Query 012155
Match_columns 470
No_of_seqs 320 out of 1526
Neff 6.2
Searched_HMMs 46136
Date Thu Mar 28 23:38:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012155.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012155hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02365 NAM: No apical merist 100.0 3.2E-36 6.9E-41 268.2 6.4 126 49-193 1-129 (129)
2 PF11498 Activator_LAG-3: Tran 96.9 0.00025 5.4E-09 72.1 0.0 8 419-426 429-436 (468)
3 KOG1883 Cofactor required for 84.2 2.2 4.8E-05 50.1 6.6 22 329-350 1430-1451(1517)
4 KOG4369 RTK signaling protein 82.7 0.78 1.7E-05 53.8 2.3 9 143-151 1675-1683(2131)
5 KOG1151 Tousled-like protein k 73.7 2.9 6.3E-05 45.1 3.2 6 241-246 30-35 (775)
6 PF10571 UPF0547: Uncharacteri 69.1 2.5 5.4E-05 27.5 0.9 14 27-40 11-24 (26)
7 PF13248 zf-ribbon_3: zinc-rib 68.1 3 6.5E-05 26.9 1.2 10 31-40 3-12 (26)
8 PHA00692 hypothetical protein 68.0 1.9 4.1E-05 33.4 0.3 30 21-57 16-45 (74)
9 PF13240 zinc_ribbon_2: zinc-r 58.5 5.1 0.00011 25.2 0.9 11 32-42 1-11 (23)
10 KOG1819 FYVE finger-containing 58.0 3.6 7.7E-05 44.5 0.2 25 312-336 566-590 (990)
11 KOG4369 RTK signaling protein 57.5 7.9 0.00017 46.0 2.8 23 442-464 1946-1968(2131)
12 PF03604 DNA_RNApol_7kD: DNA d 53.3 7.2 0.00016 26.6 1.0 14 28-41 15-28 (32)
13 COG1996 RPC10 DNA-directed RNA 50.7 6.3 0.00014 29.6 0.5 17 27-43 21-37 (49)
14 PF04684 BAF1_ABF1: BAF1 / ABF 45.5 19 0.00042 38.8 3.3 8 201-208 187-194 (496)
15 KOG3648 Golgi apparatus protei 45.1 26 0.00055 39.4 4.2 6 453-459 110-115 (1179)
16 smart00659 RPOLCX RNA polymera 44.1 10 0.00022 27.8 0.6 16 28-43 17-32 (44)
17 PF08882 Acetone_carb_G: Aceto 41.0 21 0.00045 31.3 2.2 32 31-62 75-106 (112)
18 PF07282 OrfB_Zn_ribbon: Putat 37.9 21 0.00045 27.9 1.7 26 29-54 27-55 (69)
19 PRK12495 hypothetical protein; 37.4 17 0.00037 35.6 1.3 29 29-64 41-69 (226)
20 PF07131 DUF1382: Protein of u 34.2 35 0.00077 26.6 2.3 21 51-71 22-49 (61)
21 KOG2991 Splicing regulator [RN 34.2 56 0.0012 32.9 4.3 8 306-313 48-55 (330)
22 PF13717 zinc_ribbon_4: zinc-r 32.8 20 0.00043 25.0 0.7 14 32-45 4-17 (36)
23 PF00301 Rubredoxin: Rubredoxi 32.1 15 0.00032 27.3 -0.1 25 32-56 3-29 (47)
24 COG1327 Predicted transcriptio 31.8 16 0.00035 33.8 0.1 29 13-41 9-39 (156)
25 PF12672 DUF3793: Protein of u 31.5 22 0.00048 33.6 1.0 40 51-105 82-122 (176)
26 PF09889 DUF2116: Uncharacteri 29.5 28 0.0006 27.2 1.1 11 31-41 4-14 (59)
27 cd00730 rubredoxin Rubredoxin; 28.9 40 0.00087 25.4 1.8 25 31-55 2-28 (50)
28 PF09538 FYDLN_acid: Protein o 28.7 25 0.00053 30.8 0.7 11 31-41 10-20 (108)
29 TIGR01206 lysW lysine biosynth 27.6 36 0.00079 26.0 1.4 14 31-44 3-16 (54)
30 PF03119 DNA_ligase_ZBD: NAD-d 27.5 27 0.00059 23.0 0.6 15 32-46 1-15 (28)
31 PRK06393 rpoE DNA-directed RNA 27.4 45 0.00097 26.5 1.9 36 29-67 16-51 (64)
32 PF14255 Cys_rich_CPXG: Cystei 27.0 23 0.0005 26.9 0.2 14 32-45 2-15 (52)
33 PF05865 Cypo_polyhedrin: Cypo 26.9 55 0.0012 30.7 2.7 27 144-170 141-168 (248)
34 TIGR02098 MJ0042_CXXC MJ0042 f 26.8 24 0.00051 24.3 0.2 12 30-41 25-36 (38)
35 PRK08351 DNA-directed RNA poly 26.6 51 0.0011 25.9 2.1 31 30-63 15-45 (61)
36 COG4647 AcxC Acetone carboxyla 25.8 42 0.00091 30.3 1.7 37 31-70 121-157 (165)
37 TIGR00155 pqiA_fam integral me 25.6 37 0.00079 36.3 1.5 33 9-42 13-45 (403)
38 TIGR00244 transcriptional regu 25.2 28 0.0006 32.1 0.4 60 13-73 9-77 (147)
39 PF14353 CpXC: CpXC protein 24.7 34 0.00073 30.1 0.9 22 21-42 26-50 (128)
40 PF07754 DUF1610: Domain of un 24.7 33 0.00071 22.0 0.6 12 27-38 13-24 (24)
41 PF09862 DUF2089: Protein of u 24.2 36 0.00079 30.0 1.0 34 31-67 13-47 (113)
42 PF14149 YhfH: YhfH-like prote 23.1 20 0.00044 25.4 -0.7 17 25-41 8-24 (37)
43 COG5624 TAF61 Transcription in 23.1 81 0.0018 33.7 3.4 13 431-443 290-302 (505)
44 COG1885 Uncharacterized protei 22.6 44 0.00096 29.1 1.1 49 27-75 46-100 (115)
45 COG2995 PqiA Uncharacterized p 22.4 47 0.001 35.4 1.5 36 11-47 20-55 (418)
46 PF07960 CBP4: CBP4; InterPro 22.2 57 0.0012 29.4 1.8 17 55-71 29-49 (128)
47 KOG4140 Nuclear protein Ataxin 22.0 76 0.0017 34.7 3.0 53 11-63 53-112 (659)
48 PRK15103 paraquat-inducible me 21.8 45 0.00097 35.9 1.3 33 9-42 10-42 (419)
49 PF08274 PhnA_Zn_Ribbon: PhnA 21.0 32 0.00068 23.2 -0.1 14 28-41 17-30 (30)
50 TIGR02300 FYDLN_acid conserved 20.4 45 0.00097 30.1 0.8 11 31-41 10-20 (129)
51 PF12760 Zn_Tnp_IS1595: Transp 20.0 65 0.0014 23.3 1.5 19 21-39 9-27 (46)
No 1
>PF02365 NAM: No apical meristem (NAM) protein; InterPro: IPR003441 The NAC domain (for Petunia hybrida (Petunia) NAM and for Arabidopsis ATAF1, ATAF2, and CUC2) is an N-terminal module of ~160 amino acids, which is found in proteins of the NAC family of plant-specific transcriptional regulators (no apical meristem (NAM) proteins) []. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain (DBD) and a dimerization domain [,]. The NAC domain can be subdivided into five subdomains (A-E). Each subdomain is distinguishable by blocks of heterogeneous amino acids or gaps. While the NAC domains were rich in basic amino acids (R, K and H) as a whole, the distribution of positive and negative amino acids in each subdomain were unequal. Subdomains C and D are rich in basic amino acids but poor in acidic amino acids, while subdomain B contains a high proportion of acidic amino acids. Putative nuclear localization signals (NLS) have been detected in subdomains C and D []. The DBD is contained within a 60 amino acid region located within subdomains D and E []. The overall structure of the NAC domain monomer consists of a very twisted antiparallel beta-sheet, which packs against an N-terminal alpha-helix on one side and one shorter helix on the other side surrounded by a few helical elements. The structure suggests that the NAC domain mediates dimerization through conserved interactions including a salt bridge, and DNA binding through the NAC dimer face rich in positive charges [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1UT4_A 3SWM_B 4DUL_B 3SWP_D 1UT7_B 3ULX_A.
Probab=100.00 E-value=3.2e-36 Score=268.20 Aligned_cols=126 Identities=40% Similarity=0.699 Sum_probs=88.3
Q ss_pred CCCCceeCCChHHHHH-HHHHhhhcCCCCCCCCccccccccccccCCCCCCCCCCCCCc-ccCCcceEEeecCCCCCCCC
Q 012155 49 LPAGVKFDPTDQELID-HLEAKVEAKDMVKPHPLIDEFIPTIEGEDGICYTHPEKLPGV-TRDGLSRHFFHRPSKAYTTG 126 (470)
Q Consensus 49 LPpG~RF~PTDeELI~-yL~~Ki~~~~~~~~~Pl~~~~I~~id~e~diy~~~Pw~Lp~~-~~~g~~~yFF~~~~~k~~~G 126 (470)
|||||||+|||+|||. ||++|+.+.++ |. .++|++ +|||++|||+||.. ...++.||||+++.+++.+|
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~----~~-~~~i~~----~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~ 71 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPL----PC-EDVIHD----VDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNG 71 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HH----CS--CHSEE------GGGS-GGGCHHHSSS-SSEEEEEEE--------
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCC----Cc-ccceee----cccCccChHHhhhhccCCCceEEEEEecccccCCc
Confidence 8999999999999997 69999998865 22 245654 47999999999942 23456899999998888999
Q ss_pred CcccccccccccCCCCCcEEeecCCCceEEe-CCeeeeeeEEEeeEeecCCCCCCCCcCeEEEEEeeC
Q 012155 127 TRKRRKIQTECDLQGGETRWHKTGKTRPVMV-NGKQKGCKKILVLYTNFGKNRKPEKTNWVMHQYHLG 193 (470)
Q Consensus 127 ~R~~R~~~~~~~~~~g~G~Wk~tG~~k~V~~-~g~~vG~Kk~l~Fy~~~G~~~~g~kT~WvMhEY~L~ 193 (470)
.|++|++ ++|+||.+|++++|.+ +|.+||+|++|+||. |+.+++.+|+|+||||+|.
T Consensus 72 ~r~~R~~--------~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~--~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 72 GRPNRVT--------GGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYS--GKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp --S-EEE--------TTEEEEEECEEEEEEE-TTCEEEEEEEEEEEE--SSTTS-EEEEEEEEEEEE-
T ss_pred ccccccc--------cceEEeecccccccccccceeeeeEEEEEEEe--ccCCCCCcCCeEEEEEEeC
Confidence 9999964 5899999999999998 899999999999997 6777889999999999984
No 2
>PF11498 Activator_LAG-3: Transcriptional activator LAG-3; InterPro: IPR021587 The C.elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12 []. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1 []. ; PDB: 2FO1_D.
Probab=96.87 E-value=0.00025 Score=72.14 Aligned_cols=8 Identities=13% Similarity=0.169 Sum_probs=0.0
Q ss_pred CCCCcccc
Q 012155 419 GGRSASGL 426 (470)
Q Consensus 419 ~~~~~~g~ 426 (470)
.+...+|.
T Consensus 429 hQn~~MGY 436 (468)
T PF11498_consen 429 HQNGGMGY 436 (468)
T ss_dssp --------
T ss_pred hhccCccc
Confidence 34444443
No 3
>KOG1883 consensus Cofactor required for Sp1 transcriptional activation, subunit 3 [Transcription]
Probab=84.19 E-value=2.2 Score=50.15 Aligned_cols=22 Identities=27% Similarity=0.360 Sum_probs=8.1
Q ss_pred hhhHHHhHHHHhhhhhhhccch
Q 012155 329 HRQQQQQHQQQHQQQQQQQHHT 350 (470)
Q Consensus 329 qqqqqqqqQQQQQQQQQQQq~q 350 (470)
|.|++.|||++|||+++++|||
T Consensus 1430 q~q~t~q~q~~Qqq~~~~~qqq 1451 (1517)
T KOG1883|consen 1430 QMQDTSQHQTIQQQSNHPTQQQ 1451 (1517)
T ss_pred hhhhhhHHHHHHHHhcchHHHH
Confidence 3333333333333333333333
No 4
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=82.68 E-value=0.78 Score=53.83 Aligned_cols=9 Identities=11% Similarity=0.254 Sum_probs=4.7
Q ss_pred CcEEeecCC
Q 012155 143 ETRWHKTGK 151 (470)
Q Consensus 143 ~G~Wk~tG~ 151 (470)
-|.|+..+.
T Consensus 1675 ~gq~~p~i~ 1683 (2131)
T KOG4369|consen 1675 PGQWAPHIG 1683 (2131)
T ss_pred ccccccccc
Confidence 456655443
No 5
>KOG1151 consensus Tousled-like protein kinase [Signal transduction mechanisms]
Probab=73.71 E-value=2.9 Score=45.07 Aligned_cols=6 Identities=33% Similarity=0.168 Sum_probs=2.3
Q ss_pred CCCCCC
Q 012155 241 SGSCSS 246 (470)
Q Consensus 241 s~scss 246 (470)
++.||.
T Consensus 30 sshpst 35 (775)
T KOG1151|consen 30 SSHPST 35 (775)
T ss_pred CCCCcc
Confidence 334433
No 6
>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. Several members are annotated as putative helicases.
Probab=69.10 E-value=2.5 Score=27.51 Aligned_cols=14 Identities=36% Similarity=0.783 Sum_probs=9.2
Q ss_pred ccCCCCCCCCCccc
Q 012155 27 LCGSKQCPGCGHKL 40 (470)
Q Consensus 27 ~~~~~~~~~~~~~~ 40 (470)
+...+.||.|||.+
T Consensus 11 ~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 11 PESAKFCPHCGYDF 24 (26)
T ss_pred hhhcCcCCCCCCCC
Confidence 44557777777765
No 7
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=68.11 E-value=3 Score=26.87 Aligned_cols=10 Identities=40% Similarity=1.225 Sum_probs=7.1
Q ss_pred CCCCCCCccc
Q 012155 31 KQCPGCGHKL 40 (470)
Q Consensus 31 ~~~~~~~~~~ 40 (470)
+.||+||..|
T Consensus 3 ~~Cp~Cg~~~ 12 (26)
T PF13248_consen 3 MFCPNCGAEI 12 (26)
T ss_pred CCCcccCCcC
Confidence 5688888755
No 8
>PHA00692 hypothetical protein
Probab=68.00 E-value=1.9 Score=33.41 Aligned_cols=30 Identities=20% Similarity=0.536 Sum_probs=19.9
Q ss_pred hhhhhhccCCCCCCCCCccccCCCCCCCCCCCceeCC
Q 012155 21 KLEEHQLCGSKQCPGCGHKLEAKPDWLGLPAGVKFDP 57 (470)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~LPpG~RF~P 57 (470)
|..||-+|+-- +-++.-..+..||||||--
T Consensus 16 rvqehcmcarf-------hedrthyfveyppgfrfgg 45 (74)
T PHA00692 16 RVQEHCMCARF-------HEDRTHYFVEYPPGFRFGG 45 (74)
T ss_pred hhHhhhhhhhh-------cccceeEeEecCCCccccc
Confidence 45566565543 2345567888999999964
No 9
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=58.53 E-value=5.1 Score=25.21 Aligned_cols=11 Identities=45% Similarity=1.283 Sum_probs=9.2
Q ss_pred CCCCCCccccC
Q 012155 32 QCPGCGHKLEA 42 (470)
Q Consensus 32 ~~~~~~~~~~~ 42 (470)
.||+||++|+.
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 49999999964
No 10
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=58.00 E-value=3.6 Score=44.52 Aligned_cols=25 Identities=32% Similarity=0.615 Sum_probs=11.4
Q ss_pred ccccccCCCCCCCCccchhhHHHhH
Q 012155 312 EDIRDHHQRPHHHLAHDHRQQQQQH 336 (470)
Q Consensus 312 ~~~~~~~~~~~~~~~~~qqqqqqqq 336 (470)
+++.|.||+.|||+|||.+-+|+||
T Consensus 566 dshshrhhqrhhhhhhhrhphqhqh 590 (990)
T KOG1819|consen 566 DSHSHRHHQRHHHHHHHRHPHQHQH 590 (990)
T ss_pred cccccchhhhccccccccCcchhcc
Confidence 3444444444444444444444443
No 11
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=57.49 E-value=7.9 Score=46.03 Aligned_cols=23 Identities=30% Similarity=0.467 Sum_probs=14.5
Q ss_pred CCCCCCccccceeeccCCCCCCC
Q 012155 442 ESSMTNPQEAEWLKYSSFWPDPD 464 (470)
Q Consensus 442 ~~s~~~~~~~~~~~~~~~~~~~~ 464 (470)
|++.+.+-.|..---.||.|+|-
T Consensus 1946 e~~~g~~~~~~s~~a~s~~~~~~ 1968 (2131)
T KOG4369|consen 1946 ESSTGAPGPTSSQLANSYYPSPS 1968 (2131)
T ss_pred hccCCCCCCCCCccccCCCCCcc
Confidence 55666666666655667777753
No 12
>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. 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 ....
Probab=53.29 E-value=7.2 Score=26.64 Aligned_cols=14 Identities=36% Similarity=1.023 Sum_probs=10.6
Q ss_pred cCCCCCCCCCcccc
Q 012155 28 CGSKQCPGCGHKLE 41 (470)
Q Consensus 28 ~~~~~~~~~~~~~~ 41 (470)
-+...||.||++|-
T Consensus 15 ~~~irC~~CG~RIl 28 (32)
T PF03604_consen 15 GDPIRCPECGHRIL 28 (32)
T ss_dssp SSTSSBSSSS-SEE
T ss_pred CCcEECCcCCCeEE
Confidence 45589999999985
No 13
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=50.74 E-value=6.3 Score=29.63 Aligned_cols=17 Identities=29% Similarity=0.677 Sum_probs=12.9
Q ss_pred ccCCCCCCCCCccccCC
Q 012155 27 LCGSKQCPGCGHKLEAK 43 (470)
Q Consensus 27 ~~~~~~~~~~~~~~~~~ 43 (470)
.-.-..||.||++|--+
T Consensus 21 ~~~~irCp~Cg~rIl~K 37 (49)
T COG1996 21 ETRGIRCPYCGSRILVK 37 (49)
T ss_pred ccCceeCCCCCcEEEEe
Confidence 34458899999999654
No 14
>PF04684 BAF1_ABF1: BAF1 / ABF1 chromatin reorganising factor; InterPro: IPR006774 ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture []. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 Saccharomyces cerevisiae (P14164 from SWISSPROT)) []. The N-terminal two thirds of the protein are necessary for DNA binding, and the N terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilise the protein structure [].; GO: 0003677 DNA binding, 0006338 chromatin remodeling, 0005634 nucleus
Probab=45.51 E-value=19 Score=38.83 Aligned_cols=8 Identities=38% Similarity=0.717 Sum_probs=4.5
Q ss_pred CCeEEEEE
Q 012155 201 GELVVSKI 208 (470)
Q Consensus 201 ~~~VLCKI 208 (470)
..|||.||
T Consensus 187 ~~fvltki 194 (496)
T PF04684_consen 187 DKFVLTKI 194 (496)
T ss_pred HHHHHhcc
Confidence 35566655
No 15
>KOG3648 consensus Golgi apparatus protein (cysteine-rich fibroblast growth factor receptor) [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.10 E-value=26 Score=39.44 Aligned_cols=6 Identities=33% Similarity=0.822 Sum_probs=3.0
Q ss_pred eeeccCC
Q 012155 453 WLKYSSF 459 (470)
Q Consensus 453 ~~~~~~~ 459 (470)
| |..+|
T Consensus 110 ~-KLA~~ 115 (1179)
T KOG3648|consen 110 W-KLAEE 115 (1179)
T ss_pred c-cccch
Confidence 5 55444
No 16
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=44.07 E-value=10 Score=27.78 Aligned_cols=16 Identities=25% Similarity=0.532 Sum_probs=12.7
Q ss_pred cCCCCCCCCCccccCC
Q 012155 28 CGSKQCPGCGHKLEAK 43 (470)
Q Consensus 28 ~~~~~~~~~~~~~~~~ 43 (470)
-+...||.||++|.-+
T Consensus 17 ~~~irC~~CG~rIlyK 32 (44)
T smart00659 17 KDVVRCRECGYRILYK 32 (44)
T ss_pred CCceECCCCCceEEEE
Confidence 3558999999999733
No 17
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=41.04 E-value=21 Score=31.35 Aligned_cols=32 Identities=34% Similarity=0.700 Sum_probs=25.8
Q ss_pred CCCCCCCccccCCCCCCCCCCCceeCCChHHH
Q 012155 31 KQCPGCGHKLEAKPDWLGLPAGVKFDPTDQEL 62 (470)
Q Consensus 31 ~~~~~~~~~~~~~~~~~~LPpG~RF~PTDeEL 62 (470)
-.||+||-.+|+.-.-++.||=+-|-|.-+-|
T Consensus 75 yyCP~Cgt~levE~~~Pg~P~~hD~epDid~f 106 (112)
T PF08882_consen 75 YYCPGCGTQLEVEAPPPGYPPIHDFEPDIDTF 106 (112)
T ss_pred EECCCCcceeEEccCCCCCCceEecccCHHHH
Confidence 46999999999887777788888888865544
No 18
>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. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=37.91 E-value=21 Score=27.88 Aligned_cols=26 Identities=31% Similarity=0.722 Sum_probs=17.7
Q ss_pred CCCCCCCCCccccC--CCCCCCCC-CCce
Q 012155 29 GSKQCPGCGHKLEA--KPDWLGLP-AGVK 54 (470)
Q Consensus 29 ~~~~~~~~~~~~~~--~~~~~~LP-pG~R 54 (470)
.|..||.||+..+. ....+..| =|+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 46899999999986 34444445 4555
No 19
>PRK12495 hypothetical protein; Provisional
Probab=37.45 E-value=17 Score=35.62 Aligned_cols=29 Identities=28% Similarity=0.534 Sum_probs=24.3
Q ss_pred CCCCCCCCCccccCCCCCCCCCCCceeCCChHHHHH
Q 012155 29 GSKQCPGCGHKLEAKPDWLGLPAGVKFDPTDQELID 64 (470)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~~~LPpG~RF~PTDeELI~ 64 (470)
....|+.||..|- .| +|+.|.|+=++++.
T Consensus 41 sa~hC~~CG~PIp------a~-pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 41 TNAHCDECGDPIF------RH-DGQEFCPTCQQPVT 69 (226)
T ss_pred chhhcccccCccc------CC-CCeeECCCCCCccc
Confidence 3489999999994 46 79999999888775
No 20
>PF07131 DUF1382: Protein of unknown function (DUF1382); InterPro: IPR009814 This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Probab=34.21 E-value=35 Score=26.62 Aligned_cols=21 Identities=43% Similarity=0.735 Sum_probs=15.8
Q ss_pred CCceeCC----ChHHHHHH---HHHhhh
Q 012155 51 AGVKFDP----TDQELIDH---LEAKVE 71 (470)
Q Consensus 51 pG~RF~P----TDeELI~y---L~~Ki~ 71 (470)
.|+||.| ||+|+..+ |.+|+.
T Consensus 22 ~GIRFVpiPv~~dee~~~L~s~~~~kLe 49 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHTLSSQLSQKLE 49 (61)
T ss_pred cCceeeccccccHHHHHHHHHHHHHHHH
Confidence 5999999 78888753 666654
No 21
>KOG2991 consensus Splicing regulator [RNA processing and modification]
Probab=34.20 E-value=56 Score=32.87 Aligned_cols=8 Identities=0% Similarity=-0.442 Sum_probs=3.1
Q ss_pred CCCCCCcc
Q 012155 306 PAHGTCED 313 (470)
Q Consensus 306 ~~~~~~~~ 313 (470)
+..+++..
T Consensus 48 ~~~tGm~~ 55 (330)
T KOG2991|consen 48 GVRTGMIL 55 (330)
T ss_pred CCccchhh
Confidence 33344433
No 22
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=32.77 E-value=20 Score=24.97 Aligned_cols=14 Identities=36% Similarity=0.897 Sum_probs=8.0
Q ss_pred CCCCCCccccCCCC
Q 012155 32 QCPGCGHKLEAKPD 45 (470)
Q Consensus 32 ~~~~~~~~~~~~~~ 45 (470)
.||+|+.+.+.+++
T Consensus 4 ~Cp~C~~~y~i~d~ 17 (36)
T PF13717_consen 4 TCPNCQAKYEIDDE 17 (36)
T ss_pred ECCCCCCEEeCCHH
Confidence 46666666654433
No 23
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=32.06 E-value=15 Score=27.33 Aligned_cols=25 Identities=36% Similarity=0.817 Sum_probs=16.5
Q ss_pred CCCCCCccccCCC--CCCCCCCCceeC
Q 012155 32 QCPGCGHKLEAKP--DWLGLPAGVKFD 56 (470)
Q Consensus 32 ~~~~~~~~~~~~~--~~~~LPpG~RF~ 56 (470)
.|+.||+-.+-.. ..-++|||..|.
T Consensus 3 ~C~~CgyvYd~~~Gd~~~~i~pGt~F~ 29 (47)
T PF00301_consen 3 QCPVCGYVYDPEKGDPENGIPPGTPFE 29 (47)
T ss_dssp EETTTSBEEETTTBBGGGTB-TT--GG
T ss_pred CCCCCCEEEcCCcCCcccCcCCCCCHH
Confidence 5999998887553 346899998884
No 24
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=31.83 E-value=16 Score=33.80 Aligned_cols=29 Identities=21% Similarity=0.534 Sum_probs=21.5
Q ss_pred CcchhhhhhhhhhhccC--CCCCCCCCcccc
Q 012155 13 SSSDLIDAKLEEHQLCG--SKQCPGCGHKLE 41 (470)
Q Consensus 13 ~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~ 41 (470)
..+.+||+|+-|....- -+.|++||+.+-
T Consensus 9 ~~tkViDSR~~edg~aIRRRReC~~C~~RFT 39 (156)
T COG1327 9 EDTKVIDSRPAEEGNAIRRRRECLECGERFT 39 (156)
T ss_pred CCCeeeecccccccchhhhhhcccccccccc
Confidence 35678999988854222 289999999984
No 25
>PF12672 DUF3793: Protein of unknown function (DUF3793); InterPro: IPR024523 This family of bacterial proteins is functionally uncharacterised. The proteins in this family contain two conserved sequence motifs: PHE and LGYP.
Probab=31.54 E-value=22 Score=33.58 Aligned_cols=40 Identities=25% Similarity=0.339 Sum_probs=24.8
Q ss_pred CCceeCCChHHHHHHHHHhhhcCCCCCCCCccccccccccccCCCC-CCCCCCCCC
Q 012155 51 AGVKFDPTDQELIDHLEAKVEAKDMVKPHPLIDEFIPTIEGEDGIC-YTHPEKLPG 105 (470)
Q Consensus 51 pG~RF~PTDeELI~yL~~Ki~~~~~~~~~Pl~~~~I~~id~e~diy-~~~Pw~Lp~ 105 (470)
-|| ..-+-+++|.+|..|+....+ -+ |++|+ +++..|.-|
T Consensus 82 ~GY-~~~~~~~~L~~L~~R~~~~~F----------PH----EIGiFLGYPleDV~G 122 (176)
T PF12672_consen 82 YGY-PDSSLEDCLEHLKKRFESGEF----------PH----EIGIFLGYPLEDVKG 122 (176)
T ss_pred CCc-CCCCHHHHHHHHHHHhcCCCC----------Cc----hhHhccCCCHHHHHH
Confidence 477 556667777899988854443 12 23454 667777644
No 26
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=29.48 E-value=28 Score=27.20 Aligned_cols=11 Identities=45% Similarity=1.229 Sum_probs=9.6
Q ss_pred CCCCCCCcccc
Q 012155 31 KQCPGCGHKLE 41 (470)
Q Consensus 31 ~~~~~~~~~~~ 41 (470)
+.||.||..|+
T Consensus 4 kHC~~CG~~Ip 14 (59)
T PF09889_consen 4 KHCPVCGKPIP 14 (59)
T ss_pred CcCCcCCCcCC
Confidence 78999998884
No 27
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=28.87 E-value=40 Score=25.36 Aligned_cols=25 Identities=28% Similarity=0.574 Sum_probs=19.4
Q ss_pred CCCCCCCccccCC--CCCCCCCCCcee
Q 012155 31 KQCPGCGHKLEAK--PDWLGLPAGVKF 55 (470)
Q Consensus 31 ~~~~~~~~~~~~~--~~~~~LPpG~RF 55 (470)
.+|..||+-.+-. ...-++|||-.|
T Consensus 2 y~C~~CgyiYd~~~Gd~~~~i~pGt~f 28 (50)
T cd00730 2 YECRICGYIYDPAEGDPDEGIPPGTPF 28 (50)
T ss_pred cCCCCCCeEECCCCCCcccCcCCCCCH
Confidence 4799999988844 345688999887
No 28
>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. The function of members of this family is unknown.
Probab=28.70 E-value=25 Score=30.75 Aligned_cols=11 Identities=45% Similarity=1.271 Sum_probs=9.6
Q ss_pred CCCCCCCcccc
Q 012155 31 KQCPGCGHKLE 41 (470)
Q Consensus 31 ~~~~~~~~~~~ 41 (470)
+.||.||.+|-
T Consensus 10 R~Cp~CG~kFY 20 (108)
T PF09538_consen 10 RTCPSCGAKFY 20 (108)
T ss_pred ccCCCCcchhc
Confidence 88999999884
No 29
>TIGR01206 lysW lysine biosynthesis protein LysW. 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.
Probab=27.64 E-value=36 Score=26.04 Aligned_cols=14 Identities=36% Similarity=0.990 Sum_probs=10.7
Q ss_pred CCCCCCCccccCCC
Q 012155 31 KQCPGCGHKLEAKP 44 (470)
Q Consensus 31 ~~~~~~~~~~~~~~ 44 (470)
..||.||..|+...
T Consensus 3 ~~CP~CG~~iev~~ 16 (54)
T TIGR01206 3 FECPDCGAEIELEN 16 (54)
T ss_pred cCCCCCCCEEecCC
Confidence 37999999996543
No 30
>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. 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.
Probab=27.48 E-value=27 Score=22.99 Aligned_cols=15 Identities=40% Similarity=0.776 Sum_probs=8.1
Q ss_pred CCCCCCccccCCCCC
Q 012155 32 QCPGCGHKLEAKPDW 46 (470)
Q Consensus 32 ~~~~~~~~~~~~~~~ 46 (470)
.||.||.+|....+.
T Consensus 1 ~CP~C~s~l~~~~~e 15 (28)
T PF03119_consen 1 TCPVCGSKLVREEGE 15 (28)
T ss_dssp B-TTT--BEEE-CCT
T ss_pred CcCCCCCEeEcCCCC
Confidence 499999999865553
No 31
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=27.41 E-value=45 Score=26.52 Aligned_cols=36 Identities=19% Similarity=0.540 Sum_probs=27.2
Q ss_pred CCCCCCCCCccccCCCCCCCCCCCceeCCChHHHHHHHH
Q 012155 29 GSKQCPGCGHKLEAKPDWLGLPAGVKFDPTDQELIDHLE 67 (470)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~~~LPpG~RF~PTDeELI~yL~ 67 (470)
+...||.||-. +.+.+|-||=. -.+|.+.|+...|.
T Consensus 16 ~~~~Cp~Cgs~-~~S~~w~G~v~--i~dPe~S~vAk~~~ 51 (64)
T PRK06393 16 PEKTCPVHGDE-KTTTEWFGFLI--ITEPEGSAIAKRAG 51 (64)
T ss_pred CCCcCCCCCCC-cCCcCcceEEE--EECCchhHHHHHhC
Confidence 34589999996 66788887742 46999999877663
No 32
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=27.02 E-value=23 Score=26.89 Aligned_cols=14 Identities=50% Similarity=0.982 Sum_probs=11.3
Q ss_pred CCCCCCccccCCCC
Q 012155 32 QCPGCGHKLEAKPD 45 (470)
Q Consensus 32 ~~~~~~~~~~~~~~ 45 (470)
.||.||+.|+...|
T Consensus 2 ~CPyCge~~~~~iD 15 (52)
T PF14255_consen 2 QCPYCGEPIEILID 15 (52)
T ss_pred CCCCCCCeeEEEEe
Confidence 69999999986544
No 33
>PF05865 Cypo_polyhedrin: Cypovirus polyhedrin protein; InterPro: IPR008464 This family consists of several Cypovirus polyhedrin proteins. Polyhedrin is known to form a crystalline matrix (polyhedra) in infected insect cells [].; PDB: 2OH7_A 2OH5_A 2OH6_A.
Probab=26.91 E-value=55 Score=30.74 Aligned_cols=27 Identities=30% Similarity=0.543 Sum_probs=17.7
Q ss_pred cEEeecC-CCceEEeCCeeeeeeEEEee
Q 012155 144 TRWHKTG-KTRPVMVNGKQKGCKKILVL 170 (470)
Q Consensus 144 G~Wk~tG-~~k~V~~~g~~vG~Kk~l~F 170 (470)
--|.+|| +-+.|..+|++||+...|.+
T Consensus 141 hpweatgikyrki~~dgeivgyshyfel 168 (248)
T PF05865_consen 141 HPWEATGIKYRKIHRDGEIVGYSHYFEL 168 (248)
T ss_dssp -S-B--GGG-EEEEETTEEEEEEEEEE-
T ss_pred CCccccCceEEEeeccceEeeeeeeeec
Confidence 4699999 46778899999999887754
No 34
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. 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.
Probab=26.77 E-value=24 Score=24.34 Aligned_cols=12 Identities=33% Similarity=0.769 Sum_probs=7.9
Q ss_pred CCCCCCCCcccc
Q 012155 30 SKQCPGCGHKLE 41 (470)
Q Consensus 30 ~~~~~~~~~~~~ 41 (470)
...||+||+.|.
T Consensus 25 ~v~C~~C~~~~~ 36 (38)
T TIGR02098 25 KVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEE
Confidence 356777777664
No 35
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=26.62 E-value=51 Score=25.92 Aligned_cols=31 Identities=23% Similarity=0.642 Sum_probs=23.9
Q ss_pred CCCCCCCCccccCCCCCCCCCCCceeCCChHHHH
Q 012155 30 SKQCPGCGHKLEAKPDWLGLPAGVKFDPTDQELI 63 (470)
Q Consensus 30 ~~~~~~~~~~~~~~~~~~~LPpG~RF~PTDeELI 63 (470)
...||+||-.- -+.+|.+|=. -.+|...|+.
T Consensus 15 ~~~CP~Cgs~~-~T~~W~G~vi--I~dPe~S~IA 45 (61)
T PRK08351 15 EDRCPVCGSRD-LSDEWFDLVI--IIDVENSRIA 45 (61)
T ss_pred CCcCCCCcCCc-cccccccEEE--EeCCcHhHHH
Confidence 34799999843 5679998654 7899988887
No 36
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=25.85 E-value=42 Score=30.32 Aligned_cols=37 Identities=27% Similarity=0.448 Sum_probs=29.3
Q ss_pred CCCCCCCccccCCCCCCCCCCCceeCCChHHHHHHHHHhh
Q 012155 31 KQCPGCGHKLEAKPDWLGLPAGVKFDPTDQELIDHLEAKV 70 (470)
Q Consensus 31 ~~~~~~~~~~~~~~~~~~LPpG~RF~PTDeELI~yL~~Ki 70 (470)
-.||.||+-.|..-..++.|.=--|.|. |-.|++.++
T Consensus 121 ficpecg~l~eveaaap~ypivhdfepd---legfyrdwl 157 (165)
T COG4647 121 FICPECGILHEVEAAAPGYPIVHDFEPD---LEGFYRDWL 157 (165)
T ss_pred hhCccccceeeeccCCCCCceeccCCcc---HHHHHHHHc
Confidence 5799999999988888888888899995 334666553
No 37
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. 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.
Probab=25.65 E-value=37 Score=36.30 Aligned_cols=33 Identities=24% Similarity=0.417 Sum_probs=23.8
Q ss_pred ccccCcchhhhhhhhhhhccCCCCCCCCCccccC
Q 012155 9 GTNISSSDLIDAKLEEHQLCGSKQCPGCGHKLEA 42 (470)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 42 (470)
...|..++++- ++.....-+.-.||+||+.+-+
T Consensus 13 ~~~C~~Cd~l~-~~~~l~~g~~a~CpRCg~~L~~ 45 (403)
T TIGR00155 13 HILCSQCDMLV-ALPRIESGQKAACPRCGTTLTV 45 (403)
T ss_pred eeeCCCCCCcc-cccCCCCCCeeECCCCCCCCcC
Confidence 34799999886 4444445556789999999954
No 38
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=25.18 E-value=28 Score=32.12 Aligned_cols=60 Identities=18% Similarity=0.382 Sum_probs=33.3
Q ss_pred Ccchhhhhhhhhhhcc--CCCCCCCCCccccCCCCCCCC-CCCc-----eeCCChHHHHHH-HHHhhhcC
Q 012155 13 SSSDLIDAKLEEHQLC--GSKQCPGCGHKLEAKPDWLGL-PAGV-----KFDPTDQELIDH-LEAKVEAK 73 (470)
Q Consensus 13 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~L-PpG~-----RF~PTDeELI~y-L~~Ki~~~ 73 (470)
..+.+||+|+-+.... --+.|+.||+.+- +-+.+.+ |+=+ +-.|=|.+=|.- |.+-+..+
T Consensus 9 ~dtkViDSR~~~dg~~IRRRReC~~C~~RFT-TyErve~~~l~ViKkdG~re~Fdr~Kl~~gl~~Ac~KR 77 (147)
T TIGR00244 9 HNTRVLDSRLVEDGQSIRRRRECLECHERFT-TFERAELLPPTVIKQDGVREPFNREKLLRGMVRACEKR 77 (147)
T ss_pred CCCEeeeccccCCCCeeeecccCCccCCccc-eeeeccccccEEEcCCCCCCCCCHHHHHHHHHHHhcCC
Confidence 4567889888764422 2289999999994 3343333 2212 344555554443 44433333
No 39
>PF14353 CpXC: CpXC protein
Probab=24.74 E-value=34 Score=30.13 Aligned_cols=22 Identities=50% Similarity=0.954 Sum_probs=15.5
Q ss_pred hhhhhhccCC---CCCCCCCccccC
Q 012155 21 KLEEHQLCGS---KQCPGCGHKLEA 42 (470)
Q Consensus 21 ~~~~~~~~~~---~~~~~~~~~~~~ 42 (470)
.|.|..+.++ ..||.||+.+--
T Consensus 26 ~l~e~il~g~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 26 ELKEKILDGSLFSFTCPSCGHKFRL 50 (128)
T ss_pred HHHHHHHcCCcCEEECCCCCCceec
Confidence 3445555555 889999999853
No 40
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=24.70 E-value=33 Score=22.01 Aligned_cols=12 Identities=33% Similarity=0.833 Sum_probs=8.7
Q ss_pred ccCCCCCCCCCc
Q 012155 27 LCGSKQCPGCGH 38 (470)
Q Consensus 27 ~~~~~~~~~~~~ 38 (470)
....-.||+||.
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 344578999994
No 41
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=24.23 E-value=36 Score=30.00 Aligned_cols=34 Identities=29% Similarity=0.724 Sum_probs=23.4
Q ss_pred CCCCCCCccccCCCCCCCCCCCceeCCChHHHHH-HHH
Q 012155 31 KQCPGCGHKLEAKPDWLGLPAGVKFDPTDQELID-HLE 67 (470)
Q Consensus 31 ~~~~~~~~~~~~~~~~~~LPpG~RF~PTDeELI~-yL~ 67 (470)
..|++|+-.|++... ||.=.+..+-|.+.|. |++
T Consensus 13 l~C~~C~t~i~G~F~---l~~~~~L~~E~~~Fi~~Fi~ 47 (113)
T PF09862_consen 13 LKCPSCGTEIEGEFE---LPWFARLSPEQLEFIKLFIK 47 (113)
T ss_pred EEcCCCCCEEEeeec---cchhhcCCHHHHHHHHHHHH
Confidence 579999999987544 6655566666666665 653
No 42
>PF14149 YhfH: YhfH-like protein
Probab=23.10 E-value=20 Score=25.39 Aligned_cols=17 Identities=29% Similarity=0.735 Sum_probs=13.8
Q ss_pred hhccCCCCCCCCCcccc
Q 012155 25 HQLCGSKQCPGCGHKLE 41 (470)
Q Consensus 25 ~~~~~~~~~~~~~~~~~ 41 (470)
-+.-..+.|+.||..|+
T Consensus 8 frnLp~K~C~~CG~~i~ 24 (37)
T PF14149_consen 8 FRNLPPKKCTECGKEIE 24 (37)
T ss_pred HHhCCCcccHHHHHHHH
Confidence 34667799999999986
No 43
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=23.07 E-value=81 Score=33.74 Aligned_cols=13 Identities=23% Similarity=0.503 Sum_probs=5.6
Q ss_pred cCCCCCCCCCCCC
Q 012155 431 MGCTSSSDIKEES 443 (470)
Q Consensus 431 ~~~ts~~~~~~~~ 443 (470)
..|.+++.++++.
T Consensus 290 ~~~~~~e~s~~~~ 302 (505)
T COG5624 290 FRCPSPESSRGEP 302 (505)
T ss_pred ccCCCchhccccc
Confidence 3344444444443
No 44
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.58 E-value=44 Score=29.05 Aligned_cols=49 Identities=24% Similarity=0.512 Sum_probs=27.8
Q ss_pred ccCCCCCCCCCccccCC-----CCCCCCCCCc-eeCCChHHHHHHHHHhhhcCCC
Q 012155 27 LCGSKQCPGCGHKLEAK-----PDWLGLPAGV-KFDPTDQELIDHLEAKVEAKDM 75 (470)
Q Consensus 27 ~~~~~~~~~~~~~~~~~-----~~~~~LPpG~-RF~PTDeELI~yL~~Ki~~~~~ 75 (470)
.-++..||-||..+|.- ...++|---. -|+-.-.|=..-..++..|+.+
T Consensus 46 e~G~t~CP~Cg~~~e~~fvva~~aLVgl~l~mkVFNaes~EHA~RIAK~eIGk~L 100 (115)
T COG1885 46 EVGSTSCPKCGEPFESAFVVANTALVGLILSMKVFNAESDEHAERIAKAEIGKAL 100 (115)
T ss_pred ecccccCCCCCCccceeEEEecceeEEEEEEEEEecCCCHHHHHHHHHHHHhhHh
Confidence 56889999999999732 2222222112 3776655554444444444444
No 45
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=22.44 E-value=47 Score=35.36 Aligned_cols=36 Identities=31% Similarity=0.581 Sum_probs=22.0
Q ss_pred ccCcchhhhhhhhhhhccCCCCCCCCCccccCCCCCC
Q 012155 11 NISSSDLIDAKLEEHQLCGSKQCPGCGHKLEAKPDWL 47 (470)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (470)
-|+.++++-. +-+..-..+-.||+|||+|-+..+|.
T Consensus 20 ~C~eCd~~~~-~P~l~~~q~A~CPRC~~~l~~~~~~s 55 (418)
T COG2995 20 LCPECDMLVS-LPRLDSGQSAYCPRCGHTLTRGGDWS 55 (418)
T ss_pred cCCCCCceec-cccCCCCCcccCCCCCCccccCCCCC
Confidence 3444444332 22333445689999999998766664
No 46
>PF07960 CBP4: CBP4; InterPro: IPR012420 The CBP4 gene in Saccharomyces cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase [, ]. This family appears to be fungal specific.
Probab=22.15 E-value=57 Score=29.44 Aligned_cols=17 Identities=29% Similarity=0.432 Sum_probs=12.5
Q ss_pred eCCChHHHHH-H---HHHhhh
Q 012155 55 FDPTDQELID-H---LEAKVE 71 (470)
Q Consensus 55 F~PTDeELI~-y---L~~Ki~ 71 (470)
-.||||||+. | |+++..
T Consensus 29 ~tPTeEeL~~r~sPELrkr~~ 49 (128)
T PF07960_consen 29 TTPTEEELFKRYSPELRKRYL 49 (128)
T ss_pred cCCCHHHHHHhcCHHHHHHHH
Confidence 4799999996 5 655544
No 47
>KOG4140 consensus Nuclear protein Ataxin-7 [Chromatin structure and dynamics]
Probab=22.01 E-value=76 Score=34.69 Aligned_cols=53 Identities=17% Similarity=0.105 Sum_probs=36.3
Q ss_pred ccCcchhhhhhhhhhhccC--C-CCCCCCCccccCC----CCCCCCCCCceeCCChHHHH
Q 012155 11 NISSSDLIDAKLEEHQLCG--S-KQCPGCGHKLEAK----PDWLGLPAGVKFDPTDQELI 63 (470)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~--~-~~~~~~~~~~~~~----~~~~~LPpG~RF~PTDeELI 63 (470)
+.+..-+-++++.|..+-- | ..|--|+.-..-+ .+..++=.|--|.|.-+|+=
T Consensus 53 ~L~K~~~a~a~v~e~~~~~~~~~~~~E~~~~p~~~T~Ild~~~~~~c~G~~~~p~~d~~D 112 (659)
T KOG4140|consen 53 ALSKSAAAMATVGERRPLPSSWNLWVEASKLPGKDTTILDEEVMGLCRGDMFCPAHDDFD 112 (659)
T ss_pred ccccccccccccccCCCCCchhhhhhHhhcCccccceeccHhhhccccccccCCCCCcch
Confidence 4455566778888887433 3 7899999877532 33567778999999766553
No 48
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=21.83 E-value=45 Score=35.86 Aligned_cols=33 Identities=21% Similarity=0.404 Sum_probs=24.0
Q ss_pred ccccCcchhhhhhhhhhhccCCCCCCCCCccccC
Q 012155 9 GTNISSSDLIDAKLEEHQLCGSKQCPGCGHKLEA 42 (470)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 42 (470)
.+.|..++++- ++.....-+.-.||+||+.+.+
T Consensus 10 ~~~C~~Cd~l~-~~~~l~~g~~a~CpRCg~~L~~ 42 (419)
T PRK15103 10 HILCPQCDMLV-ALPRLEHGQKAACPRCGTTLTV 42 (419)
T ss_pred cccCCCCCcee-ecCCCCCCCeeECCCCCCCCcC
Confidence 35799999886 4444444556789999999953
No 49
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. 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.
Probab=20.97 E-value=32 Score=23.22 Aligned_cols=14 Identities=36% Similarity=0.840 Sum_probs=10.2
Q ss_pred cCCCCCCCCCcccc
Q 012155 28 CGSKQCPGCGHKLE 41 (470)
Q Consensus 28 ~~~~~~~~~~~~~~ 41 (470)
...-+||.|+|.++
T Consensus 17 ~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 17 GELLVCPECGHEWN 30 (30)
T ss_dssp SSSEEETTTTEEE-
T ss_pred CCEEeCCcccccCC
Confidence 34478999999873
No 50
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. 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.
Probab=20.38 E-value=45 Score=30.06 Aligned_cols=11 Identities=36% Similarity=0.869 Sum_probs=9.8
Q ss_pred CCCCCCCcccc
Q 012155 31 KQCPGCGHKLE 41 (470)
Q Consensus 31 ~~~~~~~~~~~ 41 (470)
+.||+||.++-
T Consensus 10 r~Cp~cg~kFY 20 (129)
T TIGR02300 10 RICPNTGSKFY 20 (129)
T ss_pred ccCCCcCcccc
Confidence 88999999984
No 51
>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. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=20.04 E-value=65 Score=23.33 Aligned_cols=19 Identities=37% Similarity=0.632 Sum_probs=14.1
Q ss_pred hhhhhhccCCCCCCCCCcc
Q 012155 21 KLEEHQLCGSKQCPGCGHK 39 (470)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~ 39 (470)
-|++.+-..-.+||.||+.
T Consensus 9 ~l~~~RW~~g~~CP~Cg~~ 27 (46)
T PF12760_consen 9 YLEEIRWPDGFVCPHCGST 27 (46)
T ss_pred HHHHhcCCCCCCCCCCCCe
Confidence 5667774455889999985
Done!