Identities=38%  Similarity=0.831  Sum_probs=7.6

Q ss_pred             cCCCcEECCCCCC
Q 033949           17 LKSGAGRCINCGS   29 (107)
Q Consensus        17 ~~~~~~~C~~Cg~   29 (107)
                      .+.+...|.+||.
T Consensus       108 ~g~G~l~C~~Cg~  120 (146)
T PF07295_consen  108 VGPGTLVCENCGH  120 (146)
T ss_pred             ecCceEecccCCC
Confidence            3445566666666

Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.

>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function

Probab=86.26  E-value=0.38  Score=27.55  Aligned_cols=22  Identities=36%  Similarity=1.032  Sum_probs=12.5

Q ss_pred             cccccCCceecC----------CCccCcCCCC
Q 033949           84 SKCRFCDRLVEP----------DFSFCPYCGS  105 (107)
Q Consensus        84 ~~C~~CG~~i~~----------~~~fCP~CG~  105 (107)
                      ..|..|+-.|++          .-.+||+||.
T Consensus        23 ~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR   54 (56)
T PF02591_consen   23 GTCSGCHMELPPQELNEIRKGDEIVFCPNCGR   54 (56)
T ss_pred             CccCCCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence            356666665544          3456666664

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=86.21  E-value=0.64  Score=33.47  Aligned_cols=34  Identities=18%  Similarity=0.461  Sum_probs=26.6

Q ss_pred             CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      ...+|..|++.-              +||||... ....|+.|++.+..
T Consensus       151 kGfiCe~C~~~~--------------~IfPF~~~-~~~~C~~C~~v~H~  184 (202)
T PF13901_consen  151 KGFICEICNSDD--------------IIFPFQID-TTVRCPKCKSVFHK  184 (202)
T ss_pred             CCCCCccCCCCC--------------CCCCCCCC-CeeeCCcCccccch
Confidence            346788998832              57999985 89999999999843

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=86.17  E-value=0.43  Score=33.23  Aligned_cols=10  Identities=20%  Similarity=0.673  Sum_probs=8.2

Q ss_pred             cccccCCcee
Q 033949           84 SKCRFCDRLV   93 (107)
Q Consensus        84 ~~C~~CG~~i   93 (107)
                      +.|++||...
T Consensus        29 ~~c~~c~~~f   38 (154)
T PRK00464         29 RECLACGKRF   38 (154)
T ss_pred             eeccccCCcc
Confidence            7899999764

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=86.15  E-value=0.59  Score=29.48  Aligned_cols=33  Identities=12%  Similarity=0.409  Sum_probs=23.3

Q ss_pred             CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      ..++||.|++..                +=|+.....+.|..||..+..
T Consensus        34 m~VkCp~C~n~q----------------~VFShA~t~V~C~~Cg~~L~~   66 (85)
T PTZ00083         34 MDVKCPGCSQIT----------------TVFSHAQTVVLCGGCSSQLCQ   66 (85)
T ss_pred             EEEECCCCCCee----------------EEEecCceEEEccccCCEeec
Confidence            367899999921                115555568999999998743

>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.03  E-value=0.23  Score=24.89  Aligned_cols=19  Identities=37%  Similarity=0.884  Sum_probs=8.1

Q ss_pred             ccccCCceecC------CCccCcCC
Q 033949           85 KCRFCDRLVEP------DFSFCPYC  103 (107)
Q Consensus        85 ~C~~CG~~i~~------~~~fCP~C  103 (107)
                      .|+.|+..++.      +..+||.|
T Consensus         3 ~C~rC~~~~~~~~~~~r~~~~C~rC   27 (30)
T PF06827_consen    3 KCPRCWNYIEDIGINGRSTYLCPRC   27 (30)
T ss_dssp             B-TTT--BBEEEEETTEEEEE-TTT
T ss_pred             cCccCCCcceEeEecCCCCeECcCC
Confidence            45666655543      35566665

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....

>PRK05978 hypothetical protein; Provisional

Probab=86.00  E-value=0.49  Score=32.79  Aligned_cols=11  Identities=18%  Similarity=0.537  Sum_probs=5.7

Q ss_pred             cccccCCceec
Q 033949           84 SKCRFCDRLVE   94 (107)
Q Consensus        84 ~~C~~CG~~i~   94 (107)
                      ..|+.||.+..
T Consensus        53 ~~C~~CG~~~~   63 (148)
T PRK05978         53 DHCAACGEDFT   63 (148)
T ss_pred             CCccccCCccc
Confidence            34555555543

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=85.95  E-value=0.24  Score=35.10  Aligned_cols=12  Identities=25%  Similarity=0.121  Sum_probs=6.6

Q ss_pred             CcEECCCCCCCc
Q 033949           20 GAGRCINCGSTA   31 (107)
Q Consensus        20 ~~~~C~~Cg~~~   31 (107)
                      .-..||+||.++
T Consensus       116 ~~Y~Cp~C~~ry  127 (178)
T PRK06266        116 MFFFCPNCHIRF  127 (178)
T ss_pred             CEEECCCCCcEE
Confidence            344566666643

>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed

Probab=85.90  E-value=0.41  Score=39.54  Aligned_cols=26  Identities=31%  Similarity=0.791  Sum_probs=23.7

Q ss_pred             CccccccCCceecCCCccCcCCCCCC
Q 033949           82 DVSKCRFCDRLVEPDFSFCPYCGSAL  107 (107)
Q Consensus        82 ~~~~C~~CG~~i~~~~~fCP~CG~~l  107 (107)
                      ....|++||+.+.+..+||+.||.+|
T Consensus       591 ~~~~~~~~~~~~~~~~~f~~~~g~~~  616 (616)
T PRK07418        591 ELIYCSNCGAKNPSTHRFCPECGTKL  616 (616)
T ss_pred             CcccCCCCCCcCccccccchhhCCCC
Confidence            45789999999999999999999986

>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV

Probab=85.79  E-value=0.37  Score=36.38  Aligned_cols=24  Identities=38%  Similarity=0.735  Sum_probs=18.6

Q ss_pred             ccccccCCceecCCCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      ...|.+||+.+..=-+-||+||+.
T Consensus        82 l~~C~~CGa~V~~~e~~Cp~C~St  105 (314)
T PF09567_consen   82 LGKCNNCGANVSRLEESCPNCGST  105 (314)
T ss_pred             hhhhccccceeeehhhcCCCCCcc
Confidence            356888888888777888888863

All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system

>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i

Probab=85.73  E-value=1  Score=24.08  Aligned_cols=32  Identities=28%  Similarity=0.538  Sum_probs=20.4

Q ss_pred             EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCC---CCCCCCC
Q 033949           22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNN---CNLLFPS   68 (107)
Q Consensus        22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~---CG~~~~~   68 (107)
                      ..||.||+.+.               .+.++.+.++.|+.   |.....+
T Consensus         2 ~~CP~Cg~~lv---------------~r~~k~g~F~~Cs~yP~C~~~~~~   36 (39)
T PF01396_consen    2 EKCPKCGGPLV---------------LRRGKKGKFLGCSNYPECKYTEPL   36 (39)
T ss_pred             cCCCCCCceeE---------------EEECCCCCEEECCCCCCcCCeEeC
Confidence            46999997331               33455557788865   7776544

e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=85.69  E-value=1.5  Score=23.57  Aligned_cols=7  Identities=43%  Similarity=1.322  Sum_probs=5.6

Q ss_pred             ECCCCCC
Q 033949           23 RCINCGS   29 (107)
Q Consensus        23 ~C~~Cg~   29 (107)
                      .||+||+
T Consensus         2 ~Cp~C~~    8 (40)
T smart00440        2 PCPKCGN    8 (40)
T ss_pred             cCCCCCC
Confidence            5888887

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function

Probab=85.66  E-value=0.78  Score=33.32  Aligned_cols=10  Identities=30%  Similarity=0.624  Sum_probs=7.8

Q ss_pred             CcEECCCCCC
Q 033949           20 GAGRCINCGS   29 (107)
Q Consensus        20 ~~~~C~~Cg~   29 (107)
                      ++++||.|++
T Consensus         4 k~~~CPvC~~   13 (214)
T PF09986_consen    4 KKITCPVCGK   13 (214)
T ss_pred             CceECCCCCC
Confidence            5677888888

>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=85.58  E-value=0.52  Score=39.71  Aligned_cols=23  Identities=35%  Similarity=0.756  Sum_probs=16.9

Q ss_pred             ccccccCCceecCCCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      ..+|+.||.. ......||.||+.
T Consensus       626 ~~~C~~CG~~-~g~~~~CP~CG~~  648 (656)
T PRK08270        626 FSICPKHGYL-SGEHEFCPKCGEE  648 (656)
T ss_pred             CcccCCCCCc-CCCCCCCcCCcCc
Confidence            4568888873 4556789998875

>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=85.35  E-value=0.53  Score=39.48  Aligned_cols=23  Identities=30%  Similarity=0.766  Sum_probs=16.4

Q ss_pred             ccccccCCceecCCCccCcCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~  105 (107)
                      ..+|++||......-..||.||+
T Consensus       566 ~~iC~~CG~~~~g~~~~CP~CGs  588 (623)
T PRK08271        566 ITICNDCHHIDKRTGKRCPICGS  588 (623)
T ss_pred             CccCCCCCCcCCCCCcCCcCCCC
Confidence            45688888764555678888885

>PRK07219 DNA topoisomerase I; Validated

Probab=85.28  E-value=1.3  Score=38.29  Aligned_cols=21  Identities=33%  Similarity=0.770  Sum_probs=13.0

Q ss_pred             cccCCceecC-----CCccCcCCCCC
Q 033949           86 CRFCDRLVEP-----DFSFCPYCGSA  106 (107)
Q Consensus        86 C~~CG~~i~~-----~~~fCP~CG~~  106 (107)
                      ||.|......     .-.-||.||..
T Consensus       672 CP~C~~~~~~~~~~~~~~~CP~Cg~~  697 (822)
T PRK07219        672 CPDCEAEKEEEDPDEVIGPCPKCGGE  697 (822)
T ss_pred             CCCCCCCccccccccccccCCCCCCe
Confidence            7777765432     23568888754

>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=85.16  E-value=0.2  Score=35.78  Aligned_cols=21  Identities=24%  Similarity=0.585  Sum_probs=12.8

Q ss_pred             cccCCceecCCCccCcCCCCC
Q 033949           86 CRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        86 C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      |..|-++......-||-|+.+
T Consensus       156 C~~Cik~alk~~~~CP~C~kk  176 (187)
T KOG0320|consen  156 CSQCIKDALKNTNKCPTCRKK  176 (187)
T ss_pred             HHHHHHHHHHhCCCCCCcccc
Confidence            666666656666666666654

>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements

Probab=85.15  E-value=0.31  Score=36.41  Aligned_cols=37  Identities=27%  Similarity=0.486  Sum_probs=15.0

Q ss_pred             CcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949           20 GAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        20 ~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~   70 (107)
                      .+..||+||+ ....++.              ++..-...|++|++.|++..
T Consensus        30 ~n~yCP~Cg~~~L~~f~N--------------N~PVaDF~C~~C~eeyELKS   67 (254)
T PF06044_consen   30 ENMYCPNCGSKPLSKFEN--------------NRPVADFYCPNCNEEYELKS   67 (254)
T ss_dssp             HH---TTT--SS-EE----------------------EEE-TTT--EEEEEE
T ss_pred             HCCcCCCCCChhHhhccC--------------CCccceeECCCCchHHhhhh
Confidence            5778999999 4543332              33334778999999998743

The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.

>PRK06260 threonine synthase; Validated

Probab=85.13  E-value=0.69  Score=36.31  Aligned_cols=11  Identities=27%  Similarity=0.658  Sum_probs=5.1

Q ss_pred             eeCCCCCCCCC
Q 033949           57 LFCNNCNLLFP   67 (107)
Q Consensus        57 ~~C~~CG~~~~   67 (107)
                      +.|..||..++
T Consensus         4 ~~C~~cg~~~~   14 (397)
T PRK06260          4 LKCIECGKEYD   14 (397)
T ss_pred             EEECCCCCCCC
Confidence            44444444443

>PRK11595 DNA utilization protein GntX; Provisional

Probab=85.06  E-value=0.58  Score=34.04  Aligned_cols=21  Identities=19%  Similarity=0.338  Sum_probs=14.5

Q ss_pred             cccccCCceecCCCccCcCCC
Q 033949           84 SKCRFCDRLVEPDFSFCPYCG  104 (107)
Q Consensus        84 ~~C~~CG~~i~~~~~fCP~CG  104 (107)
                      ..|+.||.++......|+.|-
T Consensus        35 ~~C~~Cg~~~~~~~~~C~~C~   55 (227)
T PRK11595         35 TCCPQCGLPATHPHLPCGRCL   55 (227)
T ss_pred             CcCccCCCcCCCCCCCcHHHH
Confidence            469999987654334688874

>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A

Probab=85.04  E-value=0.3  Score=40.20  Aligned_cols=10  Identities=20%  Similarity=0.790  Sum_probs=3.6

Q ss_pred             ceeCCCCCCC
Q 033949           56 ALFCNNCNLL   65 (107)
Q Consensus        56 ~~~C~~CG~~   65 (107)
                      .-.|+.||..
T Consensus       491 ~~~C~~CG~~  500 (546)
T PF13597_consen  491 IDICPDCGYI  500 (546)
T ss_dssp             EEEETTT---
T ss_pred             cccccCCCcC
Confidence            4455555554

>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]

Probab=84.95  E-value=0.52  Score=40.07  Aligned_cols=73  Identities=25%  Similarity=0.430  Sum_probs=42.7

Q ss_pred             CCCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCC--CCCceeCCCCCCCCCCCCCCCCCCCCC--ccCccccccCCcee
Q 033949           18 KSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPA--KEPALFCNNCNLLFPSSLPPPPPPPPL--VSDVSKCRFCDRLV   93 (107)
Q Consensus        18 ~~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~--~~~~~~C~~CG~~~~~~~~~~~~~~~~--~~~~~~C~~CG~~i   93 (107)
                      .++..+|+.|-....               =|-++  ..++..|++||-.+.+-+. .|++.+-  ...-.-|+.|..+-
T Consensus        98 ~pD~a~C~~Cl~Ei~---------------dp~~rrY~YPF~~CT~CGPRfTIi~a-lPYDR~nTsM~~F~lC~~C~~EY  161 (750)
T COG0068          98 PPDAATCEDCLEEIF---------------DPNSRRYLYPFINCTNCGPRFTIIEA-LPYDRENTSMADFPLCPFCDKEY  161 (750)
T ss_pred             CCchhhhHHHHHHhc---------------CCCCcceeccccccCCCCcceeeecc-CCCCcccCccccCcCCHHHHHHh
Confidence            356678999987210               01111  2247789999999877442 2333221  11345688887776


Q ss_pred             cC--------CCccCcCCCCC
Q 033949           94 EP--------DFSFCPYCGSA  106 (107)
Q Consensus        94 ~~--------~~~fCP~CG~~  106 (107)
                      ..        ...-||.||=+
T Consensus       162 ~dP~nRRfHAQp~aCp~CGP~  182 (750)
T COG0068         162 KDPLNRRFHAQPIACPKCGPH  182 (750)
T ss_pred             cCccccccccccccCcccCCC
Confidence            44        56778888854

>COG4640 Predicted membrane protein [Function unknown]

Probab=84.80  E-value=0.52  Score=37.65  Aligned_cols=8  Identities=38%  Similarity=1.148  Sum_probs=3.6

Q ss_pred             CCCCCCCC
Q 033949           59 CNNCNLLF   66 (107)
Q Consensus        59 C~~CG~~~   66 (107)
                      |+-||+.+
T Consensus        18 C~qCG~~~   25 (465)
T COG4640          18 CTQCGHKF   25 (465)
T ss_pred             ccccCCcC
Confidence            44444444

>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]

Probab=84.35  E-value=0.48  Score=36.10  Aligned_cols=10  Identities=40%  Similarity=1.308  Sum_probs=5.0

Q ss_pred             CCccCcCCCC
Q 033949           96 DFSFCPYCGS  105 (107)
Q Consensus        96 ~~~fCP~CG~  105 (107)
                      +...||+||.
T Consensus        46 n~~vcp~c~~   55 (294)
T COG0777          46 NLKVCPKCGH   55 (294)
T ss_pred             hhhcccccCc
Confidence            4555555544

>PRK11032 hypothetical protein; Provisional

Probab=84.34  E-value=0.86  Score=31.97  Aligned_cols=14  Identities=29%  Similarity=0.510  Sum_probs=9.2

Q ss_pred             ecCCCcEECCCCCC
Q 033949           16 VLKSGAGRCINCGS   29 (107)
Q Consensus        16 ~~~~~~~~C~~Cg~   29 (107)
                      +.+.++..|.+||.
T Consensus       119 vvg~G~LvC~~Cg~  132 (160)
T PRK11032        119 VVGLGNLVCEKCHH  132 (160)
T ss_pred             eeecceEEecCCCC
Confidence            44456667777777

>PRK10445 endonuclease VIII; Provisional

Probab=84.28  E-value=0.49  Score=35.36  Aligned_cols=21  Identities=33%  Similarity=0.977  Sum_probs=14.1

Q ss_pred             cccccCCceecC------CCccCcCCC
Q 033949           84 SKCRFCDRLVEP------DFSFCPYCG  104 (107)
Q Consensus        84 ~~C~~CG~~i~~------~~~fCP~CG  104 (107)
                      ..||.||..|..      +.-|||.|-
T Consensus       236 ~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ  262 (263)
T PRK10445        236 EACERCGGIIEKTTLSSRPFYWCPGCQ  262 (263)
T ss_pred             CCCCCCCCEeEEEEECCCCcEECCCCc
Confidence            457777777754      667777773

>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional

Probab=84.08  E-value=0.5  Score=35.51  Aligned_cols=22  Identities=23%  Similarity=0.676  Sum_probs=17.2

Q ss_pred             ccccccCCceecC------CCccCcCCC
Q 033949           83 VSKCRFCDRLVEP------DFSFCPYCG  104 (107)
Q Consensus        83 ~~~C~~CG~~i~~------~~~fCP~CG  104 (107)
                      ...||.||++|..      +.-|||.|-
T Consensus       244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ  271 (272)
T PRK14810        244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ  271 (272)
T ss_pred             CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence            3569999988865      788899884

>PRK03922 hypothetical protein; Provisional

Probab=84.06  E-value=0.63  Score=30.73  Aligned_cols=13  Identities=15%  Similarity=0.549  Sum_probs=8.4

Q ss_pred             ccccccCCceecC
Q 033949           83 VSKCRFCDRLVEP   95 (107)
Q Consensus        83 ~~~C~~CG~~i~~   95 (107)
                      ...||.||+++++
T Consensus        49 ~~~cP~cge~~~~   61 (113)
T PRK03922         49 LTICPKCGEPFDS   61 (113)
T ss_pred             cccCCCCCCcCCc
Confidence            4567777777655

>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated

Probab=83.77  E-value=0.51  Score=35.36  Aligned_cols=22  Identities=36%  Similarity=0.881  Sum_probs=17.3

Q ss_pred             cccccCCceecC------CCccCcCCCC
Q 033949           84 SKCRFCDRLVEP------DFSFCPYCGS  105 (107)
Q Consensus        84 ~~C~~CG~~i~~------~~~fCP~CG~  105 (107)
                      ..|+.||+.|..      +.-|||.|-.
T Consensus       246 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ~  273 (274)
T PRK01103        246 EPCRRCGTPIEKIKQGGRSTFFCPRCQK  273 (274)
T ss_pred             CCCCCCCCeeEEEEECCCCcEECcCCCC
Confidence            459999988864      7889999854

>PF14353 CpXC: CpXC protein

Probab=83.75  E-value=1.6  Score=28.77  Aligned_cols=29  Identities=24%  Similarity=0.380  Sum_probs=17.0

Q ss_pred             CCcEECCCCCC----CcEEEE--EeeEEEEEEEee
Q 033949           19 SGAGRCINCGS----TADLVE--YEKVLKAFFVPV   47 (107)
Q Consensus        19 ~~~~~C~~Cg~----~~~~~~--~~~~f~lFFIP~   47 (107)
                      ...++||+||.    .+.+..  ..+.|.+++.|=
T Consensus        36 l~~~~CP~Cg~~~~~~~p~lY~D~~~~~~i~~~P~   70 (128)
T PF14353_consen   36 LFSFTCPSCGHKFRLEYPLLYHDPEKKFMIYYFPD   70 (128)
T ss_pred             cCEEECCCCCCceecCCCEEEEcCCCCEEEEEcCC
Confidence            35678888888    222222  233677777664

>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=83.70  E-value=0.69  Score=27.05  Aligned_cols=11  Identities=36%  Similarity=0.694  Sum_probs=6.2

Q ss_pred             ceeCCCCCCCC
Q 033949           56 ALFCNNCNLLF   66 (107)
Q Consensus        56 ~~~C~~CG~~~   66 (107)
                      +--|.+||..+
T Consensus        18 ~~NCl~CGkIi   28 (57)
T PF06221_consen   18 APNCLNCGKII   28 (57)
T ss_pred             cccccccChhh
Confidence            33466666655

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>COG1592 Rubrerythrin [Energy production and conversion]

Probab=83.66  E-value=0.75  Score=32.45  Aligned_cols=24  Identities=33%  Similarity=0.718  Sum_probs=20.6

Q ss_pred             ccccccCCceecC-CCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEP-DFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~-~~~fCP~CG~~  106 (107)
                      ...|+-||..... ....||-||.+
T Consensus       134 ~~vC~vCGy~~~ge~P~~CPiCga~  158 (166)
T COG1592         134 VWVCPVCGYTHEGEAPEVCPICGAP  158 (166)
T ss_pred             EEEcCCCCCcccCCCCCcCCCCCCh
Confidence            5889999998866 68899999964

>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg)

Probab=83.46  E-value=0.56  Score=35.21  Aligned_cols=20  Identities=40%  Similarity=1.022  Sum_probs=16.2

Q ss_pred             cccccCCceecC------CCccCcCC
Q 033949           84 SKCRFCDRLVEP------DFSFCPYC  103 (107)
Q Consensus        84 ~~C~~CG~~i~~------~~~fCP~C  103 (107)
                      ..|+.||++|..      +.-|||.|
T Consensus       246 ~pC~~Cg~~I~~~~~~gR~t~~CP~C  271 (272)
T TIGR00577       246 EPCRRCGTPIEKIKVGGRGTHFCPQC  271 (272)
T ss_pred             CCCCCCCCeeEEEEECCCCCEECCCC
Confidence            468999988865      78889988

All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>cd01675 RNR_III Class III ribonucleotide reductase

Probab=83.20  E-value=0.74  Score=37.96  Aligned_cols=23  Identities=35%  Similarity=0.662  Sum_probs=17.5

Q ss_pred             cccccCCceecCCCccCcCCCCC
Q 033949           84 SKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        84 ~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      .+|++||......-..||.||++
T Consensus       519 ~~C~~CG~~~~~~~~~CP~CGs~  541 (555)
T cd01675         519 DICNDCGYIGEGEGFKCPKCGSE  541 (555)
T ss_pred             ccCCCCCCCCcCCCCCCcCCCCc
Confidence            37999998655667889999864

Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w

>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]

Probab=83.18  E-value=0.7  Score=31.48  Aligned_cols=12  Identities=25%  Similarity=0.753  Sum_probs=8.8

Q ss_pred             CceeCCCCCCCC
Q 033949           55 PALFCNNCNLLF   66 (107)
Q Consensus        55 ~~~~C~~CG~~~   66 (107)
                      +...|+.||+.-
T Consensus        42 Pr~~Cp~C~~~~   53 (140)
T COG1545          42 PRAYCPKCGSET   53 (140)
T ss_pred             CcccCCCCCCCC
Confidence            567788888774

>PRK03988 translation initiation factor IF-2 subunit beta; Validated

Probab=83.06  E-value=1.9  Score=29.49  Aligned_cols=33  Identities=27%  Similarity=0.516  Sum_probs=20.9

Q ss_pred             cEECCCCCCCc-EEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           21 AGRCINCGSTA-DLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        21 ~~~C~~Cg~~~-~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      -+.|+.||+.- .+++               ..+...+.|..||+.-.+
T Consensus       102 yVlC~~C~spdT~l~k---------------~~r~~~l~C~ACGa~~~V  135 (138)
T PRK03988        102 YVICPECGSPDTKLIK---------------EGRIWVLKCEACGAETPV  135 (138)
T ss_pred             cEECCCCCCCCcEEEE---------------cCCeEEEEcccCCCCCcC
Confidence            46799999932 2222               123367889889887544

>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=83.04  E-value=0.4  Score=23.93  Aligned_cols=8  Identities=25%  Similarity=0.754  Sum_probs=2.4

Q ss_pred             CCCCCCCC
Q 033949           59 CNNCNLLF   66 (107)
Q Consensus        59 C~~CG~~~   66 (107)
                      ||.||+.+
T Consensus         2 CP~C~s~l    9 (28)
T PF03119_consen    2 CPVCGSKL    9 (28)
T ss_dssp             -TTT--BE
T ss_pred             cCCCCCEe
Confidence            45555544

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.

>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]

Probab=83.00  E-value=0.93  Score=25.82  Aligned_cols=11  Identities=18%  Similarity=0.576  Sum_probs=8.2

Q ss_pred             CceeCCCCCCC
Q 033949           55 PALFCNNCNLL   65 (107)
Q Consensus        55 ~~~~C~~CG~~   65 (107)
                      +.+.|..||..
T Consensus        36 dR~~CGkCgyT   46 (51)
T COG1998          36 DRWACGKCGYT   46 (51)
T ss_pred             ceeEeccccce
Confidence            57778888765

>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative

Probab=82.86  E-value=2  Score=29.21  Aligned_cols=33  Identities=18%  Similarity=0.441  Sum_probs=21.0

Q ss_pred             cEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           21 AGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        21 ~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      -+.|+.|++ .-.+++.               .+.+.+.|..||+.-.+
T Consensus        97 yVlC~~C~sPdT~l~k~---------------~r~~~l~C~ACGa~~~v  130 (133)
T TIGR00311        97 YVICRECNRPDTRIIKE---------------GRVSLLKCEACGAKAPL  130 (133)
T ss_pred             eEECCCCCCCCcEEEEe---------------CCeEEEecccCCCCCcc
Confidence            467999999 3222221               23357789999987654

>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins

Probab=82.84  E-value=0.75  Score=29.86  Aligned_cols=13  Identities=15%  Similarity=0.460  Sum_probs=9.0

Q ss_pred             ccccccCCceecC
Q 033949           83 VSKCRFCDRLVEP   95 (107)
Q Consensus        83 ~~~C~~CG~~i~~   95 (107)
                      ...||.||.++++
T Consensus        47 ~~~cP~Cge~~~~   59 (102)
T PF04475_consen   47 DTICPKCGEELDS   59 (102)
T ss_pred             cccCCCCCCccCc
Confidence            4567777777765

>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]

Probab=82.66  E-value=0.97  Score=28.69  Aligned_cols=31  Identities=23%  Similarity=0.486  Sum_probs=22.3

Q ss_pred             CcEECCCCCCC-cEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           20 GAGRCINCGST-ADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        20 ~~~~C~~Cg~~-~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      +...||.||.. +.  +                .......|.+||+.+.-
T Consensus        34 ~~~~Cp~C~~~~Vk--R----------------~a~GIW~C~kCg~~fAG   65 (89)
T COG1997          34 AKHVCPFCGRTTVK--R----------------IATGIWKCRKCGAKFAG   65 (89)
T ss_pred             cCCcCCCCCCccee--e----------------eccCeEEcCCCCCeecc
Confidence            34579999993 31  1                13479999999999854

>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=82.60  E-value=1  Score=26.73  Aligned_cols=14  Identities=21%  Similarity=0.437  Sum_probs=7.2

Q ss_pred             cCCCcEECCCCCCC
Q 033949           17 LKSGAGRCINCGST   30 (107)
Q Consensus        17 ~~~~~~~C~~Cg~~   30 (107)
                      ++.+.+.||+|+..
T Consensus        44 g~~gev~CPYC~t~   57 (62)
T COG4391          44 GDEGEVVCPYCSTR   57 (62)
T ss_pred             CCCCcEecCccccE
Confidence            33445555555553

>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5

Probab=82.44  E-value=1.7  Score=28.54  Aligned_cols=29  Identities=28%  Similarity=0.557  Sum_probs=17.6

Q ss_pred             cEECCCCCCC-cEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCC
Q 033949           21 AGRCINCGST-ADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNL   64 (107)
Q Consensus        21 ~~~C~~Cg~~-~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~   64 (107)
                      -+.|+.|+++ -++++.               .+...+.|..||+
T Consensus        80 yVlC~~C~spdT~l~k~---------------~r~~~l~C~aCGa  109 (110)
T smart00653       80 YVLCPECGSPDTELIKE---------------NRLFFLKCEACGA  109 (110)
T ss_pred             cEECCCCCCCCcEEEEe---------------CCeEEEEccccCC
Confidence            3679999982 222221               1335777888886

>COG1885 Uncharacterized protein conserved in archaea [Function unknown]

Probab=82.36  E-value=0.84  Score=29.98  Aligned_cols=13  Identities=23%  Similarity=0.557  Sum_probs=8.3

Q ss_pred             ccccccCCceecC
Q 033949           83 VSKCRFCDRLVEP   95 (107)
Q Consensus        83 ~~~C~~CG~~i~~   95 (107)
                      ...||.||+.+++
T Consensus        49 ~t~CP~Cg~~~e~   61 (115)
T COG1885          49 STSCPKCGEPFES   61 (115)
T ss_pred             cccCCCCCCccce
Confidence            3457777776655

>TIGR00155 pqiA_fam integral membrane protein, PqiA family

Probab=82.31  E-value=0.95  Score=35.98  Aligned_cols=15  Identities=13%  Similarity=0.366  Sum_probs=11.3

Q ss_pred             CCceeCCCCCCCCCC
Q 033949           54 EPALFCNNCNLLFPS   68 (107)
Q Consensus        54 ~~~~~C~~CG~~~~~   68 (107)
                      ++...||.||+....
T Consensus        31 g~~a~CpRCg~~L~~   45 (403)
T TIGR00155        31 GQKAACPRCGTTLTV   45 (403)
T ss_pred             CCeeECCCCCCCCcC
Confidence            367888888888744

This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=82.21  E-value=2.4  Score=23.92  Aligned_cols=13  Identities=23%  Similarity=0.483  Sum_probs=8.8

Q ss_pred             ceeCCCCCCCCCC
Q 033949           56 ALFCNNCNLLFPS   68 (107)
Q Consensus        56 ~~~C~~CG~~~~~   68 (107)
                      +..|+.||+..+.
T Consensus        26 ~~~C~~Cga~~~~   38 (53)
T TIGR03655        26 YFECSTCGASGPV   38 (53)
T ss_pred             EEECCCCCCCccc
Confidence            3468888877654

Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.

>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional

Probab=82.02  E-value=0.66  Score=34.80  Aligned_cols=21  Identities=33%  Similarity=0.869  Sum_probs=13.3

Q ss_pred             cccccCCceecC------CCccCcCCC
Q 033949           84 SKCRFCDRLVEP------DFSFCPYCG  104 (107)
Q Consensus        84 ~~C~~CG~~i~~------~~~fCP~CG  104 (107)
                      ..|+.||+.|..      +.-|||.|-
T Consensus       236 ~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ  262 (269)
T PRK14811        236 QPCPRCGTPIEKIVVGGRGTHFCPQCQ  262 (269)
T ss_pred             CCCCcCCCeeEEEEECCCCcEECCCCc
Confidence            357777766654      566777764

>TIGR00354 polC DNA polymerase, archaeal type II, large subunit

Probab=81.97  E-value=0.77  Score=40.38  Aligned_cols=22  Identities=32%  Similarity=0.830  Sum_probs=17.7

Q ss_pred             ccccccCCceecCCCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      .++||+||..  .-...||.||++
T Consensus       625 ~RKCPkCG~y--Tlk~rCP~CG~~  646 (1095)
T TIGR00354       625 IRKCPQCGKE--SFWLKCPVCGEL  646 (1095)
T ss_pred             EEECCCCCcc--cccccCCCCCCc
Confidence            5779999987  556789999975

This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.

>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]

Probab=81.97  E-value=0.76  Score=34.97  Aligned_cols=25  Identities=28%  Similarity=0.585  Sum_probs=19.0

Q ss_pred             CccccccCCceecC----CCccCcCCCCC
Q 033949           82 DVSKCRFCDRLVEP----DFSFCPYCGSA  106 (107)
Q Consensus        82 ~~~~C~~CG~~i~~----~~~fCP~CG~~  106 (107)
                      ..+.|+.||+++.+    -+..||.||..
T Consensus       110 ~~RFCg~CG~~~~~~~~g~~~~C~~cg~~  138 (279)
T COG2816         110 SHRFCGRCGTKTYPREGGWARVCPKCGHE  138 (279)
T ss_pred             hCcCCCCCCCcCccccCceeeeCCCCCCc
Confidence            35778888888876    57788888864

>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function

Probab=81.95  E-value=0.91  Score=32.97  Aligned_cols=16  Identities=19%  Similarity=0.436  Sum_probs=12.8

Q ss_pred             CceeCCCCCCCCCCCC
Q 033949           55 PALFCNNCNLLFPSSL   70 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~   70 (107)
                      ..+.||.|++.+....
T Consensus         4 k~~~CPvC~~~F~~~~   19 (214)
T PF09986_consen    4 KKITCPVCGKEFKTKK   19 (214)
T ss_pred             CceECCCCCCeeeeeE
Confidence            4689999999997643

>TIGR00155 pqiA_fam integral membrane protein, PqiA family

Probab=81.89  E-value=1.6  Score=34.64  Aligned_cols=34  Identities=15%  Similarity=0.476  Sum_probs=22.3

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      +...|+.||..++...-..       .....||.||+++..
T Consensus        12 ~~~~C~~Cd~l~~~~~l~~-------g~~a~CpRCg~~L~~   45 (403)
T TIGR00155        12 KHILCSQCDMLVALPRIES-------GQKAACPRCGTTLTV   45 (403)
T ss_pred             CeeeCCCCCCcccccCCCC-------CCeeECCCCCCCCcC
Confidence            4667999998876533111       024579999998854

This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.

>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A

Probab=81.73  E-value=0.9  Score=28.27  Aligned_cols=14  Identities=14%  Similarity=0.266  Sum_probs=3.7

Q ss_pred             ceeCCCCCCCCCCC
Q 033949           56 ALFCNNCNLLFPSS   69 (107)
Q Consensus        56 ~~~C~~CG~~~~~~   69 (107)
                      ...|..||..+.++
T Consensus         9 ~qiCqiCGD~VGl~   22 (80)
T PF14569_consen    9 GQICQICGDDVGLT   22 (80)
T ss_dssp             S-B-SSS--B--B-
T ss_pred             CcccccccCccccC
Confidence            34555566555443

>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=81.61  E-value=0.71  Score=27.13  Aligned_cols=16  Identities=25%  Similarity=0.353  Sum_probs=5.8

Q ss_pred             CCCceeCCCCCCCCCC
Q 033949           53 KEPALFCNNCNLLFPS   68 (107)
Q Consensus        53 ~~~~~~C~~CG~~~~~   68 (107)
                      +.....|..|+..+..
T Consensus         6 d~~~~~C~~C~~~F~~   21 (69)
T PF01363_consen    6 DSEASNCMICGKKFSL   21 (69)
T ss_dssp             GGG-SB-TTT--B-BS
T ss_pred             CCCCCcCcCcCCcCCC
Confidence            3345566666666643

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=81.60  E-value=0.92  Score=27.74  Aligned_cols=38  Identities=24%  Similarity=0.417  Sum_probs=25.5

Q ss_pred             EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCC--CCCCCCCC
Q 033949           22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCN--NCNLLFPS   68 (107)
Q Consensus        22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~--~CG~~~~~   68 (107)
                      ..||.||+.+ .++.+++.+-        ..+.-+-.|.  .||..+..
T Consensus         2 m~CP~Cg~~a-~irtSr~~s~--------~~~~~Y~qC~N~eCg~tF~t   41 (72)
T PRK09678          2 FHCPLCQHAA-HARTSRYITD--------TTKERYHQCQNVNCSATFIT   41 (72)
T ss_pred             ccCCCCCCcc-EEEEChhcCh--------hhheeeeecCCCCCCCEEEE
Confidence            4699999965 5666666551        1123577788  89998854

>PRK00481 NAD-dependent deacetylase; Provisional

Probab=81.59  E-value=1.8  Score=31.71  Aligned_cols=13  Identities=15%  Similarity=0.485  Sum_probs=7.1

Q ss_pred             CceeCCCCCCCCC
Q 033949           55 PALFCNNCNLLFP   67 (107)
Q Consensus        55 ~~~~C~~CG~~~~   67 (107)
                      ..+.|..|+..++
T Consensus       121 ~~~~C~~C~~~~~  133 (242)
T PRK00481        121 LRARCTKCGQTYD  133 (242)
T ss_pred             CceeeCCCCCCcC
Confidence            4555666655543

>PRK07591 threonine synthase; Validated

Probab=81.52  E-value=1  Score=35.80  Aligned_cols=12  Identities=17%  Similarity=0.382  Sum_probs=6.2

Q ss_pred             eeCCCCCCCCCC
Q 033949           57 LFCNNCNLLFPS   68 (107)
Q Consensus        57 ~~C~~CG~~~~~   68 (107)
                      ..||.||..++.
T Consensus        34 ~~C~~cg~~l~~   45 (421)
T PRK07591         34 HVCEECFGPLEV   45 (421)
T ss_pred             ccCCCCCCeEEE
Confidence            455555554443

>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase

Probab=81.32  E-value=0.97  Score=37.50  Aligned_cols=24  Identities=38%  Similarity=0.603  Sum_probs=15.3

Q ss_pred             ccccccCCceecCCCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      ..+|++||..-+.....||.||++
T Consensus       524 ~~~C~~CG~~g~~~~~~CP~Cgs~  547 (579)
T TIGR02487       524 VDVCEDCGYTGEGLNDKCPKCGSH  547 (579)
T ss_pred             CccCCCCCCCCCCCCCcCcCCCCc
Confidence            456888887322233578888864

This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.

>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

Probab=81.09  E-value=0.78  Score=34.16  Aligned_cols=22  Identities=36%  Similarity=1.025  Sum_probs=12.7

Q ss_pred             cccccCCceecC----------CCccCcCCCC
Q 033949           84 SKCRFCDRLVEP----------DFSFCPYCGS  105 (107)
Q Consensus        84 ~~C~~CG~~i~~----------~~~fCP~CG~  105 (107)
                      ..|..|+-.|++          +-.+||+||+
T Consensus       198 ~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgR  229 (239)
T COG1579         198 RVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGR  229 (239)
T ss_pred             CcccCCeeeecHHHHHHHhcCCCCccCCccch
Confidence            456666555544          4566666664

>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length

Probab=81.06  E-value=1  Score=31.13  Aligned_cols=29  Identities=24%  Similarity=0.571  Sum_probs=18.8

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      +.+.|.+||+.+.+.... .        ...||.||..
T Consensus       111 G~l~C~~Cg~~~~~~~~~-~--------l~~Cp~C~~~  139 (146)
T PF07295_consen  111 GTLVCENCGHEVELTHPE-R--------LPPCPKCGHT  139 (146)
T ss_pred             ceEecccCCCEEEecCCC-c--------CCCCCCCCCC
Confidence            577788888877665421 1        2368888764

Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.

>PRK09710 lar restriction alleviation and modification protein; Reviewed

Probab=81.05  E-value=2.5  Score=25.32  Aligned_cols=34  Identities=21%  Similarity=0.227  Sum_probs=21.2

Q ss_pred             ECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949           23 RCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        23 ~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~   70 (107)
                      -||.||....+++..              ...+++.|..||+.-+...
T Consensus         8 PCPFCG~~~~~v~~~--------------~g~~~v~C~~CgA~~~~~~   41 (64)
T PRK09710          8 PCPFCGCPSVTVKAI--------------SGYYRAKCNGCESRTGYGG   41 (64)
T ss_pred             CCCCCCCceeEEEec--------------CceEEEEcCCCCcCccccc
Confidence            399999954444431              1223688999998765533

>TIGR00310 ZPR1_znf ZPR1 zinc finger domain

Probab=80.75  E-value=1.1  Score=32.25  Aligned_cols=39  Identities=21%  Similarity=0.542  Sum_probs=21.3

Q ss_pred             ECCCCCCCcEEEEEeeEEEEEE-EeeeecCCCCCceeCCCCCCCCC
Q 033949           23 RCINCGSTADLVEYEKVLKAFF-VPVWKWPAKEPALFCNNCNLLFP   67 (107)
Q Consensus        23 ~C~~Cg~~~~~~~~~~~f~lFF-IP~~~~~~~~~~~~C~~CG~~~~   67 (107)
                      .||+||......     ..+.= ||-|+==.- -...|++||....
T Consensus         2 ~Cp~C~~~~~~~-----~~~~~~IP~F~evii-~sf~C~~CGyr~~   41 (192)
T TIGR00310         2 DCPSCGGECETV-----MKTVNDIPYFGEVLE-TSTICEHCGYRSN   41 (192)
T ss_pred             cCCCCCCCCEEE-----EEEEcCCCCcceEEE-EEEECCCCCCccc
Confidence            599999832111     11222 554441111 2567999999863

>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]

Probab=80.72  E-value=1.1  Score=35.82  Aligned_cols=35  Identities=14%  Similarity=0.440  Sum_probs=19.6

Q ss_pred             CCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949           54 EPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        54 ~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      .....|+.|+.......-..       ...-.||.||+.+..
T Consensus        16 ~~~~~C~eCd~~~~~P~l~~-------~q~A~CPRC~~~l~~   50 (418)
T COG2995          16 GHLILCPECDMLVSLPRLDS-------GQSAYCPRCGHTLTR   50 (418)
T ss_pred             cceecCCCCCceeccccCCC-------CCcccCCCCCCcccc
Confidence            35667777777665432110       023567777777655

>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]

Probab=80.56  E-value=1.1  Score=26.23  Aligned_cols=21  Identities=29%  Similarity=0.610  Sum_probs=11.6

Q ss_pred             cccccCCceecCCCccCcCCCC
Q 033949           84 SKCRFCDRLVEPDFSFCPYCGS  105 (107)
Q Consensus        84 ~~C~~CG~~i~~~~~fCP~CG~  105 (107)
                      ..|++||... -.-..|++||.
T Consensus        28 ~~c~~cG~~~-l~Hrvc~~cg~   48 (57)
T COG0333          28 SVCPNCGEYK-LPHRVCLKCGY   48 (57)
T ss_pred             eeccCCCCcc-cCceEcCCCCC
Confidence            4566666653 33455666664

>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6

Probab=80.55  E-value=0.42  Score=37.63  Aligned_cols=36  Identities=31%  Similarity=0.594  Sum_probs=21.9

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC---CCccCcCCCCC
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP---DFSFCPYCGSA  106 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~---~~~fCP~CG~~  106 (107)
                      -.||.||..-..              ...|.+||..+++   ..-.|.-||++
T Consensus       137 g~CP~C~~~~a~--------------g~~Ce~cG~~~~~~~l~~p~~~~~g~~  175 (391)
T PF09334_consen  137 GTCPYCGSDKAR--------------GDQCENCGRPLEPEELINPVCKICGSP  175 (391)
T ss_dssp             CEETTT--SSCT--------------TTEETTTSSBEECCCSECEEETTTS-B
T ss_pred             ccccCcCccccC--------------CCcccCCCCCcccccccCCcccccccc
Confidence            579999854321              3468888888875   45566666654

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....

>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family

Probab=80.47  E-value=0.95  Score=34.87  Aligned_cols=42  Identities=17%  Similarity=0.374  Sum_probs=30.3

Q ss_pred             CCcEECCCCCC------CcEEEEE--ee--EEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           19 SGAGRCINCGS------TADLVEY--EK--VLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        19 ~~~~~C~~Cg~------~~~~~~~--~~--~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      +-++.|..||+      ++...+.  .+  |++   ||||.|.     +.|+.|+..+.+
T Consensus        38 Pf~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls---~~I~rF~-----~kC~~C~~~i~~   89 (324)
T PF04502_consen   38 PFNIWCNTCGEYIYKGVRFNARKEKVGNEKYLS---TPIYRFY-----IKCPRCSNEIEF   89 (324)
T ss_pred             CccCcCCCCccccccceeeeeeeEecCCCcccc---ceEEEEE-----EEcCCCCCEEee
Confidence            56788999999      2223322  34  665   9999865     569999999876

>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases []

Probab=80.32  E-value=2.3  Score=23.07  Aligned_cols=7  Identities=43%  Similarity=1.379  Sum_probs=4.0

Q ss_pred             ECCCCCC
Q 033949           23 RCINCGS   29 (107)
Q Consensus        23 ~C~~Cg~   29 (107)
                      .||.||.
T Consensus         4 ~C~~Cg~   10 (47)
T PF13005_consen    4 ACPDCGG   10 (47)
T ss_pred             cCCCCCc
Confidence            4555555

>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr

Probab=80.19  E-value=0.45  Score=26.43  Aligned_cols=7  Identities=57%  Similarity=1.450  Sum_probs=3.8

Q ss_pred             CCCCCCC
Q 033949           24 CINCGST   30 (107)
Q Consensus        24 C~~Cg~~   30 (107)
                      ||+||+.
T Consensus         2 CP~Cg~~    8 (47)
T PF04606_consen    2 CPHCGSK    8 (47)
T ss_pred             cCCCCCe
Confidence            5555553

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent

>PRK11827 hypothetical protein; Provisional

Probab=80.06  E-value=2.7  Score=24.77  Aligned_cols=33  Identities=24%  Similarity=0.385  Sum_probs=24.6

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~   70 (107)
                      -..||.|+....                 ++.....+.|..||-.|++..
T Consensus         8 ILaCP~ckg~L~-----------------~~~~~~~Lic~~~~laYPI~d   40 (60)
T PRK11827          8 IIACPVCNGKLW-----------------YNQEKQELICKLDNLAFPLRD   40 (60)
T ss_pred             heECCCCCCcCe-----------------EcCCCCeEECCccCeeccccC
Confidence            357999998542                 344446899999999998854

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	107
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	98.11
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	97.82
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	97.13
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	96.51
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	96.49
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	96.35
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	96.15
2jne_A	101	Hypothetical protein YFGJ; zinc fingers, two zinc,	96.07
2jne_A	101	Hypothetical protein YFGJ; zinc fingers, two zinc,	96.04
2apo_B	60	Ribosome biogenesis protein NOP10; protein-protein	95.62
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	95.45
2aus_D	60	NOP10, ribosome biogenesis protein NOP10; isomeras	95.33
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	94.85
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	94.54
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	94.28
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	94.0
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	93.87
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	93.82
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	93.78
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	93.6
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	93.53
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	93.39
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	93.24
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	92.64
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	92.59
3a43_A	139	HYPD, hydrogenase nickel incorporation protein HYP	92.42
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	92.33
3a43_A	139	HYPD, hydrogenase nickel incorporation protein HYP	92.3
2ayj_A	56	50S ribosomal protein L40E; Zn-binding, beta-stran	92.29
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	92.25
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	91.91
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	91.8
2apo_B	60	Ribosome biogenesis protein NOP10; protein-protein	91.53
2con_A	79	RUH-035 protein, NIN one binding protein; ribosome	91.14
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	90.78
2zjr_Z	60	50S ribosomal protein L32; ribosome, large ribosom	90.68
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	90.5
3irb_A	145	Uncharacterized protein from DUF35 family; 1381535	90.33
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	90.21
3v2d_5	60	50S ribosomal protein L32; ribosome associated inh	90.01
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	88.54
6rxn_A	46	Rubredoxin; electron transfer(iron-sulfur protein)	88.42
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	88.42
3pwf_A	170	Rubrerythrin; non heme iron peroxidases, oxidative	88.4
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	87.96
2k2d_A	79	Ring finger and CHY zinc finger domain- containing	87.85
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	87.7
1wii_A	85	Hypothetical UPF0222 protein MGC4549; domain of un	87.42
4esj_A	257	Type-2 restriction enzyme DPNI; restriction endonu	87.34
2gnr_A	145	Conserved hypothetical protein; 13815350, structur	87.28
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	87.14
3pwf_A	170	Rubrerythrin; non heme iron peroxidases, oxidative	86.63
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	86.26
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	86.2
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	85.97
2gmg_A	105	Hypothetical protein PF0610; winged-helix like pro	85.6
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	85.19
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	85.16
1k81_A	36	EIF-2-beta, probable translation initiation factor	84.96
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	84.95
2gmg_A	105	Hypothetical protein PF0610; winged-helix like pro	84.41
2kn9_A	81	Rubredoxin; metalloprotein, ssgcid, structural gen	84.37
1e8j_A	52	Rubredoxin; iron-sulfur-protein, zinc-substitution	84.21
4rxn_A	54	Rubredoxin; electron transfer(iron-sulfur protein)	84.1
2l7x_A	77	Envelope glycoprotein; cytoplasmic tail, viral pro	83.92
1dx8_A	70	Rubredoxin; electron transport, zinc-substitution;	83.87
1yuz_A	202	Nigerythrin; rubrythrin, rubredoxin, hemerythrin,	83.63
1x4u_A	84	Zinc finger, FYVE domain containing 27 isoform B;	83.59
1ryq_A	69	DNA-directed RNA polymerase, subunit E''; structur	83.52
1lko_A	191	Rubrerythrin all-iron(II) form; reduced form, DIIR	83.45
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	83.38
4esj_A	257	Type-2 restriction enzyme DPNI; restriction endonu	83.04
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	82.79
2v3b_B	55	Rubredoxin 2, rubredoxin; alkane degradation, iron	82.64
1nj3_A	31	NPL4; NZF domain, rubredoxin knuckle, beta-ribbon,	82.62
1y02_A	120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	82.42
2lk0_A	32	RNA-binding protein 5; zinc finger; NMR {Homo sapi	82.03
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	81.67
2akl_A	138	PHNA-like protein PA0128; two domains, Zn binding	80.33
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	80.23
3nw0_A	238	Non-structural maintenance of chromosomes element	80.2
1joc_A	125	EEA1, early endosomal autoantigen 1; FYVE domain,	80.19

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=98.11  E-value=8.2e-07  Score=54.71  Aligned_cols=37  Identities=19%  Similarity=0.381  Sum_probs=24.3

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC------CCccCcCCCC
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP------DFSFCPYCGS  105 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~------~~~fCP~CG~  105 (107)
                      ....|..|+..+..              ...||.||.+++.      ...||+.||.
T Consensus        17 ~~~~C~~C~~~~~~--------------~afCPeCgq~Le~lkACGA~~yFC~~C~~   59 (81)
T 2jrp_A           17 DTAHCETCAKDFSL--------------QALCPDCRQPLQVLKACGAVDYFCQNGHG   59 (81)
T ss_dssp             SEEECTTTCCEEEE--------------EEECSSSCSCCCEEEETTEEEECCTTTTC
T ss_pred             CceECccccccCCC--------------cccCcchhhHHHHHHhcCCcCeeeccCCC
Confidence            46678888887644              2367777766644      3667777774

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=97.82  E-value=4.7e-06  Score=51.29  Aligned_cols=39  Identities=23%  Similarity=0.618  Sum_probs=24.5

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCCC
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL  107 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~l  107 (107)
                      +.||.|+..++.+.           ....|..|++.+...+ |||.||++|
T Consensus         3 ~~CP~C~~~l~~~~-----------~~~~C~~C~~~~~~~a-fCPeCgq~L   41 (81)
T 2jrp_A            3 ITCPVCHHALERNG-----------DTAHCETCAKDFSLQA-LCPDCRQPL   41 (81)
T ss_dssp             CCCSSSCSCCEECS-----------SEEECTTTCCEEEEEE-ECSSSCSCC
T ss_pred             CCCCCCCCccccCC-----------CceECccccccCCCcc-cCcchhhHH
Confidence            45667766654432           1345777777777777 777777665

>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ...

Probab=97.13  E-value=0.00027  Score=42.27  Aligned_cols=24  Identities=25%  Similarity=0.477  Sum_probs=16.5

Q ss_pred             ccccccCCceecC---CCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEP---DFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~---~~~fCP~CG~~  106 (107)
                      .+.|++||.+++.   ++..||+||.+
T Consensus        28 ~Y~C~~CG~~~e~~~~d~irCp~CG~R   54 (70)
T 1twf_L           28 KYICAECSSKLSLSRTDAVRCKDCGHR   54 (70)
T ss_dssp             CEECSSSCCEECCCTTSTTCCSSSCCC
T ss_pred             EEECCCCCCcceeCCCCCccCCCCCce
Confidence            4677777777433   56778888774

>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=96.51  E-value=0.0014  Score=36.76  Aligned_cols=25  Identities=20%  Similarity=0.297  Sum_probs=22.8

Q ss_pred             CccccccCCceecCCCccCcCCCCC
Q 033949           82 DVSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        82 ~~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      ...+|+.||+.+..++..|..||+.
T Consensus        13 ~k~iCpkC~a~~~~gaw~CrKCG~~   37 (51)
T 3j21_g           13 KKYVCLRCGATNPWGAKKCRKCGYK   37 (51)
T ss_dssp             SEEECTTTCCEECTTCSSCSSSSSC
T ss_pred             CCccCCCCCCcCCCCceecCCCCCc
Confidence            4688999999999999999999985

>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=96.49  E-value=0.0018  Score=37.86  Aligned_cols=25  Identities=20%  Similarity=0.457  Sum_probs=16.5

Q ss_pred             ccccccCCceecC---CCccCcCCCCCC
Q 033949           83 VSKCRFCDRLVEP---DFSFCPYCGSAL  107 (107)
Q Consensus        83 ~~~C~~CG~~i~~---~~~fCP~CG~~l  107 (107)
                      .+.|..||++++.   +...||+||.++
T Consensus        21 ~Y~C~~Cg~~~~l~~~~~iRC~~CG~RI   48 (63)
T 3h0g_L           21 IYLCADCGARNTIQAKEVIRCRECGHRV   48 (63)
T ss_dssp             CCBCSSSCCBCCCCSSSCCCCSSSCCCC
T ss_pred             EEECCCCCCeeecCCCCceECCCCCcEE
Confidence            4677777777655   456777777653

>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii}

Probab=96.35  E-value=0.0013  Score=44.64  Aligned_cols=24  Identities=33%  Similarity=0.581  Sum_probs=16.2

Q ss_pred             ccccccCCceecCCC--ccCcCCCCC
Q 033949           83 VSKCRFCDRLVEPDF--SFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~--~fCP~CG~~  106 (107)
                      .+.|..||...+...  .+||.||++
T Consensus       132 ~y~C~~Cg~~~~~~~~~~~Cp~CG~~  157 (165)
T 2lcq_A          132 RYVCIGCGRKFSTLPPGGVCPDCGSK  157 (165)
T ss_dssp             CEEESSSCCEESSCCGGGBCTTTCCB
T ss_pred             EEECCCCCCcccCCCCCCcCCCCCCc
Confidence            467777777766433  378888775

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=96.15  E-value=0.016  Score=37.21  Aligned_cols=16  Identities=25%  Similarity=0.426  Sum_probs=13.1

Q ss_pred             CceeCCCCCCCCCCCC
Q 033949           55 PALFCNNCNLLFPSSL   70 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~   70 (107)
                      ....|+.||...+++.
T Consensus        25 ~~~~C~~C~y~~~~~~   40 (113)
T 3h0g_I           25 LRLACRNCDYSEIAAT   40 (113)
T ss_dssp             CCEECSSSCCEECCSC
T ss_pred             eEEECCCCCCeEEcCC
Confidence            3799999999887754

>2jne_A Hypothetical protein YFGJ; zinc fingers, two zinc, structural genomics, PSI-2, protein structure initiative; NMR {Escherichia coli} SCOP: g.41.18.1

Probab=96.07  E-value=0.00076  Score=42.69  Aligned_cols=43  Identities=16%  Similarity=0.366  Sum_probs=29.4

Q ss_pred             CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949           20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      .+..||.|++..+                 |  .+....|..|+..+..              ...||.|+.+++.
T Consensus        31 M~~~CP~Cq~eL~-----------------~--~g~~~hC~~C~~~f~~--------------~a~CPdC~q~Lev   73 (101)
T 2jne_A           31 MELHCPQCQHVLD-----------------Q--DNGHARCRSCGEFIEM--------------KALCPDCHQPLQV   73 (101)
T ss_dssp             CCCBCSSSCSBEE-----------------E--ETTEEEETTTCCEEEE--------------EEECTTTCSBCEE
T ss_pred             ccccCccCCCcce-----------------e--cCCEEECccccchhhc--------------cccCcchhhHHHH
Confidence            3468999999421                 2  2356679999887743              4578888888765

>2jne_A Hypothetical protein YFGJ; zinc fingers, two zinc, structural genomics, PSI-2, protein structure initiative; NMR {Escherichia coli} SCOP: g.41.18.1

Probab=96.04  E-value=0.0011  Score=41.91  Aligned_cols=40  Identities=28%  Similarity=0.755  Sum_probs=30.1

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCCC
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL  107 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~l  107 (107)
                      .+.||.|+..++.+.           ....|..|+..... --+||.||++|
T Consensus        32 ~~~CP~Cq~eL~~~g-----------~~~hC~~C~~~f~~-~a~CPdC~q~L   71 (101)
T 2jne_A           32 ELHCPQCQHVLDQDN-----------GHARCRSCGEFIEM-KALCPDCHQPL   71 (101)
T ss_dssp             CCBCSSSCSBEEEET-----------TEEEETTTCCEEEE-EEECTTTCSBC
T ss_pred             cccCccCCCcceecC-----------CEEECccccchhhc-cccCcchhhHH
Confidence            478999998876533           24569999998554 45899999986

>2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A

Probab=95.62  E-value=0.0071  Score=34.98  Aligned_cols=12  Identities=17%  Similarity=0.301  Sum_probs=6.8

Q ss_pred             cccccCCceecC
Q 033949           84 SKCRFCDRLVEP   95 (107)
Q Consensus        84 ~~C~~CG~~i~~   95 (107)
                      ..||.||+.+..
T Consensus        19 ~~CP~CG~~T~~   30 (60)
T 2apo_B           19 EICPKCGEKTVI   30 (60)
T ss_dssp             SBCSSSCSBCBC
T ss_pred             ccCcCCCCcCCC
Confidence            356666666543

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1

Probab=95.45  E-value=0.012  Score=32.33  Aligned_cols=32  Identities=16%  Similarity=0.508  Sum_probs=22.9

Q ss_pred             cEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCC
Q 033949           21 AGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSS   69 (107)
Q Consensus        21 ~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~   69 (107)
                      ...||.||+ .+                 .++...+.+.|+.||..++..
T Consensus         5 ~~~CP~C~~~~l-----------------~~d~~~gelvC~~CG~v~~e~   37 (50)
T 1pft_A            5 QKVCPACESAEL-----------------IYDPERGEIVCAKCGYVIEEN   37 (50)
T ss_dssp             CCSCTTTSCCCE-----------------EEETTTTEEEESSSCCBCCCC
T ss_pred             cEeCcCCCCcce-----------------EEcCCCCeEECcccCCccccc
Confidence            346999988 43                 244455789999999988653

>2aus_D NOP10, ribosome biogenesis protein NOP10; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_B 3lwo_B* 3lwq_B* 3lwp_B 3lwv_B 3hax_C* 2hvy_C* 3hay_C* 2ey4_E 3hjw_B* 2rfk_B* 3hjy_B 3mqk_B

Probab=95.33  E-value=0.0092  Score=34.50  Aligned_cols=9  Identities=22%  Similarity=0.767  Sum_probs=4.7

Q ss_pred             ccccCCcee
Q 033949           85 KCRFCDRLV   93 (107)
Q Consensus        85 ~C~~CG~~i   93 (107)
                      .||.||+.+
T Consensus        19 ~CP~CG~~t   27 (60)
T 2aus_D           19 TCPVCGEKT   27 (60)
T ss_dssp             BCTTTCSBC
T ss_pred             cCcCCCCcc
Confidence            455555544

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=94.85  E-value=0.019  Score=38.10  Aligned_cols=16  Identities=19%  Similarity=0.542  Sum_probs=13.2

Q ss_pred             ceeCCCCCCCCCCCCC
Q 033949           56 ALFCNNCNLLFPSSLP   71 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~   71 (107)
                      ...|+.||...+++..
T Consensus        46 ~~~CrtCgY~~~~~~~   61 (133)
T 3qt1_I           46 LFECRTCSYVEEAGSP   61 (133)
T ss_dssp             CCBCSSSCCBCCCSCS
T ss_pred             EEECCCCCCcEEcCCc
Confidence            6899999999877554

>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ...

Probab=94.54  E-value=0.027  Score=33.45  Aligned_cols=10  Identities=30%  Similarity=0.826  Sum_probs=5.7

Q ss_pred             CceeCCCCCC
Q 033949           55 PALFCNNCNL   64 (107)
Q Consensus        55 ~~~~C~~CG~   64 (107)
                      +.+.|+.||+
T Consensus        44 d~irCp~CG~   53 (70)
T 1twf_L           44 DAVRCKDCGH   53 (70)
T ss_dssp             STTCCSSSCC
T ss_pred             CCccCCCCCc
Confidence            4555666665

>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii}

Probab=94.28  E-value=0.023  Score=38.27  Aligned_cols=30  Identities=20%  Similarity=0.352  Sum_probs=20.6

Q ss_pred             CCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949           54 EPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE   94 (107)
Q Consensus        54 ~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~   94 (107)
                      .+...|..||+.++...           ....||.||+++.
T Consensus       130 ~~~y~C~~Cg~~~~~~~-----------~~~~Cp~CG~~~~  159 (165)
T 2lcq_A          130 KWRYVCIGCGRKFSTLP-----------PGGVCPDCGSKVK  159 (165)
T ss_dssp             CCCEEESSSCCEESSCC-----------GGGBCTTTCCBEE
T ss_pred             cEEEECCCCCCcccCCC-----------CCCcCCCCCCcce
Confidence            36778888888886432           1347888888753

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=94.00  E-value=0.028  Score=36.14  Aligned_cols=23  Identities=26%  Similarity=0.618  Sum_probs=10.2

Q ss_pred             cccccCCceecC--CCc-cCcCCCCC
Q 033949           84 SKCRFCDRLVEP--DFS-FCPYCGSA  106 (107)
Q Consensus        84 ~~C~~CG~~i~~--~~~-fCP~CG~~  106 (107)
                      .+|.+||...+.  ... .||.||++
T Consensus        74 ~~C~~CG~~~e~~~~~~~~CP~Cgs~   99 (119)
T 2kdx_A           74 LECKDCSHVFKPNALDYGVCEKCHSK   99 (119)
T ss_dssp             EECSSSSCEECSCCSTTCCCSSSSSC
T ss_pred             EEcCCCCCEEeCCCCCCCcCccccCC
Confidence            445555554332  122 45555543

>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1

Probab=93.87  E-value=0.036  Score=41.44  Aligned_cols=24  Identities=25%  Similarity=0.526  Sum_probs=15.8

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      ++.|+-||+......             ..|++||..
T Consensus       208 ~l~Cs~C~t~W~~~R-------------~~C~~Cg~~  231 (309)
T 2fiy_A          208 YLSCSLCACEWHYVR-------------IKCSHCEES  231 (309)
T ss_dssp             EEEETTTCCEEECCT-------------TSCSSSCCC
T ss_pred             EEEeCCCCCEEeecC-------------cCCcCCCCC
Confidence            778888887765422             457777763

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=93.82  E-value=0.018  Score=31.97  Aligned_cols=23  Identities=30%  Similarity=0.436  Sum_probs=10.7

Q ss_pred             ccccccCCcee--c--CCCccCcCCCC
Q 033949           83 VSKCRFCDRLV--E--PDFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i--~--~~~~fCP~CG~  105 (107)
                      ...||.||+.+  .  .+-.+|+.||.
T Consensus        19 ~k~CP~CG~~~fm~~~~~R~~C~kCG~   45 (50)
T 3j20_Y           19 NKFCPRCGPGVFMADHGDRWACGKCGY   45 (50)
T ss_dssp             SEECSSSCSSCEEEECSSEEECSSSCC
T ss_pred             cccCCCCCCceEEecCCCeEECCCCCC
Confidence            34555555522  1  13445555553

>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P 2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X

Probab=93.78  E-value=0.039  Score=30.31  Aligned_cols=30  Identities=17%  Similarity=0.389  Sum_probs=20.0

Q ss_pred             eCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949           58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE   94 (107)
Q Consensus        58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~   94 (107)
                      .|-.||..+..++...       .-..+||+||..|.
T Consensus         5 ~C~rCg~~fs~~el~~-------lP~IrCpyCGyrii   34 (48)
T 4ayb_P            5 RCGKCWKTFTDEQLKV-------LPGVRCPYCGYKII   34 (48)
T ss_dssp             CCCCTTTTCCCCCSCC-------CSSSCCTTTCCSCE
T ss_pred             EeeccCCCccHHHHhh-------CCCcccCccCcEEE
Confidence            5888998886655321       01467999998764

>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P 2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X

Probab=93.60  E-value=0.063  Score=29.45  Aligned_cols=12  Identities=25%  Similarity=0.742  Sum_probs=7.3

Q ss_pred             CceeCCCCCCCC
Q 033949           55 PALFCNNCNLLF   66 (107)
Q Consensus        55 ~~~~C~~CG~~~   66 (107)
                      +.+.||+||...
T Consensus        22 P~IrCpyCGyri   33 (48)
T 4ayb_P           22 PGVRCPYCGYKI   33 (48)
T ss_dssp             SSSCCTTTCCSC
T ss_pred             CCcccCccCcEE
Confidence            455666666654

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1

Probab=93.53  E-value=0.024  Score=30.99  Aligned_cols=32  Identities=16%  Similarity=0.308  Sum_probs=19.1

Q ss_pred             CceeCCCCCC-CCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949           55 PALFCNNCNL-LFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        55 ~~~~C~~CG~-~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      ..+.||.||. .+..+...         ....|++||..++.
T Consensus         4 ~~~~CP~C~~~~l~~d~~~---------gelvC~~CG~v~~e   36 (50)
T 1pft_A            4 KQKVCPACESAELIYDPER---------GEIVCAKCGYVIEE   36 (50)
T ss_dssp             SCCSCTTTSCCCEEEETTT---------TEEEESSSCCBCCC
T ss_pred             ccEeCcCCCCcceEEcCCC---------CeEECcccCCcccc
Confidence            4567888887 43222211         24678888886654

>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=93.39  E-value=0.059  Score=31.35  Aligned_cols=13  Identities=15%  Similarity=0.447  Sum_probs=8.3

Q ss_pred             CceeCCCCCCCCC
Q 033949           55 PALFCNNCNLLFP   67 (107)
Q Consensus        55 ~~~~C~~CG~~~~   67 (107)
                      +.+.|++||..+-
T Consensus        37 ~~iRC~~CG~RIL   49 (63)
T 3h0g_L           37 EVIRCRECGHRVM   49 (63)
T ss_dssp             SCCCCSSSCCCCC
T ss_pred             CceECCCCCcEEE
Confidence            5666777776653

>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...

Probab=93.24  E-value=0.019  Score=35.20  Aligned_cols=33  Identities=21%  Similarity=0.427  Sum_probs=23.0

Q ss_pred             CCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           19 SGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        19 ~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      .....||+||....                 +....+.+.|++||..+.-
T Consensus        25 ~~~y~Cp~CG~~~v-----------------~r~atGiW~C~~Cg~~~ag   57 (83)
T 1vq8_Z           25 NEDHACPNCGEDRV-----------------DRQGTGIWQCSYCDYKFTG   57 (83)
T ss_dssp             HSCEECSSSCCEEE-----------------EEEETTEEEETTTCCEEEC
T ss_pred             cccCcCCCCCCcce-----------------eccCCCeEECCCCCCEecC
Confidence            35778999999221                 1223479999999998644

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=92.64  E-value=0.065  Score=34.37  Aligned_cols=9  Identities=22%  Similarity=0.715  Sum_probs=4.4

Q ss_pred             cEECCCCCC
Q 033949           21 AGRCINCGS   29 (107)
Q Consensus        21 ~~~C~~Cg~   29 (107)
                      ...|.+||.
T Consensus        73 ~~~C~~CG~   81 (119)
T 2kdx_A           73 ELECKDCSH   81 (119)
T ss_dssp             EEECSSSSC
T ss_pred             eEEcCCCCC
Confidence            344555554

>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...

Probab=92.59  E-value=0.033  Score=34.09  Aligned_cols=23  Identities=22%  Similarity=0.465  Sum_probs=12.5

Q ss_pred             ccccccCCceecC----CCccCcCCCC
Q 033949           83 VSKCRFCDRLVEP----DFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~----~~~fCP~CG~  105 (107)
                      .+.||+||+....    +--.|++||.
T Consensus        27 ~y~Cp~CG~~~v~r~atGiW~C~~Cg~   53 (83)
T 1vq8_Z           27 DHACPNCGEDRVDRQGTGIWQCSYCDY   53 (83)
T ss_dssp             CEECSSSCCEEEEEEETTEEEETTTCC
T ss_pred             cCcCCCCCCcceeccCCCeEECCCCCC
Confidence            4566666664432    3344666664

>3a43_A HYPD, hydrogenase nickel incorporation protein HYPA; [NIFE] hydrogenase maturation, zinc-finger, nickel binding, metal-binding; HET: FME; 2.30A {Pyrococcus kodakaraensis} PDB: 3a44_A*

Probab=92.42  E-value=0.05  Score=36.07  Aligned_cols=15  Identities=27%  Similarity=0.627  Sum_probs=8.8

Q ss_pred             CceeCCCCCCCCCCC
Q 033949           55 PALFCNNCNLLFPSS   69 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~   69 (107)
                      ....|.+||+.++.+
T Consensus        69 ~~~~C~~CG~~~~~~   83 (139)
T 3a43_A           69 AVFKCRNCNYEWKLK   83 (139)
T ss_dssp             CEEEETTTCCEEEGG
T ss_pred             CcEECCCCCCEEecc
Confidence            455666666665543

>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8

Probab=92.33  E-value=0.11  Score=29.29  Aligned_cols=23  Identities=30%  Similarity=0.423  Sum_probs=11.2

Q ss_pred             ccccccCCceec----CCCccCcCCCC
Q 033949           83 VSKCRFCDRLVE----PDFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~----~~~~fCP~CG~  105 (107)
                      ...||.||+.+-    .+.-+|+.||.
T Consensus        18 ~~fCPkCG~~~~ma~~~dr~~C~kCgy   44 (55)
T 2k4x_A           18 HRFCPRCGPGVFLAEHADRYSCGRCGY   44 (55)
T ss_dssp             SCCCTTTTTTCCCEECSSEEECTTTCC
T ss_pred             cccCcCCCCceeEeccCCEEECCCCCC
Confidence            345555555332    13445555553

>3a43_A HYPD, hydrogenase nickel incorporation protein HYPA; [NIFE] hydrogenase maturation, zinc-finger, nickel binding, metal-binding; HET: FME; 2.30A {Pyrococcus kodakaraensis} PDB: 3a44_A*

Probab=92.30  E-value=0.05  Score=36.07  Aligned_cols=25  Identities=44%  Similarity=0.821  Sum_probs=19.5

Q ss_pred             CccccccCCceecCC-----------------------CccCcCCCCC
Q 033949           82 DVSKCRFCDRLVEPD-----------------------FSFCPYCGSA  106 (107)
Q Consensus        82 ~~~~C~~CG~~i~~~-----------------------~~fCP~CG~~  106 (107)
                      ...+|.+||.+...+                       ...||.||++
T Consensus        69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~h~~p~~~~~~~~CP~Cgs~  116 (139)
T 3a43_A           69 AVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSH  116 (139)
T ss_dssp             CEEEETTTCCEEEGGGCTTCCSCCCGGGCCCCGGGCGGGCSCSSSSCC
T ss_pred             CcEECCCCCCEEecccccccccccccccccccccccccCCcCccccCC
Confidence            367899999996542                       4669999986

>2ayj_A 50S ribosomal protein L40E; Zn-binding, beta-strand protein, structural genomics, PSI, protein structure initiative; NMR {Sulfolobus solfataricus} SCOP: g.41.8.7

Probab=92.29  E-value=0.24  Score=28.08  Aligned_cols=25  Identities=28%  Similarity=0.436  Sum_probs=23.0

Q ss_pred             CccccccCCceecCCCccCcCCCCC
Q 033949           82 DVSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        82 ~~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      +.++|-.|++.+++.|+.|-.||++
T Consensus        18 ~k~ICrkC~ARnp~~A~~CRKCg~~   42 (56)
T 2ayj_A           18 LKKVCRKCGALNPIRATKCRRCHST   42 (56)
T ss_dssp             CCEEETTTCCEECTTCSSCTTTCCC
T ss_pred             chhhhccccCcCCcccccccCCCCC
Confidence            4789999999999999999999974

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4

Probab=92.25  E-value=0.14  Score=31.00  Aligned_cols=6  Identities=33%  Similarity=1.137  Sum_probs=3.1

Q ss_pred             CCCCCC
Q 033949           24 CINCGS   29 (107)
Q Consensus        24 C~~Cg~   29 (107)
                      ||+|++
T Consensus        28 CP~C~~   33 (86)
T 2ct7_A           28 CAQCSF   33 (86)
T ss_dssp             CSSSCC
T ss_pred             CcCCCc
Confidence            555554

>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4

Probab=91.91  E-value=0.098  Score=30.65  Aligned_cols=31  Identities=13%  Similarity=0.319  Sum_probs=23.9

Q ss_pred             CcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949           20 GAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP   67 (107)
Q Consensus        20 ~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~   67 (107)
                      ..++||.|++ ..                 =|+.....+.|..||..+.
T Consensus         6 m~VKCp~C~niq~-----------------VFShA~tvV~C~~Cg~~L~   37 (66)
T 1qxf_A            6 VKVKCPDCEHEQV-----------------IFDHPSTIVKCIICGRTVA   37 (66)
T ss_dssp             EEEECTTTCCEEE-----------------EESSCSSCEECSSSCCEEE
T ss_pred             EEEECCCCCCceE-----------------EEecCceEEEcccCCCEEe
Confidence            3578999999 32                 2666667999999999884

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=91.80  E-value=0.2  Score=33.02  Aligned_cols=35  Identities=23%  Similarity=0.447  Sum_probs=22.9

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE   94 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~   94 (107)
                      ...+||.||..+-+......     ..+...|++||.+.+
T Consensus        23 ~~~FCPeCgNmL~pked~~~-----~~l~~~CrtCgY~~~   57 (133)
T 3qt1_I           23 TFRFCRDCNNMLYPREDKEN-----NRLLFECRTCSYVEE   57 (133)
T ss_dssp             CCCBCTTTCCBCBCCBCTTT-----CCBCCBCSSSCCBCC
T ss_pred             CCeeCCCCCCEeeECccCCC-----ceeEEECCCCCCcEE
Confidence            47889999999866442110     013578999988643

>2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A

Probab=91.53  E-value=0.16  Score=29.20  Aligned_cols=14  Identities=14%  Similarity=0.218  Sum_probs=8.7

Q ss_pred             eeCCCCCCCCCCCC
Q 033949           57 LFCNNCNLLFPSSL   70 (107)
Q Consensus        57 ~~C~~CG~~~~~~~   70 (107)
                      ..||.||....+.+
T Consensus        19 ~~CP~CG~~T~~~h   32 (60)
T 2apo_B           19 EICPKCGEKTVIPK   32 (60)
T ss_dssp             SBCSSSCSBCBCCC
T ss_pred             ccCcCCCCcCCCCC
Confidence            34777777765544

>2con_A RUH-035 protein, NIN one binding protein; ribosome, RNA binding protein, unknown function, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.41.15.1

Probab=91.14  E-value=0.13  Score=31.11  Aligned_cols=23  Identities=26%  Similarity=0.677  Sum_probs=13.2

Q ss_pred             cccccCCceecC-CCccCcCCCCC
Q 033949           84 SKCRFCDRLVEP-DFSFCPYCGSA  106 (107)
Q Consensus        84 ~~C~~CG~~i~~-~~~fCP~CG~~  106 (107)
                      ..|..|-+.... +-.|||.||++
T Consensus        16 LrC~aCf~~t~~~~k~FCp~CGn~   39 (79)
T 2con_A           16 LRCHGCFKTTSDMNRVFCGHCGNK   39 (79)
T ss_dssp             EECSSSCCEESCSSCCSCSSSCCS
T ss_pred             eEecccceECCCcccccccccCcc
Confidence            456666655544 45566666653

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=90.78  E-value=0.21  Score=31.90  Aligned_cols=33  Identities=21%  Similarity=0.308  Sum_probs=20.7

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCcee
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLV   93 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i   93 (107)
                      ..+||.||..+.+......     ......|++||.+.
T Consensus         4 m~FCp~Cgn~L~~~~~~~~-----~~~~~~C~~C~y~~   36 (113)
T 3h0g_I            4 FQYCIECNNMLYPREDKVD-----RVLRLACRNCDYSE   36 (113)
T ss_dssp             CCCCSSSCCCCEECCCTTT-----CCCCEECSSSCCEE
T ss_pred             ceeCcCCCCEeeEcccCCC-----CeeEEECCCCCCeE
Confidence            5689999999866442110     01246788888754

>2zjr_Z 50S ribosomal protein L32; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: g.41.8.5 PDB: 1j5a_M* 1jzy_M* 1jzz_M* 1k01_M* 1nkw_Z 1ond_Z* 1sm1_Z* 1yl3_5 2b66_5 2b9n_5 2b9p_5 2zjp_Y* 2zjq_Z 1jzx_M 3cf5_Y* 3dll_Y* 3pio_Z* 3pip_Z* 1nwy_Z* 1nwx_Z* ...

Probab=90.68  E-value=0.11  Score=29.84  Aligned_cols=22  Identities=27%  Similarity=0.837  Sum_probs=13.0

Q ss_pred             ccccccCCceecCCCccCcCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~  105 (107)
                      ...|++||+. ...-..||+||.
T Consensus        30 l~~c~~cG~~-~~pH~vc~~CG~   51 (60)
T 2zjr_Z           30 LTECPQCHGK-KLSHHICPNCGY   51 (60)
T ss_dssp             CEECTTTCCE-ECTTBCCTTTCB
T ss_pred             ceECCCCCCE-eCCceEcCCCCc
Confidence            3456666666 345556666664

>3j20_W 30S ribosomal protein S27E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=90.50  E-value=0.16  Score=29.46  Aligned_cols=31  Identities=19%  Similarity=0.483  Sum_probs=23.5

Q ss_pred             CcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949           20 GAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP   67 (107)
Q Consensus        20 ~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~   67 (107)
                      ..++||.|++ ..                 =|+.....+.|..||..+.
T Consensus        14 m~VkCp~C~~~q~-----------------VFSha~t~V~C~~Cgt~L~   45 (63)
T 3j20_W           14 LRVKCIDCGNEQI-----------------VFSHPATKVRCLICGATLV   45 (63)
T ss_dssp             EEEECSSSCCEEE-----------------EESSCSSCEECSSSCCEEE
T ss_pred             EEEECCCCCCeeE-----------------EEecCCeEEEccCcCCEEe
Confidence            4678999999 32                 1666657899999999874

>3irb_A Uncharacterized protein from DUF35 family; 13815350, protein with unknown function from DUF35 family, S genomics; 1.80A {Sulfolobus solfataricus}

Probab=90.33  E-value=0.086  Score=35.11  Aligned_cols=23  Identities=39%  Similarity=0.766  Sum_probs=18.1

Q ss_pred             ccccccCCceecCCCccCcCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~  105 (107)
                      ..+|.+||+..-+-..+||.||+
T Consensus        47 ~~rC~~CG~~~~PPr~~Cp~C~s   69 (145)
T 3irb_A           47 GSKCSKCGRIFVPARSYCEHCFV   69 (145)
T ss_dssp             EEECTTTCCEEESCCSEETTTTE
T ss_pred             EEEeCCCCcEEcCchhhCcCCCC
Confidence            45788888888887788888875

>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A

Probab=90.21  E-value=0.16  Score=28.72  Aligned_cols=29  Identities=17%  Similarity=0.371  Sum_probs=20.7

Q ss_pred             ECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           23 RCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        23 ~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      .||.||+ .+                 -++.....+.|..||..++.
T Consensus        13 ~Cp~C~~~~l-----------------v~D~~~ge~vC~~CGlVl~e   42 (58)
T 1dl6_A           13 TCPNHPDAIL-----------------VEDYRAGDMICPECGLVVGD   42 (58)
T ss_dssp             SBTTBSSSCC-----------------EECSSSCCEECTTTCCEECC
T ss_pred             cCcCCCCCce-----------------eEeCCCCeEEeCCCCCEEec
Confidence            6999988 42                 13444578999999988754

>3v2d_5 50S ribosomal protein L32; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgq_4 2hgj_4 2hgu_4 2j03_5 2jl6_5 2jl8_5 2v47_5 2v49_5 2wdi_5 2wdj_5 2wdl_5 2wdn_5 2wh2_5 2wh4_5 2wrj_5 2wrl_5 2wro_5 2wrr_5 2x9s_5 2x9u_5 ...

Probab=90.01  E-value=0.14  Score=29.32  Aligned_cols=22  Identities=27%  Similarity=0.792  Sum_probs=11.8

Q ss_pred             ccccccCCceecCCCccCcCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~  105 (107)
                      ...||+||+... .-..||+||.
T Consensus        30 l~~c~~cGe~~~-~H~vc~~CG~   51 (60)
T 3v2d_5           30 LVPCPECKAMKP-PHTVCPECGY   51 (60)
T ss_dssp             CEECTTTCCEEC-TTSCCTTTCE
T ss_pred             eeECCCCCCeec-ceEEcCCCCc
Confidence            345666666533 3344666663

>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6

Probab=88.54  E-value=0.27  Score=29.84  Aligned_cols=31  Identities=13%  Similarity=0.554  Sum_probs=22.9

Q ss_pred             CcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949           20 GAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP   67 (107)
Q Consensus        20 ~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~   67 (107)
                      ..++||.|++ ..                 =|+.....+.|..||..+.
T Consensus        31 m~VkCp~C~n~q~-----------------VFShA~t~V~C~~Cg~~L~   62 (81)
T 2xzm_6           31 MDVKCAQCQNIQM-----------------IFSNAQSTIICEKCSAILC   62 (81)
T ss_dssp             EEEECSSSCCEEE-----------------EETTCSSCEECSSSCCEEE
T ss_pred             EEeECCCCCCeeE-----------------EEecCccEEEccCCCCEEe
Confidence            4678999999 32                 1566656899999998863

>6rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.50A {Desulfovibrio desulfuricans} SCOP: g.41.5.1

Probab=88.42  E-value=0.31  Score=26.48  Aligned_cols=36  Identities=19%  Similarity=0.354  Sum_probs=18.9

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      ...|+.||..++...-. +...+.......||.||+.
T Consensus         4 ~y~C~vCGyvyd~~~Gd-~t~f~~lP~dw~CP~Cg~~   39 (46)
T 6rxn_A            4 KYVCNVCGYEYDPAEHD-NVPFDQLPDDWCCPVCGVS   39 (46)
T ss_dssp             CEEETTTCCEECGGGGT-TCCGGGSCTTCBCTTTCCB
T ss_pred             EEECCCCCeEEeCCcCC-CcchhhCCCCCcCcCCCCc
Confidence            35799999888642211 0000000123578888875

>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1

Probab=88.42  E-value=0.1  Score=31.02  Aligned_cols=17  Identities=12%  Similarity=0.094  Sum_probs=13.0

Q ss_pred             CceeCCCCCCCCCCCCCC
Q 033949           55 PALFCNNCNLLFPSSLPP   72 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~   72 (107)
                      ....|| ||+.+.+.+..
T Consensus        20 kT~~C~-CG~~~~~~k~r   36 (71)
T 1gh9_A           20 KTRKCV-CGRTVNVKDRR   36 (71)
T ss_dssp             SEEEET-TTEEEECCSSS
T ss_pred             cEEECC-CCCeeeeceEE
Confidence            478898 99988776653

>3pwf_A Rubrerythrin; non heme iron peroxidases, oxidative stress, oxidoreductase; 1.64A {Pyrococcus furiosus} PDB: 3mps_A 3pza_A 3qvd_A 1nnq_A 2hr5_A

Probab=88.40  E-value=0.33  Score=33.12  Aligned_cols=13  Identities=15%  Similarity=0.381  Sum_probs=8.5

Q ss_pred             CceeCCCCCCCCC
Q 033949           55 PALFCNNCNLLFP   67 (107)
Q Consensus        55 ~~~~C~~CG~~~~   67 (107)
                      ....|+.||..++
T Consensus       137 ~~~~C~~CG~i~~  149 (170)
T 3pwf_A          137 KVYICPICGYTAV  149 (170)
T ss_dssp             CEEECTTTCCEEE
T ss_pred             CeeEeCCCCCeeC
Confidence            4556777777665

>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=87.96  E-value=0.94  Score=25.64  Aligned_cols=14  Identities=14%  Similarity=0.451  Sum_probs=9.1

Q ss_pred             CceeCCCCCCCCCC
Q 033949           55 PALFCNNCNLLFPS   68 (107)
Q Consensus        55 ~~~~C~~CG~~~~~   68 (107)
                      ....||.|+..++.
T Consensus         5 ~~k~CP~C~~~Iek   18 (60)
T 1wd2_A            5 NTKECPKCHVTIEK   18 (60)
T ss_dssp             CCCCCTTTCCCCSS
T ss_pred             cceECcCCCCeeEe
Confidence            44567777777655

>2k2d_A Ring finger and CHY zinc finger domain- containing protein 1; zinc-binding protein, cytoplasm, metal-binding, nucleus, metal binding protein; NMR {Homo sapiens}

Probab=87.85  E-value=0.2  Score=30.24  Aligned_cols=23  Identities=22%  Similarity=0.395  Sum_probs=15.9

Q ss_pred             ccccccCCceecC--CCc--cCcCCCC
Q 033949           83 VSKCRFCDRLVEP--DFS--FCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~--~~~--fCP~CG~  105 (107)
                      ...|..|++.-..  .+.  .||.||+
T Consensus        37 ~I~CnDC~~~s~v~~h~lg~kC~~C~S   63 (79)
T 2k2d_A           37 DILCNDCNGRSTVQFHILGMKCKICES   63 (79)
T ss_dssp             EEEESSSCCEEEEECCTTCCCCTTTSC
T ss_pred             EEECCCCCCCccCCceeecccCcCCCC
Confidence            3568888887655  333  6888886

>3u5c_b RP61, YS20, 40S ribosomal protein S27-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_X 3u5g_b

Probab=87.70  E-value=0.34  Score=29.49  Aligned_cols=33  Identities=15%  Similarity=0.415  Sum_probs=23.5

Q ss_pred             CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      ..++||.|++..                .=|+.....+.|..||..+..
T Consensus        33 m~VkCp~C~~~q----------------~VFSha~t~V~C~~Cg~~L~~   65 (82)
T 3u5c_b           33 LDVKCPGCLNIT----------------TVFSHAQTAVTCESCSTILCT   65 (82)
T ss_dssp             EEEECTTSCSCE----------------EEESBCSSCCCCSSSCCCCEE
T ss_pred             EEEECCCCCCee----------------EEEecCCeEEEccccCCEEec
Confidence            467899999921                115556568999999998743

>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4

Probab=87.42  E-value=0.23  Score=30.47  Aligned_cols=35  Identities=20%  Similarity=0.384  Sum_probs=24.0

Q ss_pred             CCcEECCCCCC--CcEEEEEeeEEEEEEEeeeecCC--CCCceeCCCCCCCCCC
Q 033949           19 SGAGRCINCGS--TADLVEYEKVLKAFFVPVWKWPA--KEPALFCNNCNLLFPS   68 (107)
Q Consensus        19 ~~~~~C~~Cg~--~~~~~~~~~~f~lFFIP~~~~~~--~~~~~~C~~CG~~~~~   68 (107)
                      ...+.||.||+  ++. ++              +++  ....+.|..||..++.
T Consensus        21 ~t~F~CPfCnh~~sV~-vk--------------idk~~~~g~l~C~~Cg~~~~~   59 (85)
T 1wii_A           21 ETQFTCPFCNHEKSCD-VK--------------MDRARNTGVISCTVCLEEFQT   59 (85)
T ss_dssp             SSCCCCTTTCCSSCEE-EE--------------EETTTTEEEEEESSSCCEEEE
T ss_pred             CCeEcCCCCCCCCeEE-EE--------------EEccCCEEEEEcccCCCeEEe
Confidence            35678999999  343 22              322  2358999999998854

>4esj_A Type-2 restriction enzyme DPNI; restriction endonuclease-DNA complex, type IIM, type IIE, RE enzyme, DPNI; HET: DNA 6MA; 2.05A {Streptococcus pneumoniae}

Probab=87.34  E-value=0.19  Score=36.46  Aligned_cols=37  Identities=24%  Similarity=0.536  Sum_probs=24.6

Q ss_pred             CcEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949           20 GAGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        20 ~~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~   70 (107)
                      .+.-||+||+ ..+.++.              ++..-.-+|++|++.|++..
T Consensus        33 ~n~yCPnCG~~~l~~f~n--------------N~PVaDF~C~~C~EeyELKS   70 (257)
T 4esj_A           33 RQSYCPNCGNNPLNHFEN--------------NRPVADFYCNHCSEEFELKS   70 (257)
T ss_dssp             HHCCCTTTCCSSCEEC------------------CCCEEECTTTCCEEEEEE
T ss_pred             HCCcCCCCCChhhhhccC--------------CCcccccccCCcchhheecc
Confidence            4677999999 5543332              33334678999999998744

>2gnr_A Conserved hypothetical protein; 13815350, structural genomics, PSI, protein structure initiative; 1.80A {Sulfolobus solfataricus P2} PDB: 3irb_A

Probab=87.28  E-value=0.19  Score=33.55  Aligned_cols=23  Identities=39%  Similarity=0.766  Sum_probs=17.4

Q ss_pred             ccccccCCceecCCCccCcCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~  105 (107)
                      ..+|.+||+..-+-..+||.||+
T Consensus        47 ~~rC~~CG~~~fPPr~~Cp~C~s   69 (145)
T 2gnr_A           47 GSKCSKCGRIFVPARSYCEHCFV   69 (145)
T ss_dssp             EEECTTTCCEEESCCSEETTTTE
T ss_pred             EEEECCCCcEEeCCCCCCCCCCC
Confidence            45688888877777777888875

>3iz6_X 40S ribosomal protein S27 (S27E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=87.14  E-value=0.45  Score=29.18  Aligned_cols=31  Identities=16%  Similarity=0.513  Sum_probs=23.9

Q ss_pred             cEECCCCCC-CcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           21 AGRCINCGS-TADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        21 ~~~C~~Cg~-~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      .++||.|++ ..                 =|+.....+.|..||..+..
T Consensus        36 ~VkCp~C~~~~~-----------------VFShA~t~V~C~~CgtvL~~   67 (86)
T 3iz6_X           36 DVKCQGCFNITT-----------------VFSHSQTVVVCPGCQTVLCQ   67 (86)
T ss_dssp             EEECTTTCCEEE-----------------EETTCSSCCCCSSSCCCCSC
T ss_pred             EEECCCCCCeeE-----------------EEecCCcEEEccCCCCEeec
Confidence            578999999 32                 15666579999999998854

>3pwf_A Rubrerythrin; non heme iron peroxidases, oxidative stress, oxidoreductase; 1.64A {Pyrococcus furiosus} PDB: 3mps_A 3pza_A 3qvd_A 1nnq_A 2hr5_A

Probab=86.63  E-value=0.31  Score=33.21  Aligned_cols=23  Identities=30%  Similarity=0.803  Sum_probs=12.3

Q ss_pred             ccccccCCceecC-CCccCcCCCC
Q 033949           83 VSKCRFCDRLVEP-DFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~-~~~fCP~CG~  105 (107)
                      ...|++||...+. ....||-||.
T Consensus       138 ~~~C~~CG~i~~~~~p~~CP~Cg~  161 (170)
T 3pwf_A          138 VYICPICGYTAVDEAPEYCPVCGA  161 (170)
T ss_dssp             EEECTTTCCEEESCCCSBCTTTCC
T ss_pred             eeEeCCCCCeeCCCCCCCCCCCCC
Confidence            3456666665433 2346666664

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...

Probab=86.26  E-value=0.17  Score=32.74  Aligned_cols=36  Identities=14%  Similarity=0.275  Sum_probs=23.3

Q ss_pred             EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949           22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~   70 (107)
                      .-||.||+.+.+.+..             ..+...+.|+.||+..+++.
T Consensus         5 ~FCp~CgnlL~~~~~~-------------~~~~~~~~C~~C~y~~~~~~   40 (122)
T 1twf_I            5 RFCRDCNNMLYPREDK-------------ENNRLLFECRTCSYVEEAGS   40 (122)
T ss_dssp             CBCSSSCCBCEEEEET-------------TTTEEEEECSSSSCEEECSC
T ss_pred             CcccccCccCcccccC-------------cCCCCEEECCcCCCeeecCc
Confidence            4599999954222210             12235899999999887654

>2pk7_A Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4K structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens} SCOP: b.171.1.1

Probab=86.20  E-value=0.18  Score=29.71  Aligned_cols=33  Identities=18%  Similarity=0.316  Sum_probs=24.3

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~   70 (107)
                      ...||.|++...                 ++...+.+.|+.||..|++..
T Consensus         8 iL~CP~ck~~L~-----------------~~~~~~~LiC~~cg~~YPI~d   40 (69)
T 2pk7_A            8 ILACPICKGPLK-----------------LSADKTELISKGAGLAYPIRD   40 (69)
T ss_dssp             TCCCTTTCCCCE-----------------ECTTSSEEEETTTTEEEEEET
T ss_pred             heeCCCCCCcCe-----------------EeCCCCEEEcCCCCcEecCcC
Confidence            446999999542                 344457899999999998754

>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1

Probab=85.97  E-value=0.17  Score=37.76  Aligned_cols=24  Identities=17%  Similarity=0.301  Sum_probs=21.7

Q ss_pred             ccccccCCceecCCCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      ..+|.-||++=...-.-||+||+.
T Consensus       208 ~l~Cs~C~t~W~~~R~~C~~Cg~~  231 (309)
T 2fiy_A          208 YLSCSLCACEWHYVRIKCSHCEES  231 (309)
T ss_dssp             EEEETTTCCEEECCTTSCSSSCCC
T ss_pred             EEEeCCCCCEEeecCcCCcCCCCC
Confidence            478999999999999999999974

>2gmg_A Hypothetical protein PF0610; winged-helix like protein with metal binding site, structura genomics, PSI, protein structure initiative; NMR {Pyrococcus furiosus} SCOP: a.4.5.82

Probab=85.60  E-value=0.52  Score=29.97  Aligned_cols=12  Identities=25%  Similarity=0.429  Sum_probs=6.6

Q ss_pred             cccccCCceecC
Q 033949           84 SKCRFCDRLVEP   95 (107)
Q Consensus        84 ~~C~~CG~~i~~   95 (107)
                      ..||.|+++-..
T Consensus        85 srCP~CkSe~Ie   96 (105)
T 2gmg_A           85 SRCPKCKSEWIE   96 (105)
T ss_dssp             SSCSSSCCCCBC
T ss_pred             CCCcCCCCCccC
Confidence            356666665443

>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}

Probab=85.19  E-value=0.15  Score=30.05  Aligned_cols=33  Identities=24%  Similarity=0.449  Sum_probs=24.6

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~   70 (107)
                      -..||.|++...                 ++...+.+.|+.||..|++..
T Consensus         8 iL~CP~ck~~L~-----------------~~~~~~~LiC~~cg~~YPI~d   40 (70)
T 2js4_A            8 ILVCPVCKGRLE-----------------FQRAQAELVCNADRLAFPVRD   40 (70)
T ss_dssp             CCBCTTTCCBEE-----------------EETTTTEEEETTTTEEEEEET
T ss_pred             heECCCCCCcCE-----------------EeCCCCEEEcCCCCceecCCC
Confidence            457999999543                 233457999999999998754

>2hf1_A Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthes structural genomics, PSI-2, protein structure initiative; 1.90A {Chromobacterium violaceum} SCOP: b.171.1.1

Probab=85.16  E-value=0.16  Score=29.82  Aligned_cols=32  Identities=22%  Similarity=0.375  Sum_probs=23.6

Q ss_pred             EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949           22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~   70 (107)
                      ..||.|++..+                 +....+.+.|+.||..|++..
T Consensus         9 L~CP~ck~~L~-----------------~~~~~~~LiC~~cg~~YPI~d   40 (68)
T 2hf1_A            9 LVCPLCKGPLV-----------------FDKSKDELICKGDRLAFPIKD   40 (68)
T ss_dssp             CBCTTTCCBCE-----------------EETTTTEEEETTTTEEEEEET
T ss_pred             eECCCCCCcCe-----------------EeCCCCEEEcCCCCcEecCCC
Confidence            46999999543                 223457899999999998754

>1k81_A EIF-2-beta, probable translation initiation factor 2 beta subunit; zinc ribbon; NMR {Methanocaldococcus jannaschii} SCOP: g.59.1.1

Probab=84.96  E-value=0.29  Score=25.08  Aligned_cols=30  Identities=20%  Similarity=0.548  Sum_probs=18.2

Q ss_pred             EECCCCCCC-cEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCC
Q 033949           22 GRCINCGST-ADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLF   66 (107)
Q Consensus        22 ~~C~~Cg~~-~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~   66 (107)
                      +.|+.|++. -++.+               ..+...+.|..||+.-
T Consensus         1 VlC~~C~~peT~l~~---------------~~~~~~l~C~aCG~~~   31 (36)
T 1k81_A            1 VICRECGKPDTKIIK---------------EGRVHLLKCMACGAIR   31 (36)
T ss_dssp             CCCSSSCSCEEEEEE---------------ETTEEEEEEETTTEEE
T ss_pred             CCCcCCCCCCcEEEE---------------eCCcEEEEhhcCCCcc
Confidence            368999993 22222               1233577788888754

>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}

Probab=84.95  E-value=0.16  Score=29.79  Aligned_cols=33  Identities=12%  Similarity=0.241  Sum_probs=24.3

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~   70 (107)
                      -..||.|++..+                 +....+.+.|+.||..|++..
T Consensus         8 iL~CP~ck~~L~-----------------~~~~~~~LiC~~cg~~YPI~d   40 (68)
T 2jr6_A            8 ILVCPVTKGRLE-----------------YHQDKQELWSRQAKLAYPIKD   40 (68)
T ss_dssp             CCBCSSSCCBCE-----------------EETTTTEEEETTTTEEEEEET
T ss_pred             heECCCCCCcCe-----------------EeCCCCEEEcCCCCcEecCCC
Confidence            457999999543                 223457899999999998754

>2gmg_A Hypothetical protein PF0610; winged-helix like protein with metal binding site, structura genomics, PSI, protein structure initiative; NMR {Pyrococcus furiosus} SCOP: a.4.5.82

Probab=84.41  E-value=0.85  Score=28.97  Aligned_cols=24  Identities=33%  Similarity=0.646  Sum_probs=13.3

Q ss_pred             ccccccCCceecC---CCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEP---DFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~---~~~fCP~CG~~  106 (107)
                      ...|.+||.....   ....||.|++.
T Consensus        67 p~~C~~CG~~F~~~~~kPsrCP~CkSe   93 (105)
T 2gmg_A           67 PAQCRKCGFVFKAEINIPSRCPKCKSE   93 (105)
T ss_dssp             CCBBTTTCCBCCCCSSCCSSCSSSCCC
T ss_pred             CcChhhCcCeecccCCCCCCCcCCCCC
Confidence            3556666666521   34566666653

>2kn9_A Rubredoxin; metalloprotein, ssgcid, structural genomics, seattle structural genomics center for infectious electron transport, iron; NMR {Mycobacterium tuberculosis}

Probab=84.37  E-value=0.47  Score=28.79  Aligned_cols=38  Identities=16%  Similarity=0.215  Sum_probs=20.9

Q ss_pred             CceeCCCCCCCCCCCCCC--CCCC----CCCccCccccccCCce
Q 033949           55 PALFCNNCNLLFPSSLPP--PPPP----PPLVSDVSKCRFCDRL   92 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~--~~~~----~~~~~~~~~C~~CG~~   92 (107)
                      ....|+.||..|+...-.  ..|.    ++.......||-||+.
T Consensus        26 ~~y~C~vCGyvYD~~~Gdp~~gI~pGT~fedlPddW~CPvCga~   69 (81)
T 2kn9_A           26 KLFRCIQCGFEYDEALGWPEDGIAAGTRWDDIPDDWSCPDCGAA   69 (81)
T ss_dssp             CEEEETTTCCEEETTTCBTTTTBCTTCCTTTSCTTCCCTTTCCC
T ss_pred             ceEEeCCCCEEEcCCcCCcccCcCCCCChhHCCCCCcCCCCCCC
Confidence            467899999888653310  0010    0101134579999885

>1e8j_A Rubredoxin; iron-sulfur-protein, zinc-substitution, thermostability; NMR {Desulfovibrio gigas} SCOP: g.41.5.1 PDB: 1rdg_A 2dsx_A 1spw_A

Probab=84.21  E-value=0.77  Score=25.38  Aligned_cols=37  Identities=14%  Similarity=0.244  Sum_probs=21.4

Q ss_pred             ceeCCCCCCCCCCCCCC--CCCC----CCCccCccccccCCce
Q 033949           56 ALFCNNCNLLFPSSLPP--PPPP----PPLVSDVSKCRFCDRL   92 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~--~~~~----~~~~~~~~~C~~CG~~   92 (107)
                      ...|+.||..|+...-.  ..|.    .+.....-.||.||+.
T Consensus         3 ~y~C~~CGyvYd~~~Gdp~~gi~pGt~f~~lP~dw~CP~Cg~~   45 (52)
T 1e8j_A            3 IYVCTVCGYEYDPAKGDPDSGIKPGTKFEDLPDDWACPVCGAS   45 (52)
T ss_dssp             CEECSSSCCCCCTTTCCTTTTCCSSCCTTSSCTTCCCSSSCCC
T ss_pred             cEEeCCCCeEEcCCcCCcccCcCCCCchHHCCCCCcCCCCCCc
Confidence            46899999999763311  0111    0111134579999986

>4rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.20A {Clostridium pasteurianum} SCOP: g.41.5.1 PDB: 5rxn_A 1bfy_A 1fhh_A 1fhm_A 1irn_A 1iro_A 1r0f_A 1r0g_A 1r0h_A 1r0i_A 1r0j_A 1t9q_A 1c09_A 1b2j_A 1b13_A 1smm_A 1smu_A 1smw_A 1be7_A 1t9o_A ...

Probab=84.10  E-value=0.68  Score=25.91  Aligned_cols=37  Identities=14%  Similarity=0.230  Sum_probs=21.4

Q ss_pred             ceeCCCCCCCCCCCCCC--CCCC----CCCccCccccccCCce
Q 033949           56 ALFCNNCNLLFPSSLPP--PPPP----PPLVSDVSKCRFCDRL   92 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~--~~~~----~~~~~~~~~C~~CG~~   92 (107)
                      ...|+.||..|+...-.  ..|.    .+.....-.||.||+.
T Consensus         3 ~y~C~vCGyvYd~~~Gdp~~gi~pGt~fe~lP~dw~CP~Cg~~   45 (54)
T 4rxn_A            3 KYTCTVCGYIYDPEDGDPDDGVNPGTDFKDIPDDWVCPLCGVG   45 (54)
T ss_dssp             CEEETTTCCEECTTTCBGGGTBCTTCCGGGSCTTCBCTTTCCB
T ss_pred             ceECCCCCeEECCCcCCcccCcCCCCChhHCCCCCcCcCCCCc
Confidence            35799999999764321  0010    0111135689999986

>2l7x_A Envelope glycoprotein; cytoplasmic tail, viral protein; NMR {Crimean-congo hemorrhagic fever virus}

Probab=83.92  E-value=0.44  Score=28.24  Aligned_cols=12  Identities=50%  Similarity=1.442  Sum_probs=10.2

Q ss_pred             CCccCcCCCCCC
Q 033949           96 DFSFCPYCGSAL  107 (107)
Q Consensus        96 ~~~fCP~CG~~l  107 (107)
                      +++.||||+++|
T Consensus        29 s~NiCPYC~nRl   40 (77)
T 2l7x_A           29 SYNICPYCASRL   40 (77)
T ss_dssp             TTTCCTTTCCCC
T ss_pred             CcccChhhhccC
Confidence            788899999876

>1dx8_A Rubredoxin; electron transport, zinc-substitution; NMR {Guillardia theta} SCOP: g.41.5.1 PDB: 1h7v_A

Probab=83.87  E-value=0.48  Score=27.87  Aligned_cols=38  Identities=21%  Similarity=0.419  Sum_probs=21.8

Q ss_pred             CceeCCCCCCCCCCCCCC--CCCCC----CCccCccccccCCce
Q 033949           55 PALFCNNCNLLFPSSLPP--PPPPP----PLVSDVSKCRFCDRL   92 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~--~~~~~----~~~~~~~~C~~CG~~   92 (107)
                      ....|+.||..++...-.  ..|..    +.....-.||-||+.
T Consensus         6 ~~y~C~vCGyiYd~~~Gdp~~gi~pGT~f~~lPddw~CP~Cga~   49 (70)
T 1dx8_A            6 GKYECEACGYIYEPEKGDKFAGIPPGTPFVDLSDSFMCPACRSP   49 (70)
T ss_dssp             SCEEETTTCCEECTTTCCTTTTCCSSCCGGGSCTTCBCTTTCCB
T ss_pred             ceEEeCCCCEEEcCCCCCcccCcCCCCchhhCCCCCcCCCCCCC
Confidence            467899999998764311  01110    001134579999986

>1yuz_A Nigerythrin; rubrythrin, rubredoxin, hemerythrin, electron transfer, DIIR center, oxidoreductase; 1.40A {Desulfovibrio vulgaris subsp} SCOP: a.25.1.1 g.41.5.1 PDB: 1yv1_A 1yux_A

Probab=83.63  E-value=0.53  Score=32.87  Aligned_cols=11  Identities=18%  Similarity=0.612  Sum_probs=5.5

Q ss_pred             ceeCCCCCCCC
Q 033949           56 ALFCNNCNLLF   66 (107)
Q Consensus        56 ~~~C~~CG~~~   66 (107)
                      ...|+.||..+
T Consensus       171 ~~~C~~CG~i~  181 (202)
T 1yuz_A          171 FHLCPICGYIH  181 (202)
T ss_dssp             EEECSSSCCEE
T ss_pred             EEEECCCCCEE
Confidence            44455555554

>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide binding, zinc binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=83.59  E-value=1.1  Score=26.71  Aligned_cols=11  Identities=36%  Similarity=0.739  Sum_probs=6.8

Q ss_pred             ceeCCCCCCCC
Q 033949           56 ALFCNNCNLLF   66 (107)
Q Consensus        56 ~~~C~~CG~~~   66 (107)
                      .-.|..||..+
T Consensus        30 rHHCR~CG~vf   40 (84)
T 1x4u_A           30 RRSCSNCGNSF   40 (84)
T ss_dssp             CEECSSSCCEE
T ss_pred             hhhhcCCCcEE
Confidence            45666666655

>1ryq_A DNA-directed RNA polymerase, subunit E''; structural genomics, zinc, PSI, protein structure initiative; 1.38A {Pyrococcus furiosus} SCOP: g.41.9.3 PDB: 3qqc_E

Probab=83.52  E-value=0.66  Score=27.32  Aligned_cols=10  Identities=20%  Similarity=0.803  Sum_probs=5.0

Q ss_pred             ceeCCCCCCC
Q 033949           56 ALFCNNCNLL   65 (107)
Q Consensus        56 ~~~C~~CG~~   65 (107)
                      .+.|..|...
T Consensus        11 ~~AC~~C~~~   20 (69)
T 1ryq_A           11 EKACRHCHYI   20 (69)
T ss_dssp             CEEETTTCBE
T ss_pred             hhhHHhCCcc
Confidence            3455555553

>1lko_A Rubrerythrin all-iron(II) form; reduced form, DIIRON, four-helix bundle, rubre like, electron transport; 1.63A {Desulfovibrio vulgaris} SCOP: a.25.1.1 g.41.5.1 PDB: 1dvb_A 1jyb_A 1b71_A 1lkm_A 1lkp_A 1qyb_A 1s2z_A 1s30_A 1ryt_A

Probab=83.45  E-value=0.4  Score=33.11  Aligned_cols=11  Identities=27%  Similarity=0.754  Sum_probs=5.8

Q ss_pred             ceeCCCCCCCC
Q 033949           56 ALFCNNCNLLF   66 (107)
Q Consensus        56 ~~~C~~CG~~~   66 (107)
                      ...|+.||..+
T Consensus       155 ~~~C~~CG~~~  165 (191)
T 1lko_A          155 KWRCRNCGYVH  165 (191)
T ss_dssp             EEEETTTCCEE
T ss_pred             eEEECCCCCEe
Confidence            34455555554

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=83.38  E-value=0.85  Score=27.20  Aligned_cols=11  Identities=36%  Similarity=0.999  Sum_probs=5.3

Q ss_pred             ceeCCCCCCCC
Q 033949           56 ALFCNNCNLLF   66 (107)
Q Consensus        56 ~~~C~~CG~~~   66 (107)
                      ...|..||..+
T Consensus        35 rHHCR~CG~v~   45 (82)
T 2yw8_A           35 KHHCRNCGHIF   45 (82)
T ss_dssp             CEECTTTCCEE
T ss_pred             cccCCCCCCEE
Confidence            34455555443

>4esj_A Type-2 restriction enzyme DPNI; restriction endonuclease-DNA complex, type IIM, type IIE, RE enzyme, DPNI; HET: DNA 6MA; 2.05A {Streptococcus pneumoniae}

Probab=83.04  E-value=0.44  Score=34.63  Aligned_cols=10  Identities=20%  Similarity=0.551  Sum_probs=4.7

Q ss_pred             cccccCCcee
Q 033949           84 SKCRFCDRLV   93 (107)
Q Consensus        84 ~~C~~CG~~i   93 (107)
                      ..|++|+.+.
T Consensus        57 F~C~~C~Eey   66 (257)
T 4esj_A           57 FYCNHCSEEF   66 (257)
T ss_dssp             EECTTTCCEE
T ss_pred             cccCCcchhh
Confidence            3455555443

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=82.79  E-value=1.2  Score=26.62  Aligned_cols=11  Identities=27%  Similarity=0.869  Sum_probs=6.3

Q ss_pred             ceeCCCCCCCC
Q 033949           56 ALFCNNCNLLF   66 (107)
Q Consensus        56 ~~~C~~CG~~~   66 (107)
                      ...|..||..+
T Consensus        37 rHHCR~CG~v~   47 (84)
T 1z2q_A           37 RHHCRNCGYVL   47 (84)
T ss_dssp             CEECTTTCCEE
T ss_pred             cccccCCCcEE
Confidence            45566666554

>2v3b_B Rubredoxin 2, rubredoxin; alkane degradation, iron-sulfur protein, oxidoreductase, ELE transfer, electron transport, FAD, NAD, iron; HET: FAD; 2.45A {Pseudomonas aeruginosa}

Probab=82.64  E-value=0.79  Score=25.64  Aligned_cols=37  Identities=16%  Similarity=0.283  Sum_probs=20.9

Q ss_pred             ceeCCCCCCCCCCCCCC--CCCCC----CCccCccccccCCce
Q 033949           56 ALFCNNCNLLFPSSLPP--PPPPP----PLVSDVSKCRFCDRL   92 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~--~~~~~----~~~~~~~~C~~CG~~   92 (107)
                      ...|+.||..++...-.  ..|..    +.....-.||.||+.
T Consensus         3 ~y~C~~CGyvYd~~~Gdp~~gi~pGt~f~~lP~dw~CP~Cga~   45 (55)
T 2v3b_B            3 KWQCVVCGFIYDEALGLPEEGIPAGTRWEDIPADWVCPDCGVG   45 (55)
T ss_dssp             EEEETTTCCEEETTTCBTTTTBCTTCCGGGSCTTCCCTTTCCC
T ss_pred             cEEeCCCCeEECCCcCCcccCcCCCCChhHCCCCCcCCCCCCC
Confidence            46799999999763311  01110    001134579999986

>1nj3_A NPL4; NZF domain, rubredoxin knuckle, beta-ribbon, zinc- finger, ubiquitin, protein binding; NMR {Rattus norvegicus} SCOP: g.41.11.1 PDB: 1q5w_A

Probab=82.62  E-value=1.2  Score=21.62  Aligned_cols=24  Identities=21%  Similarity=0.615  Sum_probs=18.2

Q ss_pred             cccccCCceecCCCccCcCCCCCC
Q 033949           84 SKCRFCDRLVEPDFSFCPYCGSAL  107 (107)
Q Consensus        84 ~~C~~CG~~i~~~~~fCP~CG~~l  107 (107)
                      -.|+.|.....+....|-.||.++
T Consensus         7 W~C~~CTf~N~~~~~~Ce~C~~~r   30 (31)
T 1nj3_A            7 WACQHCTFMNQPGTGHCEMCSLPR   30 (31)
T ss_dssp             EECSSSCCEECSSCSSCSSSCCCC
T ss_pred             ccCCcccccCCCCCCccCCcCCCC
Confidence            458888888788888888887753

>1y02_A CARP2, FYVE-ring finger protein sakura; zinc-binding module, phosphoinositide binding, caspase regulation, metal binding protein; 1.80A {Homo sapiens} SCOP: a.140.2.1 g.50.1.1

Probab=82.42  E-value=0.52  Score=30.52  Aligned_cols=13  Identities=23%  Similarity=0.644  Sum_probs=6.7

Q ss_pred             ceeCCCCCCCCCC
Q 033949           56 ALFCNNCNLLFPS   68 (107)
Q Consensus        56 ~~~C~~CG~~~~~   68 (107)
                      ...|..|+..+..
T Consensus        19 ~~~C~~C~~~Fs~   31 (120)
T 1y02_A           19 EPSCKSCGAHFAN   31 (120)
T ss_dssp             -CCCTTTCCCCSS
T ss_pred             cCcccCcCCcccc
Confidence            3456666666543

>2lk0_A RNA-binding protein 5; zinc finger; NMR {Homo sapiens} PDB: 2lk1_A*

Probab=82.03  E-value=0.86  Score=22.58  Aligned_cols=11  Identities=36%  Similarity=0.827  Sum_probs=5.6

Q ss_pred             CceeCCCCCCC
Q 033949           55 PALFCNNCNLL   65 (107)
Q Consensus        55 ~~~~C~~CG~~   65 (107)
                      +...|+.||..
T Consensus         4 gDW~C~~C~~~   14 (32)
T 2lk0_A            4 EDWLCNKCCLN   14 (32)
T ss_dssp             SEEECTTTCCE
T ss_pred             CCCCcCcCcCC
Confidence            34555555554

>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1

Probab=81.67  E-value=0.27  Score=28.77  Aligned_cols=33  Identities=15%  Similarity=0.114  Sum_probs=24.4

Q ss_pred             cEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949           21 AGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        21 ~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~   70 (107)
                      -..||.|++...                 ++...+.+.|+.||..|++..
T Consensus        10 iL~CP~ck~~L~-----------------~~~~~g~LvC~~c~~~YPI~d   42 (67)
T 2jny_A           10 VLACPKDKGPLR-----------------YLESEQLLVNERLNLAYRIDD   42 (67)
T ss_dssp             CCBCTTTCCBCE-----------------EETTTTEEEETTTTEEEEEET
T ss_pred             HhCCCCCCCcCe-----------------EeCCCCEEEcCCCCccccCCC
Confidence            457999999543                 233457899999999998754

>2akl_A PHNA-like protein PA0128; two domains, Zn binding protein, beta-strand protein, structural genomics, PSI; NMR {Pseudomonas aeruginosa PAO1} SCOP: b.34.11.2 g.41.3.5

Probab=80.33  E-value=0.77  Score=30.37  Aligned_cols=14  Identities=21%  Similarity=0.581  Sum_probs=9.3

Q ss_pred             CCceeCCCCCCCCC
Q 033949           54 EPALFCNNCNLLFP   67 (107)
Q Consensus        54 ~~~~~C~~CG~~~~   67 (107)
                      +..+.||.|+....
T Consensus        42 g~l~vCPeC~hEW~   55 (138)
T 2akl_A           42 GALLVCPECAHEWS   55 (138)
T ss_dssp             SSSEEETTTTEEEC
T ss_pred             CCeEECCccccccC
Confidence            35677777777663

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=80.23  E-value=2.3  Score=26.29  Aligned_cols=10  Identities=30%  Similarity=0.833  Sum_probs=5.0

Q ss_pred             ceeCCCCCCC
Q 033949           56 ALFCNNCNLL   65 (107)
Q Consensus        56 ~~~C~~CG~~   65 (107)
                      ++.|..|+..
T Consensus        35 FVAC~eC~FP   44 (93)
T 1weo_A           35 FVACNECGFP   44 (93)
T ss_dssp             CCSCSSSCCC
T ss_pred             EEeeeccCCh
Confidence            4555555544

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=80.20  E-value=1.3  Score=31.53  Aligned_cols=12  Identities=17%  Similarity=0.636  Sum_probs=8.2

Q ss_pred             CceeCCCCCCCC
Q 033949           55 PALFCNNCNLLF   66 (107)
Q Consensus        55 ~~~~C~~CG~~~   66 (107)
                      +.+.|+.|+..+
T Consensus       192 ~g~~C~~C~~~~  203 (238)
T 3nw0_A          192 QGQSCETCGIRM  203 (238)
T ss_dssp             SCEECSSSCCEE
T ss_pred             CCcccCccChHH
Confidence            457777777666

>1joc_A EEA1, early endosomal autoantigen 1; FYVE domain, inositol 3-phosphate binding, membrane protein; HET: ITP; 2.20A {Homo sapiens} SCOP: g.50.1.1 h.1.21.1 PDB: 1hyi_A* 1hyj_A

Probab=80.19  E-value=1.1  Score=28.98  Aligned_cols=11  Identities=27%  Similarity=0.510  Sum_probs=5.1

Q ss_pred             ceeCCCCCCCC
Q 033949           56 ALFCNNCNLLF   66 (107)
Q Consensus        56 ~~~C~~CG~~~   66 (107)
                      ...|..|+..+
T Consensus        69 ~~~C~~C~~~F   79 (125)
T 1joc_A           69 VQNCMACGKGF   79 (125)
T ss_dssp             CCBCTTTCCBC
T ss_pred             CCCCcCcCCcc
Confidence            33444444444

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	107
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	96.18
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	96.17
d2dkta1	74	RING finger and CHY zinc finger domain-containing	96.06
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	95.21
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	95.21
d1nnqa2	37	Rubrerythrin, C-terminal domain {Archaeon Pyrococc	95.15
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	95.13
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	94.39
d1rqga3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyro	93.76
d2ayja1	56	Ribosomal protein L40e {Sulfolobus solfataricus [T	93.33
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	93.13
d1nnqa2	37	Rubrerythrin, C-terminal domain {Archaeon Pyrococc	93.12
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	92.96
d2cona1	66	RNA-binding protein NOB1 (Nin one binding) {Mouse	92.74
d2ak3a2	37	Microbial and mitochondrial ADK, insert "zinc fing	92.34
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	92.34
d1pfva3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Esch	92.25
d2ey4e1	52	Ribosome biogenesis protein Nop10 {Archaeon Pyroco	92.23
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	92.14
d2apob1	55	Ribosome biogenesis protein Nop10 {Archaeon Methan	91.98
d1zina2	35	Microbial and mitochondrial ADK, insert "zinc fing	91.87
d2j0151	59	Ribosomal protein L32p {Thermus thermophilus [TaxI	91.8
d1twfl_	46	RBP12 subunit of RNA polymerase II {Baker's yeast	91.78
d1s3ga2	35	Microbial and mitochondrial ADK, insert "zinc fing	91.7
d1akya2	38	Microbial and mitochondrial ADK, insert "zinc fing	91.67
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	91.65
d1e4va2	35	Microbial and mitochondrial ADK, insert "zinc fing	91.45
d1lkoa2	44	Rubrerythrin, C-terminal domain {Desulfovibrio vul	91.24
d1k3xa3	40	Endonuclease VIII {Escherichia coli [TaxId: 562]}	90.67
d2zjrz1	58	Ribosomal protein L32p {Deinococcus radiodurans [T	90.66
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	90.4
d1rqga3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyro	90.27
d2gnra1	137	Hypothetical protein SSO2064 {Sulfolobus solfatari	89.87
d2dkta1	74	RING finger and CHY zinc finger domain-containing	89.73
d1vd4a_	62	Transcription initiation factor TFIIE-alpha {Human	89.49
d1k82a3	44	DNA repair protein MutM (Fpg) {Escherichia coli [T	89.19
d1wd2a_	60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	88.7
d2qam01	56	Ribosomal protein L32p {Escherichia coli [TaxId: 5	88.34
d1r2za3	46	DNA repair protein MutM (Fpg) {Bacillus stearother	88.12
d1iroa_	53	Rubredoxin {Clostridium pasteurianum [TaxId: 1501]	88.09
d1dx8a_	70	Rubredoxin {Guillardia theta [TaxId: 55529]}	87.81
d6rxna_	45	Rubredoxin {Desulfovibrio desulfuricans, strain 27	87.75
d2dsxa1	52	Rubredoxin {Desulfovibrio gigas [TaxId: 879]}	87.73
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	87.61
d1tdza3	47	DNA repair protein MutM (Fpg) {Lactococcus lactis	86.57
d1neea2	37	Zinc-binding domain of translation initiation fact	86.45
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	86.43
d1k81a_	36	Zinc-binding domain of translation initiation fact	86.39
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	84.83
d2j9ub1	47	Vacuolar protein-sorting-associated protein 36, VP	84.51
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	84.29
d1brfa_	53	Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2	83.71
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	83.51
d1wiia_	85	Hypothetical UPF0222 protein MGC4549 {Mouse (Mus m	83.46
d1ryqa_	67	putative DNA-directed RNA polymerase subunit E'' (	82.7
d1vzia2	37	Desulfoferrodoxin N-terminal domain {Desulfoarculu	82.3
d1s24a_	56	Two-iron rubredoxin {Pseudomonas oleovorans [TaxId	80.81
d1dxga_	36	Desulforedoxin {Desulfovibrio gigas [TaxId: 879]}	80.72
d2gmga1	105	Hypothetical protein PF0610 {Pyrococcus furiosus [	80.61
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	80.1

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: YfgJ-like
family: YfgJ-like
domain: Hypothetical protein YfgJ
species: Escherichia coli [TaxId: 562]

Probab=96.18  E-value=0.00029  Score=40.62  Aligned_cols=28  Identities=14%  Similarity=0.396  Sum_probs=19.0

Q ss_pred             CCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949           54 EPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        54 ~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      +....|..|...+..              .-.||.|+.+++.
T Consensus        16 ~~~~~C~~C~~~~~~--------------~a~CPdC~~~Le~   43 (71)
T d2jnea1          16 NGHARCRSCGEFIEM--------------KALCPDCHQPLQV   43 (71)
T ss_dssp             TTEEEETTTCCEEEE--------------EEECTTTCSBCEE
T ss_pred             CCCEehhhhhhhhee--------------EEeCCccccHHHH
Confidence            357788888887743              3467777777654

>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.17  E-value=0.001  Score=36.88  Aligned_cols=39  Identities=18%  Similarity=0.256  Sum_probs=27.8

Q ss_pred             eeecCCCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           14 SRVLKSGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        14 k~~~~~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      +.+....+++||+||++.                +-++.+.+.+.|..||..++.
T Consensus         4 ~~~~~~~~~~Cp~Cgs~~----------------ii~D~~~Ge~vC~~CG~Vlee   42 (58)
T d1dl6a_           4 SRLDALPRVTCPNHPDAI----------------LVEDYRAGDMICPECGLVVGD   42 (58)
T ss_dssp             CSCCCCSCCSBTTBSSSC----------------CEECSSSCCEECTTTCCEECC
T ss_pred             cccccccccCCCCCCCCC----------------EEEECCCCcEecccCCCEecc
Confidence            455666788999999932                223445578999999998643

>d2dkta1 g.89.1.1 (A:8-81) RING finger and CHY zinc finger domain-containing protein 1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: CHY zinc finger-like
superfamily: CHY zinc finger-like
family: CHY zinc finger
domain: RING finger and CHY zinc finger domain-containing protein 1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.06  E-value=0.00034  Score=40.52  Aligned_cols=24  Identities=21%  Similarity=0.570  Sum_probs=19.4

Q ss_pred             CccccccCCceecCCCccCcCCCCC
Q 033949           82 DVSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        82 ~~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      ....|..||...+. ...||+||+.
T Consensus        50 ~~l~CH~Cg~~~~~-~~~C~~Cgs~   73 (74)
T d2dkta1          50 KEVQCINCEKLQHA-QQTCEDCSTL   73 (74)
T ss_dssp             CCEEESSSCCEECS-CSBCSSSCCB
T ss_pred             CEEEeccCCCcccC-CCcCCCCCCC
Confidence            46889999998644 5679999985

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.21  E-value=0.0087  Score=34.01  Aligned_cols=12  Identities=25%  Similarity=0.622  Sum_probs=7.6

Q ss_pred             CceeCCCCCCCC
Q 033949           55 PALFCNNCNLLF   66 (107)
Q Consensus        55 ~~~~C~~CG~~~   66 (107)
                      ..+.|+.||..+
T Consensus        35 ~~~~C~~C~~~f   46 (73)
T d2ct7a1          35 LEATCPQCHQTF   46 (73)
T ss_dssp             SCEECTTTCCEE
T ss_pred             CEEEcCCCCCeE
Confidence            466677776663

>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.21  E-value=0.0063  Score=32.53  Aligned_cols=33  Identities=15%  Similarity=0.485  Sum_probs=22.5

Q ss_pred             CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      ++.+||+||+..                +-.+.+.+.+.|..||..++.
T Consensus         4 ~~~~Cp~Cgs~~----------------iv~D~~~Ge~vC~~CG~Viee   36 (50)
T d1pfta_           4 KQKVCPACESAE----------------LIYDPERGEIVCAKCGYVIEE   36 (50)
T ss_dssp             SCCSCTTTSCCC----------------EEEETTTTEEEESSSCCBCCC
T ss_pred             ccccCcCCCCCc----------------EEEECCCCeEecccCCcEecc
Confidence            355799999832                113334579999999998754

>d1nnqa2 g.41.5.1 (A:135-171) Rubrerythrin, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.15  E-value=0.0051  Score=30.97  Aligned_cols=13  Identities=15%  Similarity=0.381  Sum_probs=8.3

Q ss_pred             CceeCCCCCCCCC
Q 033949           55 PALFCNNCNLLFP   67 (107)
Q Consensus        55 ~~~~C~~CG~~~~   67 (107)
                      ....|+.||..++
T Consensus         4 ~~~~C~vCG~i~~   16 (37)
T d1nnqa2           4 KVYICPICGYTAV   16 (37)
T ss_dssp             CEEECTTTCCEEE
T ss_pred             cEEECCCCCCEec
Confidence            4566777777654

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: YfgJ-like
family: YfgJ-like
domain: Hypothetical protein YfgJ
species: Escherichia coli [TaxId: 562]

Probab=95.13  E-value=0.0016  Score=37.40  Aligned_cols=39  Identities=28%  Similarity=0.806  Sum_probs=28.5

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCCC
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSAL  107 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~l  107 (107)
                      +.||.|...++...           ..++|.+|....... .+||.|+++|
T Consensus         3 ~~CP~C~~eL~~~~-----------~~~~C~~C~~~~~~~-a~CPdC~~~L   41 (71)
T d2jnea1           3 LHCPQCQHVLDQDN-----------GHARCRSCGEFIEMK-ALCPDCHQPL   41 (71)
T ss_dssp             CBCSSSCSBEEEET-----------TEEEETTTCCEEEEE-EECTTTCSBC
T ss_pred             CcCCCccCcccccC-----------CCEehhhhhhhheeE-EeCCccccHH
Confidence            56888888876532           257899998886544 4799998876

>d2fiya1 e.59.1.1 (A:19-308) FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId: 287]}

class: Multi-domain proteins (alpha and beta)
fold: FdhE-like
superfamily: FdhE-like
family: FdhE-like
domain: FdhE homolog PA4809
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.39  E-value=0.006  Score=43.58  Aligned_cols=13  Identities=23%  Similarity=0.409  Sum_probs=9.2

Q ss_pred             ceeCCCCCCCCCC
Q 033949           56 ALFCNNCNLLFPS   68 (107)
Q Consensus        56 ~~~C~~CG~~~~~   68 (107)
                      ++.|+.|++....
T Consensus       190 ~l~C~~C~teW~~  202 (290)
T d2fiya1         190 YLSCSLCACEWHY  202 (290)
T ss_dssp             EEEETTTCCEEEC
T ss_pred             EEECCCCCCcccc
Confidence            7777777777644

>d1rqga3 g.41.1.1 (A:139-173) Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyrococcus abyssi [TaxId: 29292]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Pyrococcus abyssi [TaxId: 29292]

Probab=93.76  E-value=0.022  Score=28.19  Aligned_cols=25  Identities=24%  Similarity=0.627  Sum_probs=16.0

Q ss_pred             eCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCC
Q 033949           58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPD   96 (107)
Q Consensus        58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~   96 (107)
                      .||.||+.-..              ...|.+||+.+++.
T Consensus         4 ~CP~C~~~~a~--------------GDqCe~CG~~~~p~   28 (35)
T d1rqga3           4 TCPYCGAEDQK--------------GDQCEVCGRPLTPE   28 (35)
T ss_dssp             BCSSSCCSCCC--------------TTTCSSSCCCCCTT
T ss_pred             ECCCCCCCccc--------------CcchhhcCCccCHH
Confidence            47888775322              23588888877764

>d2ayja1 g.41.8.7 (A:1-56) Ribosomal protein L40e {Sulfolobus solfataricus [TaxId: 2287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L40e
domain: Ribosomal protein L40e
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=93.33  E-value=0.067  Score=28.92  Aligned_cols=25  Identities=28%  Similarity=0.436  Sum_probs=23.1

Q ss_pred             CccccccCCceecCCCccCcCCCCC
Q 033949           82 DVSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        82 ~~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      +..+|-.|+|.++..|+.|-.||++
T Consensus        18 ~k~ICrkC~AR~p~rAt~CRKCg~~   42 (56)
T d2ayja1          18 LKKVCRKCGALNPIRATKCRRCHST   42 (56)
T ss_dssp             CCEEETTTCCEECTTCSSCTTTCCC
T ss_pred             hhHHHhhccccCCccccccccCCCC
Confidence            5789999999999999999999975

>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Nigerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=93.13  E-value=0.025  Score=28.10  Aligned_cols=26  Identities=23%  Similarity=0.515  Sum_probs=16.0

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      .+..|+.||...+-+.            -..||-||+.
T Consensus         4 ~~~vC~vCGyi~~g~~------------Pe~CPvCg~~   29 (36)
T d1yuza2           4 KFHLCPICGYIHKGED------------FEKCPICFRP   29 (36)
T ss_dssp             CEEECSSSCCEEESSC------------CSBCTTTCCB
T ss_pred             CEEECCCCCCEeeCCC------------CCcCCCCCCc
Confidence            4667777877764321            1357777765

>d1nnqa2 g.41.5.1 (A:135-171) Rubrerythrin, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=93.12  E-value=0.025  Score=28.30  Aligned_cols=24  Identities=29%  Similarity=0.815  Sum_probs=15.0

Q ss_pred             ccccccCCceecCC-CccCcCCCCC
Q 033949           83 VSKCRFCDRLVEPD-FSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~~-~~fCP~CG~~  106 (107)
                      ...|+.||.....+ ...||-||.+
T Consensus         5 ~~~C~vCG~i~~g~~P~~CPvCg~~   29 (37)
T d1nnqa2           5 VYICPICGYTAVDEAPEYCPVCGAP   29 (37)
T ss_dssp             EEECTTTCCEEESCCCSBCTTTCCB
T ss_pred             EEECCCCCCEecCCCCCcCCCCCCc
Confidence            45677777765543 3667777753

>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Nigerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=92.96  E-value=0.026  Score=28.05  Aligned_cols=24  Identities=29%  Similarity=0.736  Sum_probs=13.8

Q ss_pred             ccccccCCceecC-CCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEP-DFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~-~~~fCP~CG~~  106 (107)
                      ...|+.||..... ....||-||.+
T Consensus         5 ~~vC~vCGyi~~g~~Pe~CPvCg~~   29 (36)
T d1yuza2           5 FHLCPICGYIHKGEDFEKCPICFRP   29 (36)
T ss_dssp             EEECSSSCCEEESSCCSBCTTTCCB
T ss_pred             EEECCCCCCEeeCCCCCcCCCCCCc
Confidence            3566666666543 34566666653

>d2cona1 g.41.15.1 (A:8-73) RNA-binding protein NOB1 (Nin one binding) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: NOB1 zinc finger-like
family: NOB1 zinc finger-like
domain: RNA-binding protein NOB1 (Nin one binding)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.74  E-value=0.032  Score=31.37  Aligned_cols=11  Identities=27%  Similarity=0.455  Sum_probs=5.2

Q ss_pred             CceeCCCCCCC
Q 033949           55 PALFCNNCNLL   65 (107)
Q Consensus        55 ~~~~C~~CG~~   65 (107)
                      +.+.|..|-..
T Consensus         7 ~~LrC~aCf~~   17 (66)
T d2cona1           7 YILRCHGCFKT   17 (66)
T ss_dssp             EEEECSSSCCE
T ss_pred             eeeEeeecCcC
Confidence            44555555443

>d2ak3a2 g.41.2.1 (A:125-161) Microbial and mitochondrial ADK, insert "zinc finger" domain {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=92.34  E-value=0.024  Score=28.35  Aligned_cols=32  Identities=6%  Similarity=0.134  Sum_probs=17.6

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      ..|+.||+.|.+......       ..-.|-.||.++..
T Consensus         3 ~vc~~cG~~Yh~~~~pPk-------~~g~CD~cg~~L~q   34 (37)
T d2ak3a2           3 WIHPGSGRVYNIEFNPPK-------TMGIDDLTGEPLVQ   34 (37)
T ss_dssp             EEETTTTEEEETTTBCCS-------STTBCTTTCCBCBC
T ss_pred             eeeCCcCChhhhccCCcc-------ccCCccCCCCcCEe
Confidence            457777777755332111       13467777776643

>d1qxfa_ g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27e
domain: Ribosomal protein S27e
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=92.34  E-value=0.039  Score=30.22  Aligned_cols=33  Identities=12%  Similarity=0.271  Sum_probs=24.2

Q ss_pred             CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCC
Q 033949           20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPS   68 (107)
Q Consensus        20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~   68 (107)
                      ..++||.|++..                +=|+.....+.|..||..+..
T Consensus         6 ~~VkC~~C~n~~----------------ivFsha~t~V~C~~Cg~~L~~   38 (58)
T d1qxfa_           6 VKVKCPDCEHEQ----------------VIFDHPSTIVKCIICGRTVAE   38 (58)
T ss_dssp             EEEECTTTCCEE----------------EEESSCSSCEECSSSCCEEEE
T ss_pred             EEeECCCCCCeE----------------EEEecCceEEEccccCCEEec
Confidence            357899999921                226666679999999998743

>d1pfva3 g.41.1.1 (A:141-175) Methionyl-tRNA synthetase (MetRS), Zn-domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Escherichia coli [TaxId: 562]

Probab=92.25  E-value=0.025  Score=27.98  Aligned_cols=11  Identities=27%  Similarity=0.884  Sum_probs=7.5

Q ss_pred             ccccCCceecC
Q 033949           85 KCRFCDRLVEP   95 (107)
Q Consensus        85 ~C~~CG~~i~~   95 (107)
                      .|.+||+.+++
T Consensus        17 qCe~CG~~~~p   27 (35)
T d1pfva3          17 NCEVCGATYSP   27 (35)
T ss_dssp             BCTTTCCBCCG
T ss_pred             cHHHcCCcCCH
Confidence            57777777654

>d2ey4e1 g.41.16.1 (E:4-55) Ribosome biogenesis protein Nop10 {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Nop10-like SnoRNP
family: Nucleolar RNA-binding protein Nop10-like
domain: Ribosome biogenesis protein Nop10
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=92.23  E-value=0.042  Score=29.45  Aligned_cols=11  Identities=18%  Similarity=0.616  Sum_probs=6.1

Q ss_pred             cccccCCceec
Q 033949           84 SKCRFCDRLVE   94 (107)
Q Consensus        84 ~~C~~CG~~i~   94 (107)
                      ..||.||....
T Consensus        15 ~~CP~CG~~t~   25 (52)
T d2ey4e1          15 EVCPVCGEKTK   25 (52)
T ss_dssp             SBCTTTCCBCE
T ss_pred             ccCcCCCCccc
Confidence            35666665543

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.14  E-value=0.09  Score=29.48  Aligned_cols=38  Identities=24%  Similarity=0.581  Sum_probs=25.6

Q ss_pred             CCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCccCcCCCCC
Q 033949           54 EPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        54 ~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      .....||.|+..+..+...         ...+|+.||..      ||-.|+.+
T Consensus        16 ~~~k~CP~C~~~~~~~~~~---------~~~~C~~C~~~------fC~~C~~~   53 (73)
T d2ct7a1          16 PKFLWCAQCSFGFIYEREQ---------LEATCPQCHQT------FCVRCKRQ   53 (73)
T ss_dssp             CCEECCSSSCCCEECCCSC---------SCEECTTTCCE------ECSSSCSB
T ss_pred             CCCCCCCCCCCEeEECCCC---------CEEEcCCCCCe------ECcccCcc
Confidence            3577788888876543321         24678888876      78888753

>d2apob1 g.41.16.1 (B:403-457) Ribosome biogenesis protein Nop10 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Nop10-like SnoRNP
family: Nucleolar RNA-binding protein Nop10-like
domain: Ribosome biogenesis protein Nop10
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=91.98  E-value=0.045  Score=29.64  Aligned_cols=12  Identities=17%  Similarity=0.301  Sum_probs=7.6

Q ss_pred             cccccCCceecC
Q 033949           84 SKCRFCDRLVEP   95 (107)
Q Consensus        84 ~~C~~CG~~i~~   95 (107)
                      ..||.||....+
T Consensus        17 ~~CP~CG~~t~~   28 (55)
T d2apob1          17 EICPKCGEKTVI   28 (55)
T ss_dssp             SBCSSSCSBCBC
T ss_pred             ccCcCCCCccCc
Confidence            467777766544

>d1zina2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=91.87  E-value=0.041  Score=27.09  Aligned_cols=31  Identities=23%  Similarity=0.565  Sum_probs=17.4

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE   94 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~   94 (107)
                      ..|+.||+.|.+......       ..-+|-.||.++.
T Consensus         3 r~C~~CG~~Yh~~~~pPk-------~~g~CD~cG~~L~   33 (35)
T d1zina2           3 RICRNCGATYHLIFHPPA-------KPGVCDKCGGELY   33 (35)
T ss_dssp             EEETTTCCEEETTTBCCS-------STTBCTTTCCBEE
T ss_pred             cCCcCcCchhccccCCCC-------CCCcCCCCCCCcc
Confidence            457777777755332111       1346777777653

>d2j0151 g.41.8.5 (5:2-60) Ribosomal protein L32p {Thermus thermophilus [TaxId: 274]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L32p
domain: Ribosomal protein L32p
species: Thermus thermophilus [TaxId: 274]

Probab=91.80  E-value=0.047  Score=29.92  Aligned_cols=22  Identities=27%  Similarity=0.792  Sum_probs=12.7

Q ss_pred             ccccccCCceecCCCccCcCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~  105 (107)
                      ...|++||+... .-..||+||.
T Consensus        29 l~~C~~CG~~~~-pHrvC~~CG~   50 (59)
T d2j0151          29 LVPCPECKAMKP-PHTVCPECGY   50 (59)
T ss_dssp             CBCCSSSSSCBC-TTCBCTTTCC
T ss_pred             eeECCCCCCccc-ceeECCCCCe
Confidence            345777776533 3445777764

>d1twfl_ g.41.9.2 (L:) RBP12 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: RNA polymerase subunits
family: RBP12 subunit of RNA polymerase II
domain: RBP12 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.78  E-value=0.066  Score=27.89  Aligned_cols=27  Identities=22%  Similarity=0.595  Sum_probs=15.5

Q ss_pred             eCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949           58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE   94 (107)
Q Consensus        58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~   94 (107)
                      .|..||....+...          +...|.+||..|.
T Consensus         6 iCgeCg~~~~l~~~----------d~irCreCG~RIl   32 (46)
T d1twfl_           6 ICAECSSKLSLSRT----------DAVRCKDCGHRIL   32 (46)
T ss_dssp             ECSSSCCEECCCTT----------STTCCSSSCCCCC
T ss_pred             EcccCCCceEeCCC----------CcEEeccCCcEEE
Confidence            46667766655332          2345777776654

>d1s3ga2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus globisporus [TaxId: 1459]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus globisporus [TaxId: 1459]

Probab=91.70  E-value=0.038  Score=27.20  Aligned_cols=31  Identities=19%  Similarity=0.347  Sum_probs=17.4

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE   94 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~   94 (107)
                      ..|+.||+.|.+.-....       ..-+|-.||.++.
T Consensus         3 ~~C~~CG~~Yh~~~~pPk-------~~g~CD~cg~~L~   33 (35)
T d1s3ga2           3 RICKVCGTSYHLLFNPPQ-------VEGKCDKDGGELY   33 (35)
T ss_dssp             EEETTTCCEEETTTBCCS-------BTTBCTTTCCBEE
T ss_pred             cCCcCcCchhccccCCCC-------CCCccCCCCCCce
Confidence            457777777755322111       1356777777653

>d1akya2 g.41.2.1 (A:131-168) Microbial and mitochondrial ADK, insert "zinc finger" domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.67  E-value=0.063  Score=26.84  Aligned_cols=32  Identities=13%  Similarity=0.142  Sum_probs=16.9

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      ..|+.||+.|.+.-....       ..-.|-.||+++..
T Consensus         3 r~C~~cG~~Yh~~~~ppk-------~~g~CD~cg~~L~q   34 (38)
T d1akya2           3 LIHPASGRSYHKIFNPPK-------EDMKDDVTGEALVQ   34 (38)
T ss_dssp             EECTTTCCEEETTTBCCS-------STTBCTTTCCBCBC
T ss_pred             cCCcCccchhhhhccCcC-------cCCccCCCCCEeee
Confidence            356777776655322111       12467777766543

>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: PhnA zinc-binding domain
domain: Hypothetical protein PA0128, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=91.65  E-value=0.043  Score=27.51  Aligned_cols=10  Identities=20%  Similarity=0.311  Sum_probs=4.8

Q ss_pred             cccccCCcee
Q 033949           84 SKCRFCDRLV   93 (107)
Q Consensus        84 ~~C~~CG~~i   93 (107)
                      ..||.||.|=
T Consensus        21 ~vCPeC~hEW   30 (38)
T d2akla2          21 LVCPECAHEW   30 (38)
T ss_dssp             EEETTTTEEE
T ss_pred             EECCcccCcC
Confidence            4455555443

>d1e4va2 g.41.2.1 (A:122-156) Microbial and mitochondrial ADK, insert "zinc finger" domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Escherichia coli [TaxId: 562]

Probab=91.45  E-value=0.038  Score=27.22  Aligned_cols=31  Identities=10%  Similarity=0.095  Sum_probs=17.5

Q ss_pred             eeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceec
Q 033949           57 LFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVE   94 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~   94 (107)
                      ..|+.||..|.+.-....       ..-+|-.||+++.
T Consensus         3 r~c~~cG~~Yh~~~~PPk-------~~g~CD~cg~~L~   33 (35)
T d1e4va2           3 RVHAPSGRVYHVKFNPPK-------VEGKDDVTGEELT   33 (35)
T ss_dssp             EEETTTTEEEETTTBCCS-------STTBCTTTCCBCB
T ss_pred             cCCcCcCChhhhccCccc-------cCCcccCCCCEee
Confidence            457777777765332211       1346777777654

>d1lkoa2 g.41.5.1 (A:148-191) Rubrerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=91.24  E-value=0.04  Score=28.52  Aligned_cols=26  Identities=19%  Similarity=0.466  Sum_probs=15.7

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      ...|.+||..++-+..           -..||.||+.
T Consensus         8 ~W~C~~CGyi~~g~~a-----------P~~CPvC~~p   33 (44)
T d1lkoa2           8 KWRCRNCGYVHEGTGA-----------PELCPACAHP   33 (44)
T ss_dssp             EEEETTTCCEEEEEEC-----------CSBCTTTCCB
T ss_pred             EEEcCCCCcEEECCCC-----------CCcCCCCCCc
Confidence            5667788877653221           1357777764

>d1k3xa3 g.39.1.8 (A:223-262) Endonuclease VIII {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: Endonuclease VIII
species: Escherichia coli [TaxId: 562]

Probab=90.67  E-value=0.03  Score=28.39  Aligned_cols=21  Identities=33%  Similarity=0.986  Sum_probs=12.7

Q ss_pred             cccccCCceecC------CCccCcCCC
Q 033949           84 SKCRFCDRLVEP------DFSFCPYCG  104 (107)
Q Consensus        84 ~~C~~CG~~i~~------~~~fCP~CG  104 (107)
                      ..|+.||..|..      +.-|||.|-
T Consensus        13 ~pC~~C~~~I~~~~~~gR~t~~Cp~CQ   39 (40)
T d1k3xa3          13 EPCERCGSIIEKTTLSSRPFYWCPGCQ   39 (40)
T ss_dssp             SBCTTTCCBCEEEEETTEEEEECTTTC
T ss_pred             CccCcCCCEEEEEEECCCCCEEChhhC
Confidence            456666666644      456677663

>d2zjrz1 g.41.8.5 (Z:2-59) Ribosomal protein L32p {Deinococcus radiodurans [TaxId: 1299]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L32p
domain: Ribosomal protein L32p
species: Deinococcus radiodurans [TaxId: 1299]

Probab=90.66  E-value=0.054  Score=29.58  Aligned_cols=22  Identities=27%  Similarity=0.794  Sum_probs=14.2

Q ss_pred             ccccccCCceecCCCccCcCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~  105 (107)
                      ...|++||+.. ..-..||.||.
T Consensus        29 l~~C~~CG~~~-lpHrvC~~CG~   50 (58)
T d2zjrz1          29 LTECPQCHGKK-LSHHICPNCGY   50 (58)
T ss_dssp             CEECTTTCCEE-CTTBCCTTTCB
T ss_pred             eeECCCCCCCc-cceeeCCCCCc
Confidence            45677777763 34457777774

>d1joca1 g.50.1.1 (A:1348-1411) Eea1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Eea1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.40  E-value=0.085  Score=28.97  Aligned_cols=11  Identities=27%  Similarity=0.510  Sum_probs=5.2

Q ss_pred             ceeCCCCCCCC
Q 033949           56 ALFCNNCNLLF   66 (107)
Q Consensus        56 ~~~C~~CG~~~   66 (107)
                      ...|..|+..+
T Consensus         8 ~~~C~~C~~~F   18 (64)
T d1joca1           8 VQNCMACGKGF   18 (64)
T ss_dssp             CCBCTTTCCBC
T ss_pred             CCcCcCcCCcc
Confidence            34444554444

>d1rqga3 g.41.1.1 (A:139-173) Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyrococcus abyssi [TaxId: 29292]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Pyrococcus abyssi [TaxId: 29292]

Probab=90.27  E-value=0.21  Score=24.43  Aligned_cols=16  Identities=13%  Similarity=0.343  Sum_probs=12.2

Q ss_pred             CceeCCCCCCCCCCCC
Q 033949           55 PALFCNNCNLLFPSSL   70 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~   70 (107)
                      +--.|..||+.++..+
T Consensus        14 ~GDqCe~CG~~~~p~e   29 (35)
T d1rqga3          14 KGDQCEVCGRPLTPEI   29 (35)
T ss_dssp             CTTTCSSSCCCCCTTS
T ss_pred             cCcchhhcCCccCHHH
Confidence            5567999999987644

>d2gnra1 b.40.4.15 (A:8-144) Hypothetical protein SSO2064 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: SSO2064-like
domain: Hypothetical protein SSO2064
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=89.87  E-value=0.046  Score=34.45  Aligned_cols=24  Identities=38%  Similarity=0.729  Sum_probs=17.6

Q ss_pred             ccccccCCceecCCCccCcCCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGSA  106 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~~  106 (107)
                      ..+|.+||...-+...+||.||+.
T Consensus        39 ~~~C~~CG~v~~Ppr~~Cp~C~s~   62 (137)
T d2gnra1          39 GSKCSKCGRIFVPARSYCEHCFVK   62 (137)
T ss_dssp             EEECTTTCCEEESCCSEETTTTEE
T ss_pred             EEEcCCCCCEEeCccccCCCCCCC
Confidence            456888888777777778888753

>d2dkta1 g.89.1.1 (A:8-81) RING finger and CHY zinc finger domain-containing protein 1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: CHY zinc finger-like
superfamily: CHY zinc finger-like
family: CHY zinc finger
domain: RING finger and CHY zinc finger domain-containing protein 1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.73  E-value=0.082  Score=29.87  Aligned_cols=26  Identities=31%  Similarity=0.613  Sum_probs=20.4

Q ss_pred             CCCceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCce
Q 033949           53 KEPALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        53 ~~~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      +...+.|..||...++.              ..|++||+.
T Consensus        48 ~~~~l~CH~Cg~~~~~~--------------~~C~~Cgs~   73 (74)
T d2dkta1          48 KVKEVQCINCEKLQHAQ--------------QTCEDCSTL   73 (74)
T ss_dssp             SCCCEEESSSCCEECSC--------------SBCSSSCCB
T ss_pred             cCCEEEeccCCCcccCC--------------CcCCCCCCC
Confidence            44789999999987553              369999974

>d1vd4a_ g.41.3.1 (A:) Transcription initiation factor TFIIE-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIE-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.49  E-value=0.041  Score=30.50  Aligned_cols=42  Identities=17%  Similarity=0.301  Sum_probs=23.7

Q ss_pred             CCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCCCCC
Q 033949           19 SGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFPSSL   70 (107)
Q Consensus        19 ~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~~~~   70 (107)
                      ....+||+|++++.-.+....          ++.......|..|+..+..+.
T Consensus        12 ~~~y~Cp~C~~~ys~Lda~~L----------~d~~~~~F~C~~C~~el~eD~   53 (62)
T d1vd4a_          12 RASFKCPVCSSTFTDLEANQL----------FDPMTGTFRCTFCHTEVEEDE   53 (62)
T ss_dssp             SSEEECSSSCCEEEHHHHHHH----------EETTTTEEBCSSSCCBCEECT
T ss_pred             CCceECCCCCCCcchhhHHHh----------cCcCCCeEEecCCCCEEecCC
Confidence            456778888884432222111          122346777888887765544

>d1k82a3 g.39.1.8 (A:225-268) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Escherichia coli [TaxId: 562]

Probab=89.19  E-value=0.041  Score=28.35  Aligned_cols=21  Identities=24%  Similarity=0.725  Sum_probs=13.9

Q ss_pred             cccccCCceecC------CCccCcCCC
Q 033949           84 SKCRFCDRLVEP------DFSFCPYCG  104 (107)
Q Consensus        84 ~~C~~CG~~i~~------~~~fCP~CG  104 (107)
                      ..|+.||+.|..      ..-|||.|-
T Consensus        17 ~~C~~C~~~I~~~~~~~R~t~~Cp~CQ   43 (44)
T d1k82a3          17 EPCRVCGTPIVATKHAQRATFYCRQCQ   43 (44)
T ss_dssp             SBCTTTCCBCEEEEETTEEEEECTTTC
T ss_pred             CCcCCCCCEEEEEEECCcccEEChhhc
Confidence            467777777654      566777763

>d1wd2a_ g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Ariadne-1 protein homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.70  E-value=0.12  Score=28.10  Aligned_cols=15  Identities=13%  Similarity=0.432  Sum_probs=12.1

Q ss_pred             CceeCCCCCCCCCCC
Q 033949           55 PALFCNNCNLLFPSS   69 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~   69 (107)
                      ....||.|+..++.+
T Consensus         5 ntK~CP~C~~~ieK~   19 (60)
T d1wd2a_           5 NTKECPKCHVTIEKD   19 (60)
T ss_dssp             CCCCCTTTCCCCSSC
T ss_pred             cCcCCCCCCCeEEEC
Confidence            567899999998664

>d2qam01 g.41.8.5 (0:1-56) Ribosomal protein L32p {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L32p
domain: Ribosomal protein L32p
species: Escherichia coli [TaxId: 562]

Probab=88.34  E-value=0.11  Score=28.07  Aligned_cols=21  Identities=10%  Similarity=-0.078  Sum_probs=13.9

Q ss_pred             ccccccCCceecCCCccCcCCCC
Q 033949           83 VSKCRFCDRLVEPDFSFCPYCGS  105 (107)
Q Consensus        83 ~~~C~~CG~~i~~~~~fCP~CG~  105 (107)
                      ...|++||+...+- ..|| ||.
T Consensus        27 ~~~c~~CG~~~lpH-~vC~-cG~   47 (56)
T d2qam01          27 LSVDKTSGEKHLRH-HITA-DGY   47 (56)
T ss_dssp             CEECSSSCCEECTT-SCCT-TSC
T ss_pred             eeECCCCCCCccCc-EECC-CCC
Confidence            45678888875553 3577 875

>d1r2za3 g.39.1.8 (A:229-274) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=88.12  E-value=0.053  Score=28.11  Aligned_cols=21  Identities=29%  Similarity=0.906  Sum_probs=13.8

Q ss_pred             cccccCCceecC------CCccCcCCC
Q 033949           84 SKCRFCDRLVEP------DFSFCPYCG  104 (107)
Q Consensus        84 ~~C~~CG~~i~~------~~~fCP~CG  104 (107)
                      ..|+.||+.|..      ..-|||.|-
T Consensus        19 ~~C~~C~~~I~~~~~~gR~t~~Cp~CQ   45 (46)
T d1r2za3          19 NPCKRCGTPIEKTVVAGRGTHYCPRCQ   45 (46)
T ss_dssp             SBCTTTCCBCEEEEETTEEEEECTTTC
T ss_pred             CccCCCCCeEEEEEECCCcCEEChhhC
Confidence            467777777654      566777773

>d1iroa_ g.41.5.1 (A:) Rubredoxin {Clostridium pasteurianum [TaxId: 1501]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Clostridium pasteurianum [TaxId: 1501]

Probab=88.09  E-value=0.11  Score=27.80  Aligned_cols=37  Identities=14%  Similarity=0.226  Sum_probs=21.8

Q ss_pred             ceeCCCCCCCCCCCCCC--CCCC----CCCccCccccccCCce
Q 033949           56 ALFCNNCNLLFPSSLPP--PPPP----PPLVSDVSKCRFCDRL   92 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~--~~~~----~~~~~~~~~C~~CG~~   92 (107)
                      ...|+.||..|+...-.  ..|.    ++-......||-||+.
T Consensus         3 ky~C~~CgyiYd~~~Gd~~~gi~pGT~F~~LP~dw~CP~C~a~   45 (53)
T d1iroa_           3 KYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVG   45 (53)
T ss_dssp             CEEETTTCCEECTTTCBGGGTBCTTCCGGGSCTTCBCTTTCCB
T ss_pred             CeEcCCCCcEECcccCCcccCCCCCCCHHHCCCCCCCcCCCCc
Confidence            35799999999764321  0111    1111245789999986

>d1dx8a_ g.41.5.1 (A:) Rubredoxin {Guillardia theta [TaxId: 55529]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Guillardia theta [TaxId: 55529]

Probab=87.81  E-value=0.14  Score=28.96  Aligned_cols=40  Identities=20%  Similarity=0.338  Sum_probs=24.4

Q ss_pred             CCCceeCCCCCCCCCCCCCC--CCCC----CCCccCccccccCCce
Q 033949           53 KEPALFCNNCNLLFPSSLPP--PPPP----PPLVSDVSKCRFCDRL   92 (107)
Q Consensus        53 ~~~~~~C~~CG~~~~~~~~~--~~~~----~~~~~~~~~C~~CG~~   92 (107)
                      ......|+.||..|+...-.  ..|.    ++-......||.||+.
T Consensus         4 ~~~ky~C~~CgyiYDp~~GD~~~gI~pGT~F~dLP~dW~CP~Cga~   49 (70)
T d1dx8a_           4 DEGKYECEACGYIYEPEKGDKFAGIPPGTPFVDLSDSFMCPACRSP   49 (70)
T ss_dssp             CSSCEEETTTCCEECTTTCCTTTTCCSSCCGGGSCTTCBCTTTCCB
T ss_pred             cCCeEEcCCCCeEECcccCCcccCCCCCCChHHCCCCCCCcCCCCc
Confidence            34578899999999764321  1111    1111246789999986

>d6rxna_ g.41.5.1 (A:) Rubredoxin {Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]

Probab=87.75  E-value=0.071  Score=27.64  Aligned_cols=35  Identities=20%  Similarity=0.371  Sum_probs=20.0

Q ss_pred             ceeCCCCCCCCCCCCC-CCCCCCCCccCccccccCCce
Q 033949           56 ALFCNNCNLLFPSSLP-PPPPPPPLVSDVSKCRFCDRL   92 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~-~~~~~~~~~~~~~~C~~CG~~   92 (107)
                      ...|+.||..|+...- .++  ++......+||.||+.
T Consensus         3 ~y~C~~CgyiYd~~~Gdgt~--Fe~LP~dw~CP~C~a~   38 (45)
T d6rxna_           3 KYVCNVCGYEYDPAEHDNVP--FDQLPDDWCCPVCGVS   38 (45)
T ss_dssp             CEEETTTCCEECGGGGTTCC--GGGSCTTCBCTTTCCB
T ss_pred             CeEeCCCCeEECcccCCCCC--HHHCCCCCCCcCCCCc
Confidence            3578899988865321 110  0101135689999876

>d2dsxa1 g.41.5.1 (A:1-52) Rubredoxin {Desulfovibrio gigas [TaxId: 879]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio gigas [TaxId: 879]

Probab=87.73  E-value=0.12  Score=27.54  Aligned_cols=37  Identities=14%  Similarity=0.244  Sum_probs=21.8

Q ss_pred             ceeCCCCCCCCCCCCCC--CCCC----CCCccCccccccCCce
Q 033949           56 ALFCNNCNLLFPSSLPP--PPPP----PPLVSDVSKCRFCDRL   92 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~--~~~~----~~~~~~~~~C~~CG~~   92 (107)
                      ...|+.||..|+...-.  ..|.    ++-....-.||.||+.
T Consensus         3 ~y~C~~CgyiYdp~~Gd~~~gi~pGT~F~~LP~~w~CP~C~a~   45 (52)
T d2dsxa1           3 IYVCTVCGYEYDPAKGDPDSGIKPGTKFEDLPDDWACPVCGAS   45 (52)
T ss_dssp             CEEETTTCCEECTTTCBGGGTBCTTCCGGGSCTTCBCTTTCCB
T ss_pred             eEEeCCCCeEECcccCCcccCCCCCCCHHHCCCCCCCcCCCCc
Confidence            45799999999764321  0111    1111246789999986

>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27a
domain: Ribosomal protein S27ae
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=87.61  E-value=0.2  Score=26.86  Aligned_cols=24  Identities=29%  Similarity=0.412  Sum_probs=15.3

Q ss_pred             CccccccCCceec----CCCccCcCCCC
Q 033949           82 DVSKCRFCDRLVE----PDFSFCPYCGS  105 (107)
Q Consensus        82 ~~~~C~~CG~~i~----~~~~fCP~CG~  105 (107)
                      +...||+||.-+-    .+-.+|-.||.
T Consensus        17 ~~k~CP~CG~GvFmA~H~dR~~CGKCgy   44 (55)
T d2k4xa1          17 KHRFCPRCGPGVFLAEHADRYSCGRCGY   44 (55)
T ss_dssp             SSCCCTTTTTTCCCEECSSEEECTTTCC
T ss_pred             ecCcCcCCCCcEEeeecCCCccccCCcc
Confidence            3567888876432    26667777775

>d1tdza3 g.39.1.8 (A:225-271) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Lactococcus lactis [TaxId: 1358]

Probab=86.57  E-value=0.093  Score=27.28  Aligned_cols=22  Identities=32%  Similarity=0.868  Sum_probs=14.9

Q ss_pred             cccccCCceecC------CCccCcCCCC
Q 033949           84 SKCRFCDRLVEP------DFSFCPYCGS  105 (107)
Q Consensus        84 ~~C~~CG~~i~~------~~~fCP~CG~  105 (107)
                      ..|+.||.+|..      +.-|||.|-.
T Consensus        19 ~~C~~C~~~I~~~~~~gR~t~~Cp~CQk   46 (47)
T d1tdza3          19 EKCSRCGAEIQKIKVAGRGTHFCPVCQQ   46 (47)
T ss_dssp             SBCTTTCCBCEEEEETTEEEEECTTTSC
T ss_pred             CCcCCCCcEEEEEEECCcccEECccccC
Confidence            467777777655      5677777754

>d1neea2 g.59.1.1 (A:99-135) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Small proteins
fold: Zinc-binding domain of translation initiation factor 2 beta
superfamily: Zinc-binding domain of translation initiation factor 2 beta
family: Zinc-binding domain of translation initiation factor 2 beta
domain: Zinc-binding domain of translation initiation factor 2 beta
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=86.45  E-value=0.15  Score=25.31  Aligned_cols=15  Identities=27%  Similarity=0.470  Sum_probs=10.5

Q ss_pred             CCceeCCCCCCCCCC
Q 033949           54 EPALFCNNCNLLFPS   68 (107)
Q Consensus        54 ~~~~~C~~CG~~~~~   68 (107)
                      -+++.|..||+.-.+
T Consensus        20 ~~~l~C~aCGa~r~V   34 (37)
T d1neea2          20 ISLLKCEACGAKAPL   34 (37)
T ss_dssp             TTEEECSTTSCCCCS
T ss_pred             EEEEEeccCCCCccc
Confidence            477888888876543

>d2fiya1 e.59.1.1 (A:19-308) FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId: 287]}

class: Multi-domain proteins (alpha and beta)
fold: FdhE-like
superfamily: FdhE-like
family: FdhE-like
domain: FdhE homolog PA4809
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=86.43  E-value=0.13  Score=36.27  Aligned_cols=40  Identities=13%  Similarity=0.226  Sum_probs=23.1

Q ss_pred             CceeCCCCCCCCCCCCCCCCCCCC----CccCccccccCCceec
Q 033949           55 PALFCNNCNLLFPSSLPPPPPPPP----LVSDVSKCRFCDRLVE   94 (107)
Q Consensus        55 ~~~~C~~CG~~~~~~~~~~~~~~~----~~~~~~~C~~CG~~i~   94 (107)
                      ..+.|++||..-.++-...+..++    .......|.+|+.-+.
T Consensus       203 ~R~~C~~Cg~~~~~~~~~~~~~~~~~~~~~~r~e~C~~C~~Y~K  246 (290)
T d2fiya1         203 VRIKCSHCEESKHLAYLSLEHDGQPAEKAVLRAETCPSCQGYLK  246 (290)
T ss_dssp             CTTSCSSSCCCSCCEEECCCC-CCCSTTCSEEEEEETTTTEEEE
T ss_pred             ccccCCCCCCCCCcceEEEecCCCcccccceEEEEcCCcCCeEE
Confidence            467999999886543222221111    0113567999998764

>d1k81a_ g.59.1.1 (A:) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Small proteins
fold: Zinc-binding domain of translation initiation factor 2 beta
superfamily: Zinc-binding domain of translation initiation factor 2 beta
family: Zinc-binding domain of translation initiation factor 2 beta
domain: Zinc-binding domain of translation initiation factor 2 beta
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=86.39  E-value=0.11  Score=25.70  Aligned_cols=31  Identities=19%  Similarity=0.336  Sum_probs=18.0

Q ss_pred             EECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCC
Q 033949           22 GRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLF   66 (107)
Q Consensus        22 ~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~   66 (107)
                      ++|+.|++..+....             -+ +-+++.|..||+.-
T Consensus         1 V~C~~C~spDT~l~k-------------e~-R~~~l~C~aCGa~r   31 (36)
T d1k81a_           1 VICRECGKPDTKIIK-------------EG-RVHLLKCMACGAIR   31 (36)
T ss_dssp             CCCSSSCSCEEEEEE-------------ET-TEEEEEEETTTEEE
T ss_pred             CCCCCCCCCCCEEEE-------------cC-CEEEEEeccCCCCC
Confidence            368888883332221             12 23677888888753

>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcriptional factor SII, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.83  E-value=0.44  Score=24.95  Aligned_cols=10  Identities=20%  Similarity=0.394  Sum_probs=6.8

Q ss_pred             CcEECCCCCC
Q 033949           20 GAGRCINCGS   29 (107)
Q Consensus        20 ~~~~C~~Cg~   29 (107)
                      ..++||+||+
T Consensus         8 ~~~~C~kC~~   17 (50)
T d1tfia_           8 DLFTCGKCKK   17 (50)
T ss_dssp             CCSCCSSSCS
T ss_pred             CCEECCCCCC
Confidence            3456777777

>d2j9ub1 g.41.11.1 (B:115-161) Vacuolar protein-sorting-associated protein 36, VPS36 {Saccharomyces cerevisiae [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Ran binding protein zinc finger-like
family: Ran binding protein zinc finger-like
domain: Vacuolar protein-sorting-associated protein 36, VPS36
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=84.51  E-value=0.34  Score=24.99  Aligned_cols=36  Identities=11%  Similarity=0.128  Sum_probs=23.6

Q ss_pred             ceeCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecC
Q 033949           56 ALFCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEP   95 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~   95 (107)
                      ...||.|+..-+...+...-.    .....|.|||-+.+.
T Consensus         3 ~W~CPICm~~Ne~~~e~~~n~----~~~p~C~nCGV~~D~   38 (47)
T d2j9ub1           3 TWVCPICMVSNETQGEFTKDT----LPTPICINCGVPADY   38 (47)
T ss_dssp             EEECTTTCCEEEESSCCCTTC----SSCCBCTTTCCBCCH
T ss_pred             ceecceeeeeccceeeeccCC----CCCCcccccCCccCH
Confidence            467999999877655432100    024679999988765

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=84.29  E-value=0.67  Score=27.06  Aligned_cols=15  Identities=20%  Similarity=0.412  Sum_probs=7.4

Q ss_pred             eecCCCcEECCCCCC
Q 033949           15 RVLKSGAGRCINCGS   29 (107)
Q Consensus        15 ~~~~~~~~~C~~Cg~   29 (107)
                      .+.....-+|.-||-
T Consensus        10 p~~~~~~q~CqiCGd   24 (93)
T d1weoa_          10 PLKNLDGQFCEICGD   24 (93)
T ss_dssp             CCSCCSSCBCSSSCC
T ss_pred             Chhhcccchhhhccc
Confidence            344444445555555

>d1brfa_ g.41.5.1 (A:) Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=83.71  E-value=0.18  Score=26.90  Aligned_cols=36  Identities=14%  Similarity=0.304  Sum_probs=21.2

Q ss_pred             eeCCCCCCCCCCCCCC--CCCC----CCCccCccccccCCce
Q 033949           57 LFCNNCNLLFPSSLPP--PPPP----PPLVSDVSKCRFCDRL   92 (107)
Q Consensus        57 ~~C~~CG~~~~~~~~~--~~~~----~~~~~~~~~C~~CG~~   92 (107)
                      ..|+.||..|+...-.  ..|.    ++-......||-||+.
T Consensus         3 y~C~~CgyiYd~~~Gd~~~gi~pGT~f~dLP~dw~CP~C~a~   44 (53)
T d1brfa_           3 WVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAP   44 (53)
T ss_dssp             EEETTTCCEEETTTCBGGGTBCTTCCGGGSCTTCBCTTTCCB
T ss_pred             eECCCCCcEECcccCCcccCCCCCCCHHHCCCCCCCcCCCCc
Confidence            4799999999664321  0111    1111246789999986

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.51  E-value=0.25  Score=27.87  Aligned_cols=12  Identities=25%  Similarity=0.576  Sum_probs=9.0

Q ss_pred             CCCcEECCCCCC
Q 033949           18 KSGAGRCINCGS   29 (107)
Q Consensus        18 ~~~~~~C~~Cg~   29 (107)
                      +.....||+||+
T Consensus        20 p~t~~~CpkCg~   31 (72)
T d1twfi2          20 PRSDRECPKCHS   31 (72)
T ss_dssp             CCCCCCCTTTCC
T ss_pred             CccCCCCCCCCC
Confidence            334678999999

>d1wiia_ g.41.3.4 (A:) Hypothetical UPF0222 protein MGC4549 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Putative zinc binding domain
domain: Hypothetical UPF0222 protein MGC4549
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.46  E-value=0.24  Score=28.87  Aligned_cols=35  Identities=20%  Similarity=0.376  Sum_probs=23.7

Q ss_pred             CCcEECCCCCC--CcEEEEEeeEEEEEEEeeeecCCC--CCceeCCCCCCCCCC
Q 033949           19 SGAGRCINCGS--TADLVEYEKVLKAFFVPVWKWPAK--EPALFCNNCNLLFPS   68 (107)
Q Consensus        19 ~~~~~C~~Cg~--~~~~~~~~~~f~lFFIP~~~~~~~--~~~~~C~~CG~~~~~   68 (107)
                      ...+.||.|+.  ++.+               +++++  ...+.|..||..+..
T Consensus        21 ~t~F~CPfCnh~~sV~v---------------k~dkk~~~g~l~C~vCg~~~~~   59 (85)
T d1wiia_          21 ETQFTCPFCNHEKSCDV---------------KMDRARNTGVISCTVCLEEFQT   59 (85)
T ss_dssp             SSCCCCTTTCCSSCEEE---------------EEETTTTEEEEEESSSCCEEEE
T ss_pred             CceEcCCCCCCCCeEEE---------------EEEecCCEEEEEEecCCCeEEe
Confidence            35678999997  4432               22333  248999999998744

>d1ryqa_ g.41.9.3 (A:) putative DNA-directed RNA polymerase subunit E'' (RpoE2) {Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: RNA polymerase subunits
family: RpoE2-like
domain: putative DNA-directed RNA polymerase subunit E'' (RpoE2)
species: Pyrococcus furiosus [TaxId: 2261]

Probab=82.70  E-value=0.34  Score=26.94  Aligned_cols=12  Identities=17%  Similarity=0.620  Sum_probs=6.7

Q ss_pred             ceeCCCCCCCCC
Q 033949           56 ALFCNNCNLLFP   67 (107)
Q Consensus        56 ~~~C~~CG~~~~   67 (107)
                      ...|..|+..++
T Consensus         9 ~rAC~~C~~i~~   20 (67)
T d1ryqa_           9 EKACRHCHYITS   20 (67)
T ss_dssp             CEEETTTCBEES
T ss_pred             ChhHhhCCCccC
Confidence            455666666543

>d1vzia2 g.41.5.2 (A:1-37) Desulfoferrodoxin N-terminal domain {Desulfoarculus baarsii (Desulfovibrio baarsii) [TaxId: 887]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Desulforedoxin
domain: Desulfoferrodoxin N-terminal domain
species: Desulfoarculus baarsii (Desulfovibrio baarsii) [TaxId: 887]

Probab=82.30  E-value=0.39  Score=23.64  Aligned_cols=31  Identities=23%  Similarity=0.532  Sum_probs=20.6

Q ss_pred             CCcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949           19 SGAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP   67 (107)
Q Consensus        19 ~~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~   67 (107)
                      .+..+|..|||-++++.                .....+.|  ||..+.
T Consensus         4 ~evYkC~~CGNiVeV~~----------------~g~G~LvC--Cg~pM~   34 (37)
T d1vzia2           4 LQVYKCEVCGNIVEVLN----------------GGIGELVC--CNQDMK   34 (37)
T ss_dssp             TCEEECTTTCCEEEEEE----------------CCSSCEEE--TTEECE
T ss_pred             ccEEEecccCcEEEEEE----------------CCCccEEE--CCCccc
Confidence            35678999999554443                23467887  887764

>d1s24a_ g.41.5.1 (A:) Two-iron rubredoxin {Pseudomonas oleovorans [TaxId: 301]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Two-iron rubredoxin
species: Pseudomonas oleovorans [TaxId: 301]

Probab=80.81  E-value=0.21  Score=26.92  Aligned_cols=37  Identities=16%  Similarity=0.274  Sum_probs=21.8

Q ss_pred             ceeCCCCCCCCCCCCCC--CCCC----CCCccCccccccCCce
Q 033949           56 ALFCNNCNLLFPSSLPP--PPPP----PPLVSDVSKCRFCDRL   92 (107)
Q Consensus        56 ~~~C~~CG~~~~~~~~~--~~~~----~~~~~~~~~C~~CG~~   92 (107)
                      ...|+.||..|+...-.  ..|.    ++-....-.||-||+.
T Consensus         4 ky~C~~CgyiYdp~~Gd~~~gi~pGT~F~~LP~dw~CP~C~a~   46 (56)
T d1s24a_           4 KWICITCGHIYDEALGDEAEGFTPGTRFEDIPDDWCCPDCGAT   46 (56)
T ss_dssp             EEEETTTTEEEETTSCCTTTTCCSCCCGGGCCTTCCCSSSCCC
T ss_pred             cEECCCCCcEECcccCCcccCcCCCCChhhCCCCCCCcCCCCc
Confidence            46799999999664321  1111    1111245689999986

>d1dxga_ g.41.5.2 (A:) Desulforedoxin {Desulfovibrio gigas [TaxId: 879]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Desulforedoxin
domain: Desulforedoxin
species: Desulfovibrio gigas [TaxId: 879]

Probab=80.72  E-value=0.52  Score=22.99  Aligned_cols=30  Identities=23%  Similarity=0.538  Sum_probs=19.4

Q ss_pred             CcEECCCCCCCcEEEEEeeEEEEEEEeeeecCCCCCceeCCCCCCCCC
Q 033949           20 GAGRCINCGSTADLVEYEKVLKAFFVPVWKWPAKEPALFCNNCNLLFP   67 (107)
Q Consensus        20 ~~~~C~~Cg~~~~~~~~~~~f~lFFIP~~~~~~~~~~~~C~~CG~~~~   67 (107)
                      +..+|..|||.+++..                .....+.|  ||..+.
T Consensus         5 evYkC~~CGNiVeV~~----------------~g~G~LvC--Cg~pM~   34 (36)
T d1dxga_           5 DVYKCELCGQVVKVLE----------------EGGGTLVC--CGEDMV   34 (36)
T ss_dssp             CEEECTTTCCEEEEEE----------------CCSSCEEE--TTEECE
T ss_pred             cEEEeccCCcEEEEEE----------------CCCceEEE--CCCccC
Confidence            4568999999554443                23457777  777653

>d2gmga1 a.4.5.82 (A:1-105) Hypothetical protein PF0610 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF0610-like
domain: Hypothetical protein PF0610
species: Pyrococcus furiosus [TaxId: 2261]

Probab=80.61  E-value=0.67  Score=27.91  Aligned_cols=31  Identities=19%  Similarity=0.382  Sum_probs=18.7

Q ss_pred             eCCCCCCCCCCCCCCCCCCCCCccCccccccCCceecCCCc
Q 033949           58 FCNNCNLLFPSSLPPPPPPPPLVSDVSKCRFCDRLVEPDFS   98 (107)
Q Consensus        58 ~C~~CG~~~~~~~~~~~~~~~~~~~~~~C~~CG~~i~~~~~   98 (107)
                      .|..||..+.. ...         .-.+||.|.++-.....
T Consensus        69 ~CrkCGfvFr~-~~k---------kPSRCP~CKSE~Ie~P~   99 (105)
T d2gmga1          69 QCRKCGFVFKA-EIN---------IPSRCPKCKSEWIEEPR   99 (105)
T ss_dssp             BBTTTCCBCCC-CSS---------CCSSCSSSCCCCBCCCC
T ss_pred             hhhhcCCeecc-cCC---------CCCCCCCCCCccccCCc
Confidence            58888888732 111         12578888887655443

>d1x68a2 g.39.1.3 (A:37-70) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.10  E-value=0.39  Score=22.73  Aligned_cols=13  Identities=15%  Similarity=0.363  Sum_probs=7.5

Q ss_pred             ccccccCCceecC
Q 033949           83 VSKCRFCDRLVEP   95 (107)
Q Consensus        83 ~~~C~~CG~~i~~   95 (107)
                      ...|+.||+-++.
T Consensus        20 ~i~c~~cgsg~dt   32 (34)
T d1x68a2          20 EIFCQKCGSGMDT   32 (34)
T ss_dssp             EEEETTTTCCCCC
T ss_pred             cEEehhcCCCcCC
Confidence            3456666665544