Query psy5244
Match_columns 90
No_of_seqs 76 out of 78
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 21:24:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5244.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5244hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3252|consensus 100.0 6.6E-33 1.4E-37 205.8 5.5 88 2-89 118-216 (217)
2 PF10075 PCI_Csn8: COP9 signal 99.5 2.1E-15 4.5E-20 104.1 2.7 64 8-72 70-143 (143)
3 KOG4414|consensus 82.4 0.99 2.1E-05 33.5 2.0 43 14-56 113-163 (197)
4 PF06056 Terminase_5: Putative 79.5 1 2.2E-05 27.3 1.1 28 27-54 14-42 (58)
5 PF07037 DUF1323: Putative tra 79.3 1.7 3.6E-05 30.6 2.2 20 35-54 10-29 (122)
6 PF05687 DUF822: Plant protein 75.0 2.6 5.7E-05 30.6 2.3 24 40-63 49-72 (150)
7 PF08727 P3A: Poliovirus 3A pr 72.3 2.2 4.8E-05 26.4 1.2 17 38-54 28-44 (57)
8 PF10281 Ish1: Putative stress 69.4 4 8.7E-05 22.4 1.7 17 38-54 5-21 (38)
9 cd03742 SOCS_Rab40 SOCS (suppr 68.9 7.5 0.00016 22.6 2.9 35 15-50 6-40 (43)
10 COG5484 Uncharacterized conser 66.4 3.7 7.9E-05 32.5 1.6 19 35-53 29-47 (279)
11 KOG3151|consensus 66.1 5.9 0.00013 31.0 2.6 47 15-61 174-229 (260)
12 smart00513 SAP Putative DNA-bi 61.9 7.8 0.00017 20.7 1.9 21 36-56 3-23 (35)
13 PF13518 HTH_28: Helix-turn-he 59.4 11 0.00024 20.7 2.4 23 27-49 13-36 (52)
14 PF08887 GAD-like: GAD-like do 54.6 13 0.00027 25.2 2.4 52 15-66 4-60 (109)
15 PRK10302 hypothetical protein; 52.8 12 0.00027 28.9 2.4 35 37-71 208-243 (272)
16 PF03374 ANT: Phage antirepres 52.4 14 0.00031 23.8 2.4 38 14-54 13-53 (111)
17 PF08977 BOFC_N: Bypass of For 50.8 23 0.00051 21.4 2.9 14 41-54 25-39 (51)
18 PF10668 Phage_terminase: Phag 49.8 12 0.00026 23.1 1.6 41 17-57 11-54 (60)
19 PF07927 YcfA: YcfA-like prote 49.1 48 0.001 18.7 4.0 15 40-54 2-16 (56)
20 cd03738 SOCS_SOCS4 SOCS (suppr 47.7 23 0.00049 21.7 2.5 36 17-53 8-43 (56)
21 PF01329 Pterin_4a: Pterin 4 a 47.2 38 0.00082 21.8 3.7 19 37-55 5-24 (95)
22 PF13384 HTH_23: Homeodomain-l 46.8 7.1 0.00015 21.6 0.2 23 27-49 18-41 (50)
23 PF01418 HTH_6: Helix-turn-hel 46.5 49 0.0011 20.3 4.0 26 27-52 32-61 (77)
24 KOG4779|consensus 45.8 10 0.00022 24.8 0.8 28 43-72 25-52 (82)
25 PF11774 Lsr2: Lsr2 ; InterPr 44.5 30 0.00065 23.4 3.0 44 14-57 42-97 (110)
26 PRK10853 putative reductase; P 43.2 28 0.0006 23.4 2.7 27 27-53 25-53 (118)
27 cd03739 SOCS_SOCS5 SOCS (suppr 42.3 29 0.00063 21.4 2.4 37 16-53 7-43 (57)
28 PF14791 DNA_pol_B_thumb: DNA 40.5 38 0.00083 20.7 2.8 20 41-60 14-33 (64)
29 PF09409 PUB: PUB domain; Int 39.6 80 0.0017 19.7 4.3 33 27-61 27-70 (87)
30 TIGR01616 nitro_assoc nitrogen 39.1 35 0.00076 23.3 2.7 27 27-53 26-54 (126)
31 smart00753 PAM PCI/PINT associ 38.8 37 0.00081 20.6 2.6 40 27-66 25-72 (88)
32 smart00088 PINT motif in prote 38.8 37 0.00081 20.6 2.6 40 27-66 25-72 (88)
33 PF10671 TcpQ: Toxin co-regula 35.4 27 0.00059 21.9 1.6 16 39-54 13-28 (84)
34 PF08571 Yos1: Yos1-like; Int 35.1 12 0.00027 24.3 -0.0 28 43-71 21-49 (80)
35 PF13542 HTH_Tnp_ISL3: Helix-t 34.8 38 0.00081 18.7 2.0 36 14-49 11-51 (52)
36 PF01904 DUF72: Protein of unk 34.1 26 0.00057 25.8 1.6 30 37-66 185-216 (230)
37 TIGR00014 arsC arsenate reduct 33.9 54 0.0012 21.6 2.9 27 27-53 24-52 (114)
38 PF09012 FeoC: FeoC like trans 32.5 37 0.0008 20.4 1.8 30 18-47 4-36 (69)
39 PF02167 Cytochrom_C1: Cytochr 31.6 36 0.00077 25.8 1.9 27 23-49 28-58 (219)
40 COG1801 Uncharacterized conser 31.4 45 0.00098 25.7 2.5 34 35-68 199-234 (263)
41 PF01527 HTH_Tnp_1: Transposas 30.7 37 0.00079 20.0 1.5 24 27-50 24-48 (76)
42 cd03033 ArsC_15kD Arsenate Red 30.5 56 0.0012 21.8 2.6 27 27-53 25-53 (113)
43 PRK00823 phhB pterin-4-alpha-c 30.4 48 0.001 21.5 2.2 20 37-56 6-26 (97)
44 PF11767 SET_assoc: Histone ly 29.7 92 0.002 19.3 3.3 29 35-63 10-41 (66)
45 PRK09413 IS2 repressor TnpA; R 29.2 58 0.0013 21.6 2.5 24 27-50 30-54 (121)
46 PF01710 HTH_Tnp_IS630: Transp 28.7 59 0.0013 21.6 2.4 40 17-56 60-102 (119)
47 COG4187 RocB Arginine degradat 28.1 28 0.00061 29.9 0.9 35 40-77 150-184 (553)
48 PF13348 Y_phosphatase3C: Tyro 28.1 50 0.0011 19.5 1.8 31 18-48 30-66 (68)
49 PF07311 Dodecin: Dodecin; In 27.9 33 0.00072 21.5 1.0 21 14-34 15-36 (66)
50 PRK04351 hypothetical protein; 27.4 83 0.0018 22.3 3.1 45 5-50 47-96 (149)
51 COG0718 Uncharacterized protei 27.3 30 0.00065 23.6 0.8 35 55-89 38-77 (105)
52 PF08854 DUF1824: Domain of un 26.8 73 0.0016 22.3 2.7 49 17-65 22-85 (125)
53 PF03793 PASTA: PASTA domain; 26.4 1.1E+02 0.0024 17.4 3.1 19 35-53 7-25 (63)
54 PF13405 EF-hand_6: EF-hand do 26.1 30 0.00065 17.4 0.5 22 29-50 6-31 (31)
55 COG1393 ArsC Arsenate reductas 26.0 79 0.0017 21.4 2.7 27 27-53 26-56 (117)
56 PF09494 Slx4: Slx4 endonuclea 25.5 1.1E+02 0.0024 18.3 3.0 15 36-50 44-58 (64)
57 KOG0027|consensus 25.0 40 0.00087 22.8 1.1 52 28-88 90-149 (151)
58 PF12123 Amidase02_C: N-acetyl 24.8 61 0.0013 18.9 1.7 18 35-52 22-42 (45)
59 PF13601 HTH_34: Winged helix 24.8 48 0.001 20.8 1.4 23 27-49 15-38 (80)
60 PF11338 DUF3140: Protein of u 24.3 48 0.001 22.2 1.3 21 35-55 6-31 (92)
61 TIGR03862 flavo_PP4765 unchara 23.6 87 0.0019 25.3 2.9 25 38-62 55-81 (376)
62 PF01890 CbiG_C: Cobalamin syn 23.4 1.5E+02 0.0032 20.0 3.6 40 14-53 16-61 (121)
63 smart00874 B5 tRNA synthetase 23.2 84 0.0018 18.5 2.2 28 27-54 6-36 (71)
64 PF08281 Sigma70_r4_2: Sigma-7 23.0 51 0.0011 18.3 1.1 22 27-48 27-49 (54)
65 smart00540 LEM in nuclear memb 22.8 75 0.0016 18.4 1.8 18 36-53 5-22 (44)
66 PF10652 DUF2480: Protein of u 22.4 94 0.002 23.0 2.6 50 16-65 2-72 (167)
67 TIGR00027 mthyl_TIGR00027 meth 22.3 82 0.0018 23.8 2.4 21 35-55 227-247 (260)
68 PF11761 CbiG_mid: Cobalamin b 21.9 44 0.00094 20.4 0.7 14 41-54 3-16 (93)
69 PF03428 RP-C: Replication pro 21.7 82 0.0018 23.0 2.2 30 35-64 39-74 (177)
70 PRK14622 hypothetical protein; 21.5 38 0.00083 22.6 0.4 35 55-89 34-73 (103)
71 PHA02535 P terminase ATPase su 21.2 41 0.00088 29.1 0.6 28 27-54 19-47 (581)
72 PHA00435 capsid assembly prote 21.0 2E+02 0.0044 23.1 4.4 39 14-53 125-171 (306)
73 COG2963 Transposase and inacti 21.0 1.1E+02 0.0024 19.7 2.6 23 27-49 25-49 (116)
74 KOG2758|consensus 20.8 1.3E+02 0.0029 25.1 3.4 44 4-47 311-371 (432)
75 PF05555 DUF762: Coxiella burn 20.7 97 0.0021 24.1 2.5 39 27-67 10-48 (248)
76 PF01399 PCI: PCI domain; Int 20.4 1.1E+02 0.0023 18.5 2.3 22 27-48 56-83 (105)
77 PF03791 KNOX2: KNOX2 domain ; 20.3 56 0.0012 19.7 1.0 12 38-49 7-18 (52)
78 cd06445 ATase The DNA repair p 20.3 1E+02 0.0022 19.1 2.2 38 15-52 1-46 (79)
79 PF12936 Kri1_C: KRI1-like fam 20.2 63 0.0014 21.4 1.3 32 14-46 16-58 (93)
80 KOG1348|consensus 20.2 54 0.0012 27.6 1.1 33 27-74 68-104 (477)
No 1
>KOG3252|consensus
Probab=99.97 E-value=6.6e-33 Score=205.83 Aligned_cols=88 Identities=40% Similarity=0.654 Sum_probs=85.0
Q ss_pred hhhHHhHHHhhh--HHHHHHHHHhhcc--cccccccc-------CCCChHHHHHHHHHhCceEcCCeEEEecCCCCcccc
Q psy5244 2 DIVKSLQKACQG--ELQQSVRLSSCGP--STKDTKTK-------ADQTDSTLRLWVKKYGWKELDNGYIFIANQDENIKT 70 (90)
Q Consensus 2 ~~~~~~~~l~~~--gFedsVR~fi~~v--~Tfq~I~~-------~~l~d~~L~~~i~~~gW~~~~~g~i~~~N~dn~iKt 70 (90)
+++++||+++.+ |||||||+|+||| +|||+|++ ||++|++|+.|++++||..+++|++|+++||++|||
T Consensus 118 ~~~~~N~~mle~itGFedsvr~yachvv~iTyQkI~k~lLaellG~~sDs~le~~~~~~GW~a~e~G~ifv~~qE~~iKt 197 (217)
T KOG3252|consen 118 QEADENRDMLEGITGFEDSVRKYACHVVGITYQKIDKWLLAELLGGLSDSQLEVWMTKYGWIADESGQIFVASQEEEIKT 197 (217)
T ss_pred hhhccchHHhcCCCcHHHHHHHHHHHheechHhhchHHHHHHhhCcccHHHHHHHHHHccceecCCceEEEecccccccc
Confidence 467899999999 9999999999999 99999999 999999999999999999999999999999999999
Q ss_pred cceeeeeccchHHHHhhcc
Q psy5244 71 KNITEKIEFENAATIMTSN 89 (90)
Q Consensus 71 k~I~EkI~fe~~~~ima~s 89 (90)
|||.|||+||++++||++.
T Consensus 198 kNi~EkI~fd~Va~ima~~ 216 (217)
T KOG3252|consen 198 KNIVEKIDFDHVASIMASL 216 (217)
T ss_pred CCccccCCcchHHHHHHhc
Confidence 9999999999999999874
No 2
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=99.55 E-value=2.1e-15 Score=104.08 Aligned_cols=64 Identities=19% Similarity=0.305 Sum_probs=44.8
Q ss_pred HHHhhh--HHHHHHHHHhhcc--cccccccc------CCCChHHHHHHHHHhCceEcCCeEEEecCCCCcccccc
Q psy5244 8 QKACQG--ELQQSVRLSSCGP--STKDTKTK------ADQTDSTLRLWVKKYGWKELDNGYIFIANQDENIKTKN 72 (90)
Q Consensus 8 ~~l~~~--gFedsVR~fi~~v--~Tfq~I~~------~~l~d~~L~~~i~~~gW~~~~~g~i~~~N~dn~iKtk~ 72 (90)
+.+... ||+|.||.+|+++ .||++|+. +|+++++|.+|+++.||+.++++++|+.||+ ++|+||
T Consensus 70 ~~~~~~v~~~~~~iR~~i~~~i~~aY~sIs~~~la~~Lg~~~~el~~~~~~~gW~~d~~~~~~~~~~~-~~k~k~ 143 (143)
T PF10075_consen 70 PDYKPFVPGFEDTIRERIAHLISKAYSSISLSDLAEMLGLSEEELEKFIKSRGWTVDGDGVLFPPNPE-EIKSKN 143 (143)
T ss_dssp -HHHHTSTTHHHHHHHHHHHHHHHH-SEE-HHHHHHHTTS-HHHHHHHHHHHT-EE-----EE---HH-HTS---
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHcCHHHHHHHhCCCHHHHHHHHHHcCCEECCCccEEecCCc-ccCCCC
Confidence 455555 9999999999999 99999999 9999999999999999999999999999999 999987
No 3
>KOG4414|consensus
Probab=82.43 E-value=0.99 Score=33.52 Aligned_cols=43 Identities=7% Similarity=0.123 Sum_probs=36.6
Q ss_pred HHHHHHHHHhhcc--cccccccc------CCCChHHHHHHHHHhCceEcCC
Q psy5244 14 ELQQSVRLSSCGP--STKDTKTK------ADQTDSTLRLWVKKYGWKELDN 56 (90)
Q Consensus 14 gFedsVR~fi~~v--~Tfq~I~~------~~l~d~~L~~~i~~~gW~~~~~ 56 (90)
-|.|+-|+..-.. +.|.+|-. +||..++-..++-.+||+.+..
T Consensus 113 Af~D~~~kR~FaLl~qAYssI~~~D~A~FlGl~~ddAtk~ilEnGWqaDaa 163 (197)
T KOG4414|consen 113 AFRDATRKRAFALLLQAYSSIIADDFAAFLGLPEDDATKGILENGWQADAA 163 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcccchhhH
Confidence 6888888876555 99999987 9999999999999999998743
No 4
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=79.49 E-value=1 Score=27.32 Aligned_cols=28 Identities=25% Similarity=0.485 Sum_probs=23.6
Q ss_pred cccccccc-CCCChHHHHHHHHHhCceEc
Q psy5244 27 STKDTKTK-ADQTDSTLRLWVKKYGWKEL 54 (90)
Q Consensus 27 ~Tfq~I~~-~~l~d~~L~~~i~~~gW~~~ 54 (90)
-+...|.. +|++...+..|+++++|...
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~r~~W~~~ 42 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKDRYKWDEL 42 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHHhhCcccc
Confidence 45556666 99999999999999999864
No 5
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=79.28 E-value=1.7 Score=30.64 Aligned_cols=20 Identities=35% Similarity=0.762 Sum_probs=18.1
Q ss_pred CCCChHHHHHHHHHhCceEc
Q psy5244 35 ADQTDSTLRLWVKKYGWKEL 54 (90)
Q Consensus 35 ~~l~d~~L~~~i~~~gW~~~ 54 (90)
+|++...++.|++++||+..
T Consensus 10 tG~srQTINrWvRkegW~T~ 29 (122)
T PF07037_consen 10 TGYSRQTINRWVRKEGWKTE 29 (122)
T ss_pred hCccHHHHHHHHHhcCceec
Confidence 68888899999999999975
No 6
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=75.01 E-value=2.6 Score=30.59 Aligned_cols=24 Identities=17% Similarity=0.435 Sum_probs=20.3
Q ss_pred HHHHHHHHHhCceEcCCeEEEecC
Q psy5244 40 STLRLWVKKYGWKELDNGYIFIAN 63 (90)
Q Consensus 40 ~~L~~~i~~~gW~~~~~g~i~~~N 63 (90)
+-|++.+.+.||++++||..+..-
T Consensus 49 eVLkALc~eAGw~Ve~DGTtyr~~ 72 (150)
T PF05687_consen 49 EVLKALCREAGWTVEPDGTTYRKG 72 (150)
T ss_pred HHHHHHHHhCCEEEccCCCeeccC
Confidence 349999999999999999888643
No 7
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=72.35 E-value=2.2 Score=26.41 Aligned_cols=17 Identities=18% Similarity=0.452 Sum_probs=11.7
Q ss_pred ChHHHHHHHHHhCceEc
Q psy5244 38 TDSTLRLWVKKYGWKEL 54 (90)
Q Consensus 38 ~d~~L~~~i~~~gW~~~ 54 (90)
++.++.+||+++||...
T Consensus 28 ~~~eV~~YC~~~GWIip 44 (57)
T PF08727_consen 28 DSPEVREYCEEQGWIIP 44 (57)
T ss_dssp --HHHHHHHHHHT--TT
T ss_pred CCHHHHHHHHHCCcccc
Confidence 66789999999999865
No 8
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=69.43 E-value=4 Score=22.38 Aligned_cols=17 Identities=35% Similarity=0.591 Sum_probs=14.3
Q ss_pred ChHHHHHHHHHhCceEc
Q psy5244 38 TDSTLRLWVKKYGWKEL 54 (90)
Q Consensus 38 ~d~~L~~~i~~~gW~~~ 54 (90)
++++|+.|++++|-...
T Consensus 5 s~~~L~~wL~~~gi~~~ 21 (38)
T PF10281_consen 5 SDSDLKSWLKSHGIPVP 21 (38)
T ss_pred CHHHHHHHHHHcCCCCC
Confidence 67899999999887654
No 9
>cd03742 SOCS_Rab40 SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as membrane-associated molecular switches. Rab40 is characterized by a SOCS box c-terminal to the GTPase domain. The SOCS boxes interact with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=68.95 E-value=7.5 Score=22.62 Aligned_cols=35 Identities=14% Similarity=0.039 Sum_probs=28.0
Q ss_pred HHHHHHHHhhccccccccccCCCChHHHHHHHHHhC
Q psy5244 15 LQQSVRLSSCGPSTKDTKTKADQTDSTLRLWVKKYG 50 (90)
Q Consensus 15 FedsVR~fi~~v~Tfq~I~~~~l~d~~L~~~i~~~g 50 (90)
.++.=|.-|+..++|..|+++-|+.. |+.|+++|.
T Consensus 6 LQ~LCR~~I~~~t~~~~I~~LPLP~~-Lk~yLkey~ 40 (43)
T cd03742 6 LQDLCCRAIVSCTPVYLIDKLPLPVS-IKSHLKSFA 40 (43)
T ss_pred HHHHHHHHHHHhCCcchhhhCCCCHH-HHHHHHhcc
Confidence 45667888888888999999877654 999999884
No 10
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=66.43 E-value=3.7 Score=32.47 Aligned_cols=19 Identities=21% Similarity=0.720 Sum_probs=17.9
Q ss_pred CCCChHHHHHHHHHhCceE
Q psy5244 35 ADQTDSTLRLWVKKYGWKE 53 (90)
Q Consensus 35 ~~l~d~~L~~~i~~~gW~~ 53 (90)
+|++..+++.|..++||+.
T Consensus 29 lGvspntiksWKrr~gWs~ 47 (279)
T COG5484 29 LGVSPNTIKSWKRRDGWSA 47 (279)
T ss_pred hCCChHHHHHHHHhcCCCc
Confidence 9999999999999999973
No 11
>KOG3151|consensus
Probab=66.11 E-value=5.9 Score=31.04 Aligned_cols=47 Identities=17% Similarity=0.239 Sum_probs=37.5
Q ss_pred HHHHHHHHhhcc--cccccccc------CCC-ChHHHHHHHHHhCceEcCCeEEEe
Q psy5244 15 LQQSVRLSSCGP--STKDTKTK------ADQ-TDSTLRLWVKKYGWKELDNGYIFI 61 (90)
Q Consensus 15 FedsVR~fi~~v--~Tfq~I~~------~~l-~d~~L~~~i~~~gW~~~~~g~i~~ 61 (90)
.-+.||.-||.+ -+|-.|+. |.+ ++.+++.|..+-+|..+..++...
T Consensus 174 l~~tiRdEIA~c~EKsYd~l~~s~a~~~L~f~~~~e~~~~~~~r~W~l~~~~~~~~ 229 (260)
T KOG3151|consen 174 LLDTIRDEIAGCIEKSYDKLSASDATQMLLFNNDKELKKFATERQWPLDEKGVFSF 229 (260)
T ss_pred HHHHHHHHHHHHHHHHHhhcCHHHHHHHHhcCChHHHHHHHHhcCCcccccccccc
Confidence 357899999999 88988887 444 788999999999999986555443
No 12
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=61.87 E-value=7.8 Score=20.70 Aligned_cols=21 Identities=24% Similarity=0.120 Sum_probs=17.7
Q ss_pred CCChHHHHHHHHHhCceEcCC
Q psy5244 36 DQTDSTLRLWVKKYGWKELDN 56 (90)
Q Consensus 36 ~l~d~~L~~~i~~~gW~~~~~ 56 (90)
.++-++|+++++.+|+...|.
T Consensus 3 ~l~~~~Lk~~l~~~gl~~~G~ 23 (35)
T smart00513 3 KLKVSELKDELKKRGLSTSGT 23 (35)
T ss_pred cCcHHHHHHHHHHcCCCCCCC
Confidence 467789999999999998764
No 13
>PF13518 HTH_28: Helix-turn-helix domain
Probab=59.42 E-value=11 Score=20.70 Aligned_cols=23 Identities=22% Similarity=0.456 Sum_probs=18.6
Q ss_pred cccccccc-CCCChHHHHHHHHHh
Q psy5244 27 STKDTKTK-ADQTDSTLRLWVKKY 49 (90)
Q Consensus 27 ~Tfq~I~~-~~l~d~~L~~~i~~~ 49 (90)
.|+..+.+ +|++..+|..|+++|
T Consensus 13 ~s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 13 ESVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred CCHHHHHHHHCCCHhHHHHHHHHH
Confidence 35566666 899999999999876
No 14
>PF08887 GAD-like: GAD-like domain; InterPro: IPR014983 This domain is functionally uncharacterised, but it appears to be distantly related to the GAD domain IPR004115 from INTERPRO.
Probab=54.61 E-value=13 Score=25.23 Aligned_cols=52 Identities=15% Similarity=0.277 Sum_probs=36.4
Q ss_pred HHHHHHHH---hhcc-cccccccc-CCCChHHHHHHHHHhCceEcCCeEEEecCCCC
Q psy5244 15 LQQSVRLS---SCGP-STKDTKTK-ADQTDSTLRLWVKKYGWKELDNGYIFIANQDE 66 (90)
Q Consensus 15 FedsVR~f---i~~v-~Tfq~I~~-~~l~d~~L~~~i~~~gW~~~~~g~i~~~N~dn 66 (90)
|+..+.+| +-+. ..=..|++ =|.-.++|-.+-+.+||.--.||..=..||++
T Consensus 4 ~e~fle~fg~~~~~~~vp~~~I~kyk~~lP~~Ll~~W~~~G~g~~~dG~f~~vnP~d 60 (109)
T PF08887_consen 4 FEFFLEKFGPPIDRQEVPEESIEKYKGKLPDELLEYWKEYGFGGYGDGLFWLVNPDD 60 (109)
T ss_pred HHHHHHHcCCCcCCCcCCHHHHHHhcCCCcHHHHHHHHHcCCchhcCcEEEEECHHH
Confidence 55566666 4444 44455777 34444557778899999999999888889864
No 15
>PRK10302 hypothetical protein; Provisional
Probab=52.79 E-value=12 Score=28.91 Aligned_cols=35 Identities=23% Similarity=0.563 Sum_probs=25.1
Q ss_pred CChHHHHHHHHHh-CceEcCCeEEEecCCCCccccc
Q psy5244 37 QTDSTLRLWVKKY-GWKELDNGYIFIANQDENIKTK 71 (90)
Q Consensus 37 l~d~~L~~~i~~~-gW~~~~~g~i~~~N~dn~iKtk 71 (90)
-++++|+.|+++. .|....+-++|..|.++--=++
T Consensus 208 y~~~~L~~wa~~i~~w~~~~~~yvff~n~~~~~A~~ 243 (272)
T PRK10302 208 QNLELFQVWLQKLPQWHQTTTPYLFIHTPDIAQAPE 243 (272)
T ss_pred CCHHHHHHHHHHHHHHHhCCCEEEEEeCCchhhHHH
Confidence 4778999999986 9954434477888887654333
No 16
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=52.42 E-value=14 Score=23.79 Aligned_cols=38 Identities=18% Similarity=0.223 Sum_probs=30.1
Q ss_pred HHHHHHHHHhhcc--cccccccc-CCCChHHHHHHHHHhCceEc
Q psy5244 14 ELQQSVRLSSCGP--STKDTKTK-ADQTDSTLRLWVKKYGWKEL 54 (90)
Q Consensus 14 gFedsVR~fi~~v--~Tfq~I~~-~~l~d~~L~~~i~~~gW~~~ 54 (90)
.|.| .|++.- .|.+.+.+ +++...+|.+|+...||--.
T Consensus 13 ~~~d---~~~~~~~~~ti~~~AK~L~i~~~~l~~~Lr~~g~l~~ 53 (111)
T PF03374_consen 13 EFYD---AFVDSDGLYTIREAAKLLGIGRNKLFQWLREKGWLYR 53 (111)
T ss_pred HHHH---HHHcCCCCccHHHHHHHhCCCHHHHHHHHHhCCceEE
Confidence 4555 344444 77888888 99999999999999999876
No 17
>PF08977 BOFC_N: Bypass of Forespore C, N terminal; InterPro: IPR015071 The N-terminal domain of, bypass of forespore C, is composed of a four-stranded beta-sheet covered by an alpha-helix. The beta-sheet has a beta2-beta1-beta4-beta3 topology, where strands beta1 and beta2 and strands beta3 and beta4 are connected by beta-turns, whereas strands beta2 and beta3 are joined by an alpha-helix that runs across one face of the beta-sheet. This domain is similar to the third immunoglobulin G-binding domain of protein G from Streptococcus, the latter belonging to a large and diverse group of cell surface-associated proteins that bind to immunoglobulins. It has been hypothesised that this domain may be a mediator of protein-protein interactions involved in proteolytic events at the cell surface []. ; PDB: 2BW2_A.
Probab=50.81 E-value=23 Score=21.37 Aligned_cols=14 Identities=29% Similarity=0.800 Sum_probs=11.5
Q ss_pred HHHHHHHHh-CceEc
Q psy5244 41 TLRLWVKKY-GWKEL 54 (90)
Q Consensus 41 ~L~~~i~~~-gW~~~ 54 (90)
.+++|.++| ||+..
T Consensus 25 s~ed~w~~Y~~WqLv 39 (51)
T PF08977_consen 25 SMEDFWAKYKGWQLV 39 (51)
T ss_dssp EHHHHHHHSTTSEEE
T ss_pred cHHHHHHhhcCcEEE
Confidence 378899998 99974
No 18
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=49.77 E-value=12 Score=23.09 Aligned_cols=41 Identities=17% Similarity=0.324 Sum_probs=32.0
Q ss_pred HHHHHHhhcc--cccccccc-CCCChHHHHHHHHHhCceEcCCe
Q psy5244 17 QSVRLSSCGP--STKDTKTK-ADQTDSTLRLWVKKYGWKELDNG 57 (90)
Q Consensus 17 dsVR~fi~~v--~Tfq~I~~-~~l~d~~L~~~i~~~gW~~~~~g 57 (90)
.+.+.|.-+- ++...|.. ||+++.++..|=++..|...-+|
T Consensus 11 kA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~dkW~~~~~~ 54 (60)
T PF10668_consen 11 KAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSRDKWDEKLKG 54 (60)
T ss_pred HHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhhcchhhHhcc
Confidence 3455566665 77777777 99999999999999999976444
No 19
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=49.13 E-value=48 Score=18.74 Aligned_cols=15 Identities=27% Similarity=0.430 Sum_probs=12.0
Q ss_pred HHHHHHHHHhCceEc
Q psy5244 40 STLRLWVKKYGWKEL 54 (90)
Q Consensus 40 ~~L~~~i~~~gW~~~ 54 (90)
.+|..+++++||...
T Consensus 2 ~el~k~L~~~G~~~~ 16 (56)
T PF07927_consen 2 RELIKLLEKAGFEEV 16 (56)
T ss_dssp HHHHHHHHHTT-EEE
T ss_pred hHHHHHHHHCCCEEe
Confidence 478999999999974
No 20
>cd03738 SOCS_SOCS4 SOCS (suppressors of cytokine signaling) box of SOCS4-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=47.68 E-value=23 Score=21.75 Aligned_cols=36 Identities=25% Similarity=0.413 Sum_probs=27.3
Q ss_pred HHHHHHhhccccccccccCCCChHHHHHHHHHhCceE
Q psy5244 17 QSVRLSSCGPSTKDTKTKADQTDSTLRLWVKKYGWKE 53 (90)
Q Consensus 17 dsVR~fi~~v~Tfq~I~~~~l~d~~L~~~i~~~gW~~ 53 (90)
..-|.-|++.+++..|+.+-|... |+.|++.|-.+.
T Consensus 8 HLCR~~I~~~t~~~~I~~LPLP~~-LK~YLkeY~y~~ 43 (56)
T cd03738 8 HICRTVICNCTTYDGIDALPIPSS-MKLYLKEYHYKS 43 (56)
T ss_pred HHHHHHHHhcCCccccccCCCCHH-HHHHHHhCCCcc
Confidence 445677777777888888777655 999999997664
No 21
>PF01329 Pterin_4a: Pterin 4 alpha carbinolamine dehydratase; InterPro: IPR001533 DCoH is the dimerisation cofactor of hepatocyte nuclear factor 1 (HNF-1) that functions as both a transcriptional coactivator and a pterin dehydratase []. X-ray crystallographic studies have shown that the ligand binds at four sites per tetrameric enzyme, with little apparent conformational change in the protein.; GO: 0008124 4-alpha-hydroxytetrahydrobiopterin dehydratase activity, 0006729 tetrahydrobiopterin biosynthetic process; PDB: 2V6T_B 2V6U_A 2V6S_B 2EBB_A 1USM_A 1F93_B 1DCP_C 1DCH_E 3HXA_E 1DCO_C ....
Probab=47.24 E-value=38 Score=21.83 Aligned_cols=19 Identities=16% Similarity=0.324 Sum_probs=16.2
Q ss_pred CChHHHHHHHHHh-CceEcC
Q psy5244 37 QTDSTLRLWVKKY-GWKELD 55 (90)
Q Consensus 37 l~d~~L~~~i~~~-gW~~~~ 55 (90)
|+++++...++.. ||+..+
T Consensus 5 Ls~~ei~~~L~~l~~W~~~~ 24 (95)
T PF01329_consen 5 LSEEEIAEALAELPGWKLDG 24 (95)
T ss_dssp -THHHHHHHHHTSTTSEEET
T ss_pred CCHHHHHHhhhcCcCCEECC
Confidence 6889999999986 999987
No 22
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=46.80 E-value=7.1 Score=21.64 Aligned_cols=23 Identities=26% Similarity=0.429 Sum_probs=16.0
Q ss_pred cccccccc-CCCChHHHHHHHHHh
Q psy5244 27 STKDTKTK-ADQTDSTLRLWVKKY 49 (90)
Q Consensus 27 ~Tfq~I~~-~~l~d~~L~~~i~~~ 49 (90)
.|.+.|.+ +|++...+..|+++|
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT--
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHc
Confidence 56677777 999999999999886
No 23
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=46.53 E-value=49 Score=20.30 Aligned_cols=26 Identities=23% Similarity=0.258 Sum_probs=18.2
Q ss_pred cccccccc----CCCChHHHHHHHHHhCce
Q psy5244 27 STKDTKTK----ADQTDSTLRLWVKKYGWK 52 (90)
Q Consensus 27 ~Tfq~I~~----~~l~d~~L~~~i~~~gW~ 52 (90)
+.+-+|.. .+++.+.+-.|+++.|.+
T Consensus 32 ~~~~si~elA~~~~vS~sti~Rf~kkLG~~ 61 (77)
T PF01418_consen 32 IAFMSISELAEKAGVSPSTIVRFCKKLGFS 61 (77)
T ss_dssp HCT--HHHHHHHCTS-HHHHHHHHHHCTTT
T ss_pred HHHccHHHHHHHcCCCHHHHHHHHHHhCCC
Confidence 44444444 999999999999998764
No 24
>KOG4779|consensus
Probab=45.81 E-value=10 Score=24.80 Aligned_cols=28 Identities=25% Similarity=0.470 Sum_probs=19.1
Q ss_pred HHHHHHhCceEcCCeEEEecCCCCcccccc
Q psy5244 43 RLWVKKYGWKELDNGYIFIANQDENIKTKN 72 (90)
Q Consensus 43 ~~~i~~~gW~~~~~g~i~~~N~dn~iKtk~ 72 (90)
+.|+++.||+.+. +..|-. .++.+|++.
T Consensus 25 eRFL~riGws~d~-~~gFG~-~q~tiKS~~ 52 (82)
T KOG4779|consen 25 ERFLKRIGWSTDQ-GIGFGE-DQPTIKSQL 52 (82)
T ss_pred HHHHHHhCcCccc-CcccCC-CCccHHHHH
Confidence 5788999999874 334433 356788864
No 25
>PF11774 Lsr2: Lsr2 ; InterPro: IPR024412 This entry represents Lsr2, which is a small, basic DNA-bridging protein present in Mycobacterium and related actinomycetes. It is a functional homologue of the H-NS-like proteins []. H-NS proteins play a role in nucleoid organisation and also function as a pleiotropic regulator of gene expression [, ].; PDB: 4E1R_B 4E1P_B 2KNG_A.
Probab=44.51 E-value=30 Score=23.41 Aligned_cols=44 Identities=14% Similarity=0.394 Sum_probs=26.7
Q ss_pred HHHHHHHHHhhcc--cc--cccccc--------CCCChHHHHHHHHHhCceEcCCe
Q psy5244 14 ELQQSVRLSSCGP--ST--KDTKTK--------ADQTDSTLRLWVKKYGWKELDNG 57 (90)
Q Consensus 14 gFedsVR~fi~~v--~T--fq~I~~--------~~l~d~~L~~~i~~~gW~~~~~g 57 (90)
-|.+++..||.+. .. -++-.. ..-+-.++..|.+.+|+....-|
T Consensus 42 ~lr~~l~~yi~~arr~~g~~~~~~~~~~~~~~~~~~~~~~IR~WA~~nG~~Vs~RG 97 (110)
T PF11774_consen 42 KLRDALAPYIAAARRVGGRARRRRRRARSAAAAPREDTAAIREWARENGYEVSDRG 97 (110)
T ss_dssp HHHHHHHHHHHHSEEE---------SSGGG---SSTHHHHHHHHHHHTT----SSS
T ss_pred HHHHHHHHHHHHheEccccccccccCccccCCCCccchHHHHHHHHHcCCcCCCCC
Confidence 7899999999988 22 111111 33445779999999999987666
No 26
>PRK10853 putative reductase; Provisional
Probab=43.25 E-value=28 Score=23.45 Aligned_cols=27 Identities=11% Similarity=0.263 Sum_probs=21.3
Q ss_pred cccccccc--CCCChHHHHHHHHHhCceE
Q psy5244 27 STKDTKTK--ADQTDSTLRLWVKKYGWKE 53 (90)
Q Consensus 27 ~Tfq~I~~--~~l~d~~L~~~i~~~gW~~ 53 (90)
+.|+-++- -.++.++|..|+++.||..
T Consensus 25 i~~~~~d~~k~p~s~~eL~~~l~~~g~~~ 53 (118)
T PRK10853 25 IDYRFHDYRVDGLDSELLQGFIDELGWEA 53 (118)
T ss_pred CCcEEeehccCCcCHHHHHHHHHHcCHHH
Confidence 55555554 6789999999999999863
No 27
>cd03739 SOCS_SOCS5 SOCS (suppressors of cytokine signaling) box of SOCS5-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. SOCS5 inhibits Th2 differentiation by inhibiting IL-4 signaling. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=42.31 E-value=29 Score=21.37 Aligned_cols=37 Identities=24% Similarity=0.296 Sum_probs=27.6
Q ss_pred HHHHHHHhhccccccccccCCCChHHHHHHHHHhCceE
Q psy5244 16 QQSVRLSSCGPSTKDTKTKADQTDSTLRLWVKKYGWKE 53 (90)
Q Consensus 16 edsVR~fi~~v~Tfq~I~~~~l~d~~L~~~i~~~gW~~ 53 (90)
...-|.-|+..+++..|+.+-|... |+.|++.|-.+.
T Consensus 7 QhLCR~~In~~t~~~~I~~LPLP~~-LKdyLkeY~y~~ 43 (57)
T cd03739 7 QYICRAVICRCTTYDGIDALPLPSM-LQDFLKEYHYKQ 43 (57)
T ss_pred HHHHHHHHHHhcCCCCcccCcCCHH-HHHHHHhCCCCc
Confidence 4455777777778888887777654 999999987664
No 28
>PF14791 DNA_pol_B_thumb: DNA polymerase beta thumb ; PDB: 1HUZ_A 3K75_D 1HUO_A 2BPC_A 1RPL_A 1NOM_A 1ZQX_A 1ZQU_A 1ZQZ_A 1ZQV_A ....
Probab=40.54 E-value=38 Score=20.71 Aligned_cols=20 Identities=35% Similarity=0.419 Sum_probs=16.4
Q ss_pred HHHHHHHHhCceEcCCeEEE
Q psy5244 41 TLRLWVKKYGWKELDNGYIF 60 (90)
Q Consensus 41 ~L~~~i~~~gW~~~~~g~i~ 60 (90)
.|+.|+++.||+.+..|+.-
T Consensus 14 ~lR~~A~~~g~~L~~~Gl~~ 33 (64)
T PF14791_consen 14 DLRQYAKKKGMKLSEYGLFK 33 (64)
T ss_dssp HHHHHHHHTTEEEESSEEEE
T ss_pred HHHHHHHHcCCeeCcccccc
Confidence 58899999999999877543
No 29
>PF09409 PUB: PUB domain; InterPro: IPR018997 The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain []. This domain is also found on other proteins linked to the ubiquitin-proteasome system. ; PDB: 2CM0_A 2CCQ_A 2D5U_A 2HPL_A 2HPJ_A.
Probab=39.64 E-value=80 Score=19.66 Aligned_cols=33 Identities=9% Similarity=0.122 Sum_probs=22.3
Q ss_pred cccccccc---------CCCChHHHHHHHHHhCceEc--CCeEEEe
Q psy5244 27 STKDTKTK---------ADQTDSTLRLWVKKYGWKEL--DNGYIFI 61 (90)
Q Consensus 27 ~Tfq~I~~---------~~l~d~~L~~~i~~~gW~~~--~~g~i~~ 61 (90)
--|++|.. +.+.+ -.+++...||... ++..+++
T Consensus 27 ~kyR~Ir~~N~~f~~~i~~~~g--~~~~L~~~GF~~~~~~~~~vl~ 70 (87)
T PF09409_consen 27 EKYRRIRLSNKTFQEKILPVPG--ARELLEALGFREVTDEEFLVLP 70 (87)
T ss_dssp CGGGEEETTSHHHHHHTTTSTT--HHHHHHHHT-EE---SSEEE--
T ss_pred ccceEeecCcchHHHHhcCChh--HHHHHHHCCCEEecCCCEEEEe
Confidence 78999988 55655 6778888999998 4557777
No 30
>TIGR01616 nitro_assoc nitrogenase-associated protein. This model describes a small family of uncharacterized proteins found so far in alpha and gamma proteobacteria and in Nostoc sp. PCC 7120, a cyanobacterium. The gene for this protein is associated with nitrogenase genes. This family shows sequence similarity to TIGR00014, a glutaredoxin-dependent arsenate reductase that converts arsentate to arsenite for disposal. This family is one of several included in Pfam model pfam03960.
Probab=39.08 E-value=35 Score=23.34 Aligned_cols=27 Identities=11% Similarity=0.031 Sum_probs=20.7
Q ss_pred cccccccc--CCCChHHHHHHHHHhCceE
Q psy5244 27 STKDTKTK--ADQTDSTLRLWVKKYGWKE 53 (90)
Q Consensus 27 ~Tfq~I~~--~~l~d~~L~~~i~~~gW~~ 53 (90)
+.|+-++- =.++.++|+.|+++.||..
T Consensus 26 i~~~~~d~~~~p~t~~eL~~~l~~~g~~~ 54 (126)
T TIGR01616 26 HDVEVQDILKEPWHADTLRPYFGNKPVGS 54 (126)
T ss_pred CCcEEEeccCCCcCHHHHHHHHHHcCHHH
Confidence 55555554 6789999999999999864
No 31
>smart00753 PAM PCI/PINT associated module.
Probab=38.82 E-value=37 Score=20.65 Aligned_cols=40 Identities=18% Similarity=0.034 Sum_probs=24.4
Q ss_pred cccccccc-CCCChHHHHHHHHHh------CceEc-CCeEEEecCCCC
Q psy5244 27 STKDTKTK-ADQTDSTLRLWVKKY------GWKEL-DNGYIFIANQDE 66 (90)
Q Consensus 27 ~Tfq~I~~-~~l~d~~L~~~i~~~------gW~~~-~~g~i~~~N~dn 66 (90)
++|..|.. ++++.++++.|+.+. ..+.+ .+|++.....++
T Consensus 25 i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~ 72 (88)
T smart00753 25 ISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDP 72 (88)
T ss_pred eeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCch
Confidence 44444444 999999999998542 34554 355555544433
No 32
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=38.82 E-value=37 Score=20.65 Aligned_cols=40 Identities=18% Similarity=0.034 Sum_probs=24.4
Q ss_pred cccccccc-CCCChHHHHHHHHHh------CceEc-CCeEEEecCCCC
Q psy5244 27 STKDTKTK-ADQTDSTLRLWVKKY------GWKEL-DNGYIFIANQDE 66 (90)
Q Consensus 27 ~Tfq~I~~-~~l~d~~L~~~i~~~------gW~~~-~~g~i~~~N~dn 66 (90)
++|..|.. ++++.++++.|+.+. ..+.+ .+|++.....++
T Consensus 25 i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~ 72 (88)
T smart00088 25 ISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDP 72 (88)
T ss_pred eeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCch
Confidence 44444444 999999999998542 34554 355555544433
No 33
>PF10671 TcpQ: Toxin co-regulated pilus biosynthesis protein Q; InterPro: IPR018927 The toxin-coregulated pilus (TCP) of Vibrio cholerae and the soluble TcpF protein that is secreted via the TCP biogenesis apparatus are essential for intestinal colonisation in the disease of cholera. TCP fibres are homopolymers of TcpA pilin, encoded by the first gene in the tcp biogenesis operon. TcpQ is part of an outer membrane complex of the TCP biogenesis apparatus, comprised of TcpC and TcpQ. TcpQ is required for proper localisation of TcpC to the outer membrane [, ]. This entry represents a C-terminal domain found in TcpQ and other pilus biosynthesis proteins.; PDB: 3OV5_A 2L4W_A.
Probab=35.40 E-value=27 Score=21.93 Aligned_cols=16 Identities=31% Similarity=0.821 Sum_probs=12.6
Q ss_pred hHHHHHHHHHhCceEc
Q psy5244 39 DSTLRLWVKKYGWKEL 54 (90)
Q Consensus 39 d~~L~~~i~~~gW~~~ 54 (90)
...|..|.++.||+..
T Consensus 13 ~~~L~~Wa~~aGw~l~ 28 (84)
T PF10671_consen 13 REALERWAKQAGWTLV 28 (84)
T ss_dssp HHHHHHHHHCTT-EEE
T ss_pred HHHHHHHHHHCCCEEE
Confidence 4679999999999963
No 34
>PF08571 Yos1: Yos1-like; InterPro: IPR013880 In yeast, Yos1 is a subunit of the Yip1p-Yif1p complex and is required for transport between the endoplasmic reticulum and the Golgi complex. Yos1 appears to be conserved in eukaryotes [].
Probab=35.06 E-value=12 Score=24.26 Aligned_cols=28 Identities=25% Similarity=0.475 Sum_probs=16.8
Q ss_pred HHHHHHhCceEcCCeEEEe-cCCCCccccc
Q psy5244 43 RLWVKKYGWKELDNGYIFI-ANQDENIKTK 71 (90)
Q Consensus 43 ~~~i~~~gW~~~~~g~i~~-~N~dn~iKtk 71 (90)
+.|++++||......- .. ..+++.+|.+
T Consensus 21 ~RFL~kiGw~~~~~~~-~g~~~~~~siK~q 49 (80)
T PF08571_consen 21 DRFLAKIGWSSSQNSG-FGFGGDPNSIKAQ 49 (80)
T ss_pred HHHhccCCCCCccccc-cccCCCCcCHHHH
Confidence 4789999998763211 10 1256677774
No 35
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=34.83 E-value=38 Score=18.74 Aligned_cols=36 Identities=11% Similarity=0.082 Sum_probs=26.7
Q ss_pred HHHHHHHHHhhcc----cccccccc-CCCChHHHHHHHHHh
Q psy5244 14 ELQQSVRLSSCGP----STKDTKTK-ADQTDSTLRLWVKKY 49 (90)
Q Consensus 14 gFedsVR~fi~~v----~Tfq~I~~-~~l~d~~L~~~i~~~ 49 (90)
.+-...+.+|... .|++.|.+ +|++...+...+.++
T Consensus 11 r~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 11 RITKRLEQYILKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred cHHHHHHHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 4444555566655 48999999 999999999887654
No 36
>PF01904 DUF72: Protein of unknown function DUF72; InterPro: IPR002763 The function of this family is unknown. Aquifex aeolicus has two copies of this protein. A probable aspartyl-tRNA synthetase from Escherichia coli [] belongs to this group.; PDB: 1VPY_A 1ZTV_A 1VPQ_A.
Probab=34.11 E-value=26 Score=25.84 Aligned_cols=30 Identities=27% Similarity=0.674 Sum_probs=20.4
Q ss_pred CChHHHHHHHHHh-CceEcCCe-EEEecCCCC
Q psy5244 37 QTDSTLRLWVKKY-GWKELDNG-YIFIANQDE 66 (90)
Q Consensus 37 l~d~~L~~~i~~~-gW~~~~~g-~i~~~N~dn 66 (90)
-++++|+.|+++. +|...+.. .++.+|..+
T Consensus 185 Ys~~eL~~~a~~i~~~~~~~~~v~v~fnN~~~ 216 (230)
T PF01904_consen 185 YSDEELEEWAERIRAWAAQGKEVYVFFNNDYE 216 (230)
T ss_dssp --HHHHHHHHHHHHHHHTCSSEEEEEE-SBCC
T ss_pred CCHHHHHHHHHHHHHHHHcCCCEEEEEeCCcc
Confidence 3789999999986 89876544 557777554
No 37
>TIGR00014 arsC arsenate reductase (glutaredoxin). composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate.
Probab=33.91 E-value=54 Score=21.60 Aligned_cols=27 Identities=19% Similarity=0.111 Sum_probs=21.7
Q ss_pred cccccccc--CCCChHHHHHHHHHhCceE
Q psy5244 27 STKDTKTK--ADQTDSTLRLWVKKYGWKE 53 (90)
Q Consensus 27 ~Tfq~I~~--~~l~d~~L~~~i~~~gW~~ 53 (90)
+.|+-++- =.++.++|..|+++.||..
T Consensus 24 i~~~~~di~~~p~t~~el~~~l~~~g~~~ 52 (114)
T TIGR00014 24 IEPEVVKYLKNPPTKSELEAIFAKLGLTV 52 (114)
T ss_pred CCeEEEeccCCCcCHHHHHHHHHHcCCch
Confidence 56665554 7889999999999999864
No 38
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=32.52 E-value=37 Score=20.36 Aligned_cols=30 Identities=3% Similarity=-0.044 Sum_probs=22.6
Q ss_pred HHHHHhhcc--cccccccc-CCCChHHHHHHHH
Q psy5244 18 SVRLSSCGP--STKDTKTK-ADQTDSTLRLWVK 47 (90)
Q Consensus 18 sVR~fi~~v--~Tfq~I~~-~~l~d~~L~~~i~ 47 (90)
.||.|+..- .|++.|.+ ++++.+.|+.-+.
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~ 36 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGISPEAVEAMLE 36 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 588888777 88999998 9999988766554
No 39
>PF02167 Cytochrom_C1: Cytochrome C1 family; InterPro: IPR002326 Cytochrome bc1 complex (ubiquinol:ferricytochrome c oxidoreductase) is found in mitochondria, photosynthetic bacteria and other prokaryotes. It is minimally composed of three subunits: cytochrome b, carrying a low- and a high-potential haem group; cytochrome c1 (cyt c1); and a high-potential Rieske iron-sulphur protein. The general function of the complex is electron transfer between two mobile redox carriers, ubiquinol and cytochrome c; the electron transfer is coupled with proton translocation across the membrane, thus generating proton-motive force in the form of an electrochemical potential that can drive ATP synthesis. In its structure and functions, the cytochrome bc1 complex bears extensive analogy to the cytochrome b6f complex of chloroplasts and cyanobacteria; cyt c1 plays an analogous role to cytochrome f, in spite of their different structures [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1P84_D 2IBZ_D 1EZV_D 3CX5_O 3CXH_O 1KB9_D 1KYO_D 1ZRT_Q 2CA4_B 2C9X_B ....
Probab=31.61 E-value=36 Score=25.82 Aligned_cols=27 Identities=15% Similarity=0.261 Sum_probs=23.7
Q ss_pred hhcc---cccccccc-CCCChHHHHHHHHHh
Q psy5244 23 SCGP---STKDTKTK-ADQTDSTLRLWVKKY 49 (90)
Q Consensus 23 i~~v---~Tfq~I~~-~~l~d~~L~~~i~~~ 49 (90)
-||. .+|+++.. ++++++++++++..+
T Consensus 28 ~CHsl~~~~y~~L~~d~~~~e~~vk~~a~~~ 58 (219)
T PF02167_consen 28 SCHSLKYVRYRRLADDLGLTEDEVKAIAAEY 58 (219)
T ss_dssp GTSBCTTCBGGGGTTSTSSHHHHHHHHHHTS
T ss_pred hccccccccHHHHhhccCCCHHHHHHHHHhc
Confidence 4777 89999999 999999999999876
No 40
>COG1801 Uncharacterized conserved protein [Function unknown]
Probab=31.37 E-value=45 Score=25.66 Aligned_cols=34 Identities=21% Similarity=0.322 Sum_probs=26.0
Q ss_pred CCCChHHHHHHHHHh-CceEcC-CeEEEecCCCCcc
Q psy5244 35 ADQTDSTLRLWVKKY-GWKELD-NGYIFIANQDENI 68 (90)
Q Consensus 35 ~~l~d~~L~~~i~~~-gW~~~~-~g~i~~~N~dn~i 68 (90)
-+-++++|+.|.++. .|...+ ..+++.+|+.+--
T Consensus 199 y~Y~~~eL~~~a~ki~~~~~~~~~~yv~FnN~~~g~ 234 (263)
T COG1801 199 YRYNEEELKEWAEKIKQLAEGGKEVYVFFNNPYNGD 234 (263)
T ss_pred CCCCHHHHHHHHHHHHHHhcCCCceEEEEeCCcchh
Confidence 456899999999996 688765 4577888876543
No 41
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=30.69 E-value=37 Score=20.04 Aligned_cols=24 Identities=25% Similarity=0.368 Sum_probs=17.7
Q ss_pred cccccccc-CCCChHHHHHHHHHhC
Q psy5244 27 STKDTKTK-ADQTDSTLRLWVKKYG 50 (90)
Q Consensus 27 ~Tfq~I~~-~~l~d~~L~~~i~~~g 50 (90)
.|-..+.+ .|++...|-.|++++.
T Consensus 24 ~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 24 ESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp CHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CceEeeecccccccccccHHHHHHh
Confidence 44444444 8999999999999985
No 42
>cd03033 ArsC_15kD Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also encodes dinitrogenase reductase ADP-ribosyltransferase (DRAT) and dinitrogenase reductase activating glycohydrolase (DRAG). ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via glutaredoxin, through a single catalytic cysteine.
Probab=30.54 E-value=56 Score=21.78 Aligned_cols=27 Identities=19% Similarity=0.142 Sum_probs=21.5
Q ss_pred cccccccc--CCCChHHHHHHHHHhCceE
Q psy5244 27 STKDTKTK--ADQTDSTLRLWVKKYGWKE 53 (90)
Q Consensus 27 ~Tfq~I~~--~~l~d~~L~~~i~~~gW~~ 53 (90)
+.|+-++- -.++.++|+.|+++.||..
T Consensus 25 i~~~~~d~~~~p~s~~eL~~~l~~~g~~~ 53 (113)
T cd03033 25 HEVEVRDLLTEPWTAETLRPFFGDLPVAE 53 (113)
T ss_pred CCcEEeehhcCCCCHHHHHHHHHHcCHHH
Confidence 66666665 6789999999999999854
No 43
>PRK00823 phhB pterin-4-alpha-carbinolamine dehydratase; Validated
Probab=30.44 E-value=48 Score=21.46 Aligned_cols=20 Identities=15% Similarity=0.473 Sum_probs=16.9
Q ss_pred CChHHHHHHHHHh-CceEcCC
Q psy5244 37 QTDSTLRLWVKKY-GWKELDN 56 (90)
Q Consensus 37 l~d~~L~~~i~~~-gW~~~~~ 56 (90)
|++++++..+++. ||+..++
T Consensus 6 Ls~~ei~~~l~~l~gW~~~~~ 26 (97)
T PRK00823 6 LSDEEIAELLPQLPGWTLVGD 26 (97)
T ss_pred CCHHHHHHHhhcCCCCeEeCC
Confidence 6789999999886 9998755
No 44
>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes. This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].
Probab=29.70 E-value=92 Score=19.31 Aligned_cols=29 Identities=21% Similarity=0.472 Sum_probs=21.1
Q ss_pred CCCChHHHHHHHHHhCceE---cCCeEEEecC
Q psy5244 35 ADQTDSTLRLWVKKYGWKE---LDNGYIFIAN 63 (90)
Q Consensus 35 ~~l~d~~L~~~i~~~gW~~---~~~g~i~~~N 63 (90)
.+++-+.++.=+++|+|+. +..|..++-|
T Consensus 10 ~~~~v~d~K~~Lr~y~~~~I~~d~tGfYIvF~ 41 (66)
T PF11767_consen 10 HGVTVEDFKKRLRKYRWDRIRDDRTGFYIVFN 41 (66)
T ss_pred CCccHHHHHHHHhcCCcceEEecCCEEEEEEC
Confidence 5666778999999999996 4567544444
No 45
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=29.24 E-value=58 Score=21.65 Aligned_cols=24 Identities=29% Similarity=0.404 Sum_probs=21.5
Q ss_pred cccccccc-CCCChHHHHHHHHHhC
Q psy5244 27 STKDTKTK-ADQTDSTLRLWVKKYG 50 (90)
Q Consensus 27 ~Tfq~I~~-~~l~d~~L~~~i~~~g 50 (90)
.|+..+.+ +|++...|-.|+++|.
T Consensus 30 ~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 30 MTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 77888877 9999999999999984
No 46
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=28.72 E-value=59 Score=21.59 Aligned_cols=40 Identities=13% Similarity=0.068 Sum_probs=29.1
Q ss_pred HHHHHHhhcc--cccccccc-CCCChHHHHHHHHHhCceEcCC
Q psy5244 17 QSVRLSSCGP--STKDTKTK-ADQTDSTLRLWVKKYGWKELDN 56 (90)
Q Consensus 17 dsVR~fi~~v--~Tfq~I~~-~~l~d~~L~~~i~~~gW~~~~~ 56 (90)
|.++.+|..- .|-..+.. +|++.+.+-.++++.||+..-+
T Consensus 60 ~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t~KK~ 102 (119)
T PF01710_consen 60 DELKALVEENPDATLRELAERLGVSPSTIWRALKRLGITRKKK 102 (119)
T ss_pred HHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHcCchhccC
Confidence 4455555443 55555555 9999999999999999997644
No 47
>COG4187 RocB Arginine degradation protein (predicted deacylase) [Amino acid transport and metabolism]
Probab=28.05 E-value=28 Score=29.86 Aligned_cols=35 Identities=17% Similarity=0.420 Sum_probs=26.6
Q ss_pred HHHHHHHHHhCceEcCCeEEEecCCCCcccccceeeee
Q psy5244 40 STLRLWVKKYGWKELDNGYIFIANQDENIKTKNITEKI 77 (90)
Q Consensus 40 ~~L~~~i~~~gW~~~~~g~i~~~N~dn~iKtk~I~EkI 77 (90)
+-|++|++. +.-.+++.|++|||+++.+.-|+|-+
T Consensus 150 a~L~~fa~~---~~~~GNlLf~a~pdEE~~s~G~r~a~ 184 (553)
T COG4187 150 ACLEEFAAR---TDRQGNLLFMAVPDEEVESRGMREAR 184 (553)
T ss_pred HHHHHHhhC---CCCCCcEEEEeccchhhhcccHHHHH
Confidence 347777776 33345689999999999999888754
No 48
>PF13348 Y_phosphatase3C: Tyrosine phosphatase family C-terminal region; PDB: 1YWF_A 2OZ5_B.
Probab=28.05 E-value=50 Score=19.49 Aligned_cols=31 Identities=0% Similarity=-0.049 Sum_probs=16.1
Q ss_pred HHHHHhhcc-cccccccc-----CCCChHHHHHHHHH
Q psy5244 18 SVRLSSCGP-STKDTKTK-----ADQTDSTLRLWVKK 48 (90)
Q Consensus 18 sVR~fi~~v-~Tfq~I~~-----~~l~d~~L~~~i~~ 48 (90)
.++.++-++ ..|.+++. +|+++++++.+-.+
T Consensus 30 ~l~~~l~~i~~~yGs~e~Yl~~~lgl~~~~i~~Lr~~ 66 (68)
T PF13348_consen 30 YLEAALDAIDERYGSVENYLREELGLSEEDIERLRER 66 (68)
T ss_dssp HHHHHHHHHHHHHSSHHHHHHHT-T--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHcCCCCHHHHHHHHHH
Confidence 344444444 45666665 68888887776543
No 49
>PF07311 Dodecin: Dodecin; InterPro: IPR009923 This entry represents proteins with a Dodecin-like topology. Dodecin flavoprotein is a small dodecameric flavin-binding protein from Halobacterium salinarium (Halobacterium halobium) that contains two flavins stacked in a single binding pocket between two tryptophan residues to form an aromatic tetrade []. Dodecin binds riboflavin, although it appears to have a broad specificity for flavins. Lumichrome, a molecule associated with flavin metabolism, appears to be a ligand of dodecin, which could act as a waste-trapping device. ; PDB: 2VYX_L 2DEG_F 2V18_K 2V19_D 2UX9_B 2CZ8_E 2V21_F 2CC8_A 2CCB_A 2VX9_A ....
Probab=27.89 E-value=33 Score=21.49 Aligned_cols=21 Identities=10% Similarity=0.001 Sum_probs=17.8
Q ss_pred HHHHHHHHHhhcc-cccccccc
Q psy5244 14 ELQQSVRLSSCGP-STKDTKTK 34 (90)
Q Consensus 14 gFedsVR~fi~~v-~Tfq~I~~ 34 (90)
+|||+||.-|.++ -|-.+|.-
T Consensus 15 S~edAv~~Av~~A~kTl~ni~~ 36 (66)
T PF07311_consen 15 SWEDAVQNAVARASKTLRNIRW 36 (66)
T ss_dssp HHHHHHHHHHHHHHHHSSSEEE
T ss_pred CHHHHHHHHHHHHhhchhCcEE
Confidence 9999999999998 77776654
No 50
>PRK04351 hypothetical protein; Provisional
Probab=27.43 E-value=83 Score=22.30 Aligned_cols=45 Identities=20% Similarity=0.180 Sum_probs=32.4
Q ss_pred HHhHHHhhh----HHHHHHHHHhhccccccccccCCC-ChHHHHHHHHHhC
Q psy5244 5 KSLQKACQG----ELQQSVRLSSCGPSTKDTKTKADQ-TDSTLRLWVKKYG 50 (90)
Q Consensus 5 ~~~~~l~~~----gFedsVR~fi~~v~Tfq~I~~~~l-~d~~L~~~i~~~g 50 (90)
+=+|.+++. -|.+-|+.=+||...|+. .++-- -|.+.+.|+++.|
T Consensus 47 ~lnp~ll~~~~~~~l~~vv~HElcH~~~~~~-g~g~~h~g~~fk~~~~~v~ 96 (149)
T PRK04351 47 EFNPKMLEEYGLEELIGIIKHELCHYHLHLE-GKGYQHRDRDFKELLKQVG 96 (149)
T ss_pred EeCHHHHhhccHHHHHhhHHHHHHHHHHHHH-CCCCCCCCHHHHHHHHHhC
Confidence 336777764 677777888888877875 55333 4689999999975
No 51
>COG0718 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.28 E-value=30 Score=23.57 Aligned_cols=35 Identities=14% Similarity=0.243 Sum_probs=27.5
Q ss_pred CCe-EEEecCCCCcccccceeeee----ccchHHHHhhcc
Q psy5244 55 DNG-YIFIANQDENIKTKNITEKI----EFENAATIMTSN 89 (90)
Q Consensus 55 ~~g-~i~~~N~dn~iKtk~I~EkI----~fe~~~~ima~s 89 (90)
++| |-+..|.+.++++..|.+.+ |.|.|..++.++
T Consensus 38 ggGlVtV~~~G~~ev~~v~Idp~l~dpeD~E~LeDLi~aA 77 (105)
T COG0718 38 GGGLVTVTINGKGEVKSVEIDPSLLDPEDKEMLEDLILAA 77 (105)
T ss_pred CCcEEEEEEeCCCcEEEEEeCHHHcCcccHHHHHHHHHHH
Confidence 455 55999999999999988765 578888888654
No 52
>PF08854 DUF1824: Domain of unknown function (DUF1824); InterPro: IPR014953 This uncharacterised group of proteins are principally found in cyanobacteria. ; PDB: 2Q22_B.
Probab=26.81 E-value=73 Score=22.30 Aligned_cols=49 Identities=20% Similarity=0.158 Sum_probs=27.9
Q ss_pred HHHHHHhhcc---cccccccc--CCCCh--HHHHHHHHHhCceE-------cCCe-EEEecCCC
Q psy5244 17 QSVRLSSCGP---STKDTKTK--ADQTD--STLRLWVKKYGWKE-------LDNG-YIFIANQD 65 (90)
Q Consensus 17 dsVR~fi~~v---~Tfq~I~~--~~l~d--~~L~~~i~~~gW~~-------~~~g-~i~~~N~d 65 (90)
..+|.-+... +.|++|.. -.... .+|+.|.+++||.. ..+| |.+=.||.
T Consensus 22 ~~Lr~~L~~~~~~sd~~~lGIcA~s~~~ai~ALr~~~~alg~~~~~~~~~~~~~GpVfLK~N~~ 85 (125)
T PF08854_consen 22 KKLRQALRLLASNSDWFTLGICAPSAEEAIAALRSYEQALGYPPLEPLDSPPIEGPVFLKANQK 85 (125)
T ss_dssp HHHHHHHHHHHHTSSEEEEEEEESSHHHHHHHHHHHHHHTT------------SSSEEEEEETT
T ss_pred HHHHHHHHHHHhccCceEEEeecCCHHHHHHHHHHHHHHcCCCccCCCCCCCCCCCEEEEecCC
Confidence 3455555444 77888877 22222 45999999999998 2334 55666763
No 53
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=26.39 E-value=1.1e+02 Score=17.37 Aligned_cols=19 Identities=11% Similarity=0.027 Sum_probs=14.4
Q ss_pred CCCChHHHHHHHHHhCceE
Q psy5244 35 ADQTDSTLRLWVKKYGWKE 53 (90)
Q Consensus 35 ~~l~d~~L~~~i~~~gW~~ 53 (90)
-|++-++...+++++||+.
T Consensus 7 ~g~~~~~a~~~l~~~g~~~ 25 (63)
T PF03793_consen 7 VGMTYDEAKSILEAAGLTV 25 (63)
T ss_dssp TTSBHHHHHHHHHHTT-EE
T ss_pred CCCcHHHHHHHHHHCCCEE
Confidence 3567788899999999954
No 54
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=26.11 E-value=30 Score=17.44 Aligned_cols=22 Identities=18% Similarity=0.049 Sum_probs=14.0
Q ss_pred cccccc---CCCChHHHHHHHH-HhC
Q psy5244 29 KDTKTK---ADQTDSTLRLWVK-KYG 50 (90)
Q Consensus 29 fq~I~~---~~l~d~~L~~~i~-~~g 50 (90)
|..+++ |-++.++|..+++ +.|
T Consensus 6 F~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 6 FKMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred HHHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 444555 6667788888887 455
No 55
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=26.02 E-value=79 Score=21.39 Aligned_cols=27 Identities=15% Similarity=0.092 Sum_probs=19.6
Q ss_pred cccccccc--CCCChHHHHHHHHHhC--ceE
Q psy5244 27 STKDTKTK--ADQTDSTLRLWVKKYG--WKE 53 (90)
Q Consensus 27 ~Tfq~I~~--~~l~d~~L~~~i~~~g--W~~ 53 (90)
+.|+-++- =.++.++|.+|+++.| |..
T Consensus 26 i~~~~~~y~~~~~s~~eL~~~l~~~g~~~~~ 56 (117)
T COG1393 26 IEYTFIDYLKTPPSREELKKILSKLGDGVEE 56 (117)
T ss_pred CCcEEEEeecCCCCHHHHHHHHHHcCccHHH
Confidence 66666555 5778888888888877 654
No 56
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=25.47 E-value=1.1e+02 Score=18.34 Aligned_cols=15 Identities=27% Similarity=0.578 Sum_probs=11.6
Q ss_pred CCChHHHHHHHHHhC
Q psy5244 36 DQTDSTLRLWVKKYG 50 (90)
Q Consensus 36 ~l~d~~L~~~i~~~g 50 (90)
-++...|++|+.++|
T Consensus 44 ~~~~~~l~~~lD~~g 58 (64)
T PF09494_consen 44 KVDPSKLKEWLDSQG 58 (64)
T ss_pred eeCHHHHHHHHHHCC
Confidence 357788899988876
No 57
>KOG0027|consensus
Probab=24.98 E-value=40 Score=22.80 Aligned_cols=52 Identities=19% Similarity=0.158 Sum_probs=37.1
Q ss_pred ccccccc---CCCChHHHHHHHHHhCceEcCCe-----EEEecCCCCcccccceeeeeccchHHHHhhc
Q psy5244 28 TKDTKTK---ADQTDSTLRLWVKKYGWKELDNG-----YIFIANQDENIKTKNITEKIEFENAATIMTS 88 (90)
Q Consensus 28 Tfq~I~~---~~l~d~~L~~~i~~~gW~~~~~g-----~i~~~N~dn~iKtk~I~EkI~fe~~~~ima~ 88 (90)
+|+-.++ |-++-++|+..+...|.+....- -.+..|.|+.| +|+.+.++|..
T Consensus 90 aF~~fD~d~~G~Is~~el~~~l~~lg~~~~~~e~~~mi~~~d~d~dg~i---------~f~ef~~~m~~ 149 (151)
T KOG0027|consen 90 AFRVFDKDGDGFISASELKKVLTSLGEKLTDEECKEMIREVDVDGDGKV---------NFEEFVKMMSG 149 (151)
T ss_pred HHHHHccCCCCcCcHHHHHHHHHHhCCcCCHHHHHHHHHhcCCCCCCeE---------eHHHHHHHHhc
Confidence 4555555 77899999999999999975322 12455666666 78888888764
No 58
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=24.83 E-value=61 Score=18.91 Aligned_cols=18 Identities=28% Similarity=0.748 Sum_probs=9.7
Q ss_pred CCCChHHH---HHHHHHhCce
Q psy5244 35 ADQTDSTL---RLWVKKYGWK 52 (90)
Q Consensus 35 ~~l~d~~L---~~~i~~~gW~ 52 (90)
..+++++| +.|+.+.||-
T Consensus 22 ~~~s~~~L~k~~~wld~rgWw 42 (45)
T PF12123_consen 22 DPLSDAELDKFTAWLDERGWW 42 (45)
T ss_dssp ----HHHHHHHHHHHHHTT--
T ss_pred CCCCHHHHHHHHHHHHhcCcE
Confidence 67888875 5789999995
No 59
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=24.82 E-value=48 Score=20.76 Aligned_cols=23 Identities=26% Similarity=0.211 Sum_probs=18.1
Q ss_pred cccccccc-CCCChHHHHHHHHHh
Q psy5244 27 STKDTKTK-ADQTDSTLRLWVKKY 49 (90)
Q Consensus 27 ~Tfq~I~~-~~l~d~~L~~~i~~~ 49 (90)
.+|..|.. +++++..|..-+++.
T Consensus 15 ~~f~~L~~~l~lt~g~Ls~hL~~L 38 (80)
T PF13601_consen 15 ATFSELKEELGLTDGNLSKHLKKL 38 (80)
T ss_dssp EEHHHHHHHTT--HHHHHHHHHHH
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHH
Confidence 88999988 999999999888754
No 60
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=24.26 E-value=48 Score=22.19 Aligned_cols=21 Identities=24% Similarity=0.398 Sum_probs=16.7
Q ss_pred CCCChHHHHHHHH-----HhCceEcC
Q psy5244 35 ADQTDSTLRLWVK-----KYGWKELD 55 (90)
Q Consensus 35 ~~l~d~~L~~~i~-----~~gW~~~~ 55 (90)
-|++.++|.+|+. ..||+.++
T Consensus 6 VNMt~~EL~~WL~t~~S~~~g~~~~~ 31 (92)
T PF11338_consen 6 VNMTPAELEDWLRTDESKSVGEKKDG 31 (92)
T ss_pred hCCCHHHHHHHHcCccccccccCCCC
Confidence 3789999999994 45999863
No 61
>TIGR03862 flavo_PP4765 uncharacterized flavoprotein, PP_4765 family. This model describes a sharply distinctive clade of proteins within the larger family of flavoproteins described by Pfam model pfam03486 and TIGRFAMs model TIGR00275. The function is unknown.
Probab=23.57 E-value=87 Score=25.28 Aligned_cols=25 Identities=20% Similarity=0.322 Sum_probs=19.5
Q ss_pred ChHHHHHHHHHhC--ceEcCCeEEEec
Q psy5244 38 TDSTLRLWVKKYG--WKELDNGYIFIA 62 (90)
Q Consensus 38 ~d~~L~~~i~~~g--W~~~~~g~i~~~ 62 (90)
+-.++.+|.+++| |+.+++|.+||.
T Consensus 55 ~~~d~~~fF~~~Gi~~~~e~~grvfP~ 81 (376)
T TIGR03862 55 DAVALQDWARGLGIETFVGSSGRVFPV 81 (376)
T ss_pred CHHHHHHHHHHCCCceEECCCCEECCC
Confidence 4567889999986 577778889983
No 62
>PF01890 CbiG_C: Cobalamin synthesis G C-terminus; InterPro: IPR002750 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CbiG proteins are specific for anaerobic cobalamin biosynthesis. CbiG, which shows homology with CobE of the aerobic pathway, participates in the conversion of cobalt-precorrin 5 into cobalt-precorrin 6 []. CbiG is responsible for the opening of the delta-lactone ring and extrusion of the C2-unit []. The aerobic pathway uses molecular oxygen to trigger the events at C-20 leading to contraction and expulsion of the C2-unit as acetic acid from a metal-free intermediate, whereas the anaerobic route involves the internal delivery of oxygen from a carboxylic acid terminus to C-20 followed by extrusion of the C2-unit as acetaldehyde, using cobalt complexes as substrates []. This entry represents the core domain of CibG.; GO: 0009236 cobalamin biosynthetic process; PDB: 3BY5_A 2W6K_A 2W6L_A 3EEQ_B.
Probab=23.42 E-value=1.5e+02 Score=19.98 Aligned_cols=40 Identities=10% Similarity=0.136 Sum_probs=28.8
Q ss_pred HHHHHHHHHhhcc-cccccccc---CCC--ChHHHHHHHHHhCceE
Q psy5244 14 ELQQSVRLSSCGP-STKDTKTK---ADQ--TDSTLRLWVKKYGWKE 53 (90)
Q Consensus 14 gFedsVR~fi~~v-~Tfq~I~~---~~l--~d~~L~~~i~~~gW~~ 53 (90)
.++++|+.+.... ....+|.. .++ ++.-|.++.+++||-.
T Consensus 16 ~i~~ai~~~l~~~~~~~~~i~~iasi~~K~~E~~l~~~A~~l~~~~ 61 (121)
T PF01890_consen 16 EIEEAIEQALAEAGLSPRSIAAIASIDIKADEPGLLELAEELGIPL 61 (121)
T ss_dssp HHHHHHHHHHHHCT--GGGEEEEEESSSSS--HHHHHHHHHCTSEE
T ss_pred HHHHHHHHHHHHcCCChhhccEEEeccccCCCHHHHHHHHHhCCCe
Confidence 6777888887777 77777777 444 6678999999999875
No 63
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=23.24 E-value=84 Score=18.50 Aligned_cols=28 Identities=11% Similarity=0.242 Sum_probs=21.4
Q ss_pred cccccccc---CCCChHHHHHHHHHhCceEc
Q psy5244 27 STKDTKTK---ADQTDSTLRLWVKKYGWKEL 54 (90)
Q Consensus 27 ~Tfq~I~~---~~l~d~~L~~~i~~~gW~~~ 54 (90)
.++..+.+ ..++++++...+++.|...+
T Consensus 6 ~~~~~i~~llG~~i~~~ei~~~L~~lg~~~~ 36 (71)
T smart00874 6 LRRERINRLLGLDLSAEEIEEILKRLGFEVE 36 (71)
T ss_pred ecHHHHHHHHCCCCCHHHHHHHHHHCCCeEE
Confidence 34455555 46788999999999999875
No 64
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=23.01 E-value=51 Score=18.34 Aligned_cols=22 Identities=9% Similarity=0.170 Sum_probs=16.7
Q ss_pred cccccccc-CCCChHHHHHHHHH
Q psy5244 27 STKDTKTK-ADQTDSTLRLWVKK 48 (90)
Q Consensus 27 ~Tfq~I~~-~~l~d~~L~~~i~~ 48 (90)
.||..|.. +|++.+.++.++.+
T Consensus 27 ~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 27 MSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp --HHHHHHHCTS-HHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHH
Confidence 78888888 99999999998864
No 65
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=22.85 E-value=75 Score=18.38 Aligned_cols=18 Identities=33% Similarity=0.512 Sum_probs=15.5
Q ss_pred CCChHHHHHHHHHhCceE
Q psy5244 36 DQTDSTLRLWVKKYGWKE 53 (90)
Q Consensus 36 ~l~d~~L~~~i~~~gW~~ 53 (90)
.|+|++|.+=+.+||-..
T Consensus 5 ~LSd~eL~~~L~~~G~~~ 22 (44)
T smart00540 5 RLSDAELRAELKQYGLPP 22 (44)
T ss_pred HcCHHHHHHHHHHcCCCC
Confidence 579999999999999763
No 66
>PF10652 DUF2480: Protein of unknown function (DUF2480); InterPro: IPR018914 All the members of this family are uncharacterised proteins, but the environment in which they are found on the bacterial genome suggests a function as a glucose-6-phosphate isomerase (5.3.1.9 from EC). This could not, however, be confirmed.
Probab=22.35 E-value=94 Score=22.99 Aligned_cols=50 Identities=14% Similarity=0.303 Sum_probs=34.2
Q ss_pred HHHHHHHhhcc--cccccccc------------------CCCChHHHHHHHHHhCceEcCCeEE-EecCCC
Q psy5244 16 QQSVRLSSCGP--STKDTKTK------------------ADQTDSTLRLWVKKYGWKELDNGYI-FIANQD 65 (90)
Q Consensus 16 edsVR~fi~~v--~Tfq~I~~------------------~~l~d~~L~~~i~~~gW~~~~~g~i-~~~N~d 65 (90)
+|.|.+-+|.+ +||.=-+- +-|-+.++++.++.+.|+.=.|..| +-+.-|
T Consensus 2 ~eeIvNkVA~S~LitfDLedyyp~g~r~~~Dik~~L~~GliLkEKdFR~~lk~~DWsqY~~~~Vai~CStD 72 (167)
T PF10652_consen 2 EEEIVNKVANSGLITFDLEDYYPKGERVVFDIKDWLFEGLILKEKDFREFLKEHDWSQYQDKYVAIYCSTD 72 (167)
T ss_pred chHHHHHHhccCceEeeHHHhCCCCcEEEEecHHHHhhhhhhhhHHHHHHHHhcCHHHhCCcEEEEEcccc
Confidence 35677777777 66643221 5568899999999999998766655 444433
No 67
>TIGR00027 mthyl_TIGR00027 methyltransferase, putative, TIGR00027 family. This model represents a set of probable methyltransferases, about 300 amino acids long, with essentially full length homology. Members share an N-terminal region described by Pfam model pfam02409. Included are a paralogous family of 12 proteins in Mycobacterium tuberculosis, plus close homologs in related species, a family of 8 in the archaeon Methanosarcina acetivorans, and small numbers of members in other species, including plants.
Probab=22.28 E-value=82 Score=23.79 Aligned_cols=21 Identities=14% Similarity=0.544 Sum_probs=17.9
Q ss_pred CCCChHHHHHHHHHhCceEcC
Q psy5244 35 ADQTDSTLRLWVKKYGWKELD 55 (90)
Q Consensus 35 ~~l~d~~L~~~i~~~gW~~~~ 55 (90)
.+.+.+++..|+..+||....
T Consensus 227 ~~~~~~~~~~~l~~~Gw~~~~ 247 (260)
T TIGR00027 227 FGIDRADVAEWLAERGWRASE 247 (260)
T ss_pred cCCChhhHHHHHHHCCCeeec
Confidence 567788999999999999754
No 68
>PF11761 CbiG_mid: Cobalamin biosynthesis central region; InterPro: IPR021745 Members of this family are involved in cobalamin synthesis. The gene encoded by P72862 from SWISSPROT has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process [].
Probab=21.86 E-value=44 Score=20.38 Aligned_cols=14 Identities=21% Similarity=0.653 Sum_probs=11.5
Q ss_pred HHHHHHHHhCceEc
Q psy5244 41 TLRLWVKKYGWKEL 54 (90)
Q Consensus 41 ~L~~~i~~~gW~~~ 54 (90)
+|+.|.+++||..+
T Consensus 3 AvD~la~~~g~~i~ 16 (93)
T PF11761_consen 3 AVDLLARELGWRIE 16 (93)
T ss_pred CcchhhhhCCCEEc
Confidence 46788999999973
No 69
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=21.66 E-value=82 Score=23.02 Aligned_cols=30 Identities=17% Similarity=0.276 Sum_probs=20.9
Q ss_pred CCCChHH---HHHHHH---HhCceEcCCeEEEecCC
Q psy5244 35 ADQTDST---LRLWVK---KYGWKELDNGYIFIANQ 64 (90)
Q Consensus 35 ~~l~d~~---L~~~i~---~~gW~~~~~g~i~~~N~ 64 (90)
+||++.+ |+..+. ...|+..+.-+|||.|.
T Consensus 39 lgl~~~~l~vL~aLls~~~~~d~~~~~~piVfpSN~ 74 (177)
T PF03428_consen 39 LGLSDRALAVLDALLSFTPPDDWEPGRRPIVFPSNA 74 (177)
T ss_pred cCCChhHHHHHHHHHHhCCcccccCCCCceeecCHH
Confidence 8998866 455554 34886555558999995
No 70
>PRK14622 hypothetical protein; Provisional
Probab=21.45 E-value=38 Score=22.63 Aligned_cols=35 Identities=11% Similarity=0.134 Sum_probs=27.3
Q ss_pred CCe-EEEecCCCCcccccceeeee----ccchHHHHhhcc
Q psy5244 55 DNG-YIFIANQDENIKTKNITEKI----EFENAATIMTSN 89 (90)
Q Consensus 55 ~~g-~i~~~N~dn~iKtk~I~EkI----~fe~~~~ima~s 89 (90)
++| |-+..|-+..++.-.|...+ |.+.|..++.++
T Consensus 34 ggG~VkV~~nG~~~v~~i~Idp~~l~~ed~e~LeDLI~aA 73 (103)
T PRK14622 34 GGGLVKVAMNGKCEVTRLTVDPKAVDPNDKAMLEDLVTAA 73 (103)
T ss_pred CCceEEEEEEcCceEEEEEECHHHcCcccHHHHHHHHHHH
Confidence 455 55999999999999987665 678888887554
No 71
>PHA02535 P terminase ATPase subunit; Provisional
Probab=21.16 E-value=41 Score=29.13 Aligned_cols=28 Identities=21% Similarity=0.474 Sum_probs=23.6
Q ss_pred cccccccc-CCCChHHHHHHHHHhCceEc
Q psy5244 27 STKDTKTK-ADQTDSTLRLWVKKYGWKEL 54 (90)
Q Consensus 27 ~Tfq~I~~-~~l~d~~L~~~i~~~gW~~~ 54 (90)
-|...|.+ +|++...|..|+++++|-..
T Consensus 19 ~sv~eIA~~LGv~~~Tl~~W~kr~~w~~~ 47 (581)
T PHA02535 19 WTVAEIAEELGLKSRTIYSWKERDGWRDL 47 (581)
T ss_pred CCHHHHHHHhCCChhHHHHHhcccccccc
Confidence 45556666 99999999999999999874
No 72
>PHA00435 capsid assembly protein
Probab=21.02 E-value=2e+02 Score=23.14 Aligned_cols=39 Identities=13% Similarity=0.140 Sum_probs=28.9
Q ss_pred HHHHHHHHHhhcccccccccc--------CCCChHHHHHHHHHhCceE
Q psy5244 14 ELQQSVRLSSCGPSTKDTKTK--------ADQTDSTLRLWVKKYGWKE 53 (90)
Q Consensus 14 gFedsVR~fi~~v~Tfq~I~~--------~~l~d~~L~~~i~~~gW~~ 53 (90)
||.+.|-.-+.+=.++-+|.+ |+||+....++ .+.||+.
T Consensus 125 gf~~mv~~Ave~Glsae~i~~i~aEY~~~g~LSeeSY~~L-a~AGysR 171 (306)
T PHA00435 125 GFQAMVEQAVERGLSAETITRIQAEYEEEGGLSEESYAEL-AAAGYSK 171 (306)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCcCHHHHHHH-HHcCCcH
Confidence 999988877766666666644 99999877764 4578885
No 73
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.99 E-value=1.1e+02 Score=19.74 Aligned_cols=23 Identities=13% Similarity=0.199 Sum_probs=19.3
Q ss_pred cccccccc-CCC-ChHHHHHHHHHh
Q psy5244 27 STKDTKTK-ADQ-TDSTLRLWVKKY 49 (90)
Q Consensus 27 ~Tfq~I~~-~~l-~d~~L~~~i~~~ 49 (90)
.|+..|.+ +|+ +...|..|++++
T Consensus 25 ~sv~~vAr~~gv~~~~~l~~W~~~~ 49 (116)
T COG2963 25 DTVSEVAREFGIVSATQLYKWRIQL 49 (116)
T ss_pred ccHHHHHHHhCCCChHHHHHHHHHH
Confidence 66777777 996 999999999876
No 74
>KOG2758|consensus
Probab=20.79 E-value=1.3e+02 Score=25.10 Aligned_cols=44 Identities=11% Similarity=0.185 Sum_probs=30.9
Q ss_pred hHHhHHHhhh---------HHHHHHHHHhhcc--cccccccc------CCCChHHHHHHHH
Q psy5244 4 VKSLQKACQG---------ELQQSVRLSSCGP--STKDTKTK------ADQTDSTLRLWVK 47 (90)
Q Consensus 4 ~~~~~~l~~~---------gFedsVR~fi~~v--~Tfq~I~~------~~l~d~~L~~~i~ 47 (90)
+++|.+.+.. .|-+..|.+|.-. ---|.|+. |++++++-+.|+-
T Consensus 311 l~eCeeVl~nDfFLva~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~~eeaErwiv 371 (432)
T KOG2758|consen 311 LRECEEVLVNDFFLVALLDEFLENARLLIFETFCRIHQCITIDMLADKLNMDPEEAERWIV 371 (432)
T ss_pred HHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCCHHHHHHHHH
Confidence 5555555443 8999999998655 22344444 9999999999993
No 75
>PF05555 DUF762: Coxiella burnetii protein of unknown function (DUF762); InterPro: IPR008481 This family consists several of several uncharacterised proteins from the bacterium Coxiella burnetii. C. burnetii is the causative agent of the Q fever disease.
Probab=20.73 E-value=97 Score=24.09 Aligned_cols=39 Identities=15% Similarity=0.427 Sum_probs=26.1
Q ss_pred ccccccccCCCChHHHHHHHHHhCceEcCCeEEEecCCCCc
Q psy5244 27 STKDTKTKADQTDSTLRLWVKKYGWKELDNGYIFIANQDEN 67 (90)
Q Consensus 27 ~Tfq~I~~~~l~d~~L~~~i~~~gW~~~~~g~i~~~N~dn~ 67 (90)
+-||.++--.-.+..|+.|.+-.. ..++.-+|++|++++
T Consensus 10 ID~q~~~nSq~~E~tLqEWlRgan--~~E~A~vFI~s~~~~ 48 (248)
T PF05555_consen 10 IDMQDRSNSQCPEQTLQEWLRGAN--NQEDANVFIASSSKE 48 (248)
T ss_pred cchhhhhccCCHHHHHHHHHhccC--CccceeEEEecCccc
Confidence 667777653334677999997652 223456899998765
No 76
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=20.35 E-value=1.1e+02 Score=18.52 Aligned_cols=22 Identities=0% Similarity=-0.023 Sum_probs=16.7
Q ss_pred cccccccc------CCCChHHHHHHHHH
Q psy5244 27 STKDTKTK------ADQTDSTLRLWVKK 48 (90)
Q Consensus 27 ~Tfq~I~~------~~l~d~~L~~~i~~ 48 (90)
.+|++|+- ++++..+++.|+.+
T Consensus 56 ~~y~~i~~~~ia~~l~~~~~~vE~~l~~ 83 (105)
T PF01399_consen 56 KPYSSISISEIAKALQLSEEEVESILID 83 (105)
T ss_dssp HC-SEEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred HHhcccchHHHHHHhccchHHHHHHHHH
Confidence 56666665 99999999999965
No 77
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=20.31 E-value=56 Score=19.66 Aligned_cols=12 Identities=25% Similarity=0.598 Sum_probs=9.6
Q ss_pred ChHHHHHHHHHh
Q psy5244 38 TDSTLRLWVKKY 49 (90)
Q Consensus 38 ~d~~L~~~i~~~ 49 (90)
.|++|++||..|
T Consensus 7 ~dpELDqFMeaY 18 (52)
T PF03791_consen 7 ADPELDQFMEAY 18 (52)
T ss_pred CCccHHHHHHHH
Confidence 567899999776
No 78
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=20.26 E-value=1e+02 Score=19.05 Aligned_cols=38 Identities=13% Similarity=-0.011 Sum_probs=29.7
Q ss_pred HHHHHHHHhhcc-----cccccccc-CCCC--hHHHHHHHHHhCce
Q psy5244 15 LQQSVRLSSCGP-----STKDTKTK-ADQT--DSTLRLWVKKYGWK 52 (90)
Q Consensus 15 FedsVR~fi~~v-----~Tfq~I~~-~~l~--d~~L~~~i~~~gW~ 52 (90)
|.+.|...++.+ +||..|-+ +|.. --++...|+++...
T Consensus 1 ~~~~V~~~v~~IP~G~v~TYg~iA~~~g~p~~~R~Vg~al~~np~~ 46 (79)
T cd06445 1 FQRRVWEALRQIPYGEVTTYGQIAKLAGTPKAARAVGSALARNPIP 46 (79)
T ss_pred CHHHHHHHHhcCCCCCcCcHHHHHHHHCCCCcHHHHHHHHHhCCCC
Confidence 567788888877 99999999 7774 45688888888654
No 79
>PF12936 Kri1_C: KRI1-like family C-terminal; InterPro: IPR024626 The yeast member of the Kri1-like family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus []. This entry represents the C-terminal domain of this protein family.
Probab=20.20 E-value=63 Score=21.44 Aligned_cols=32 Identities=13% Similarity=0.130 Sum_probs=20.0
Q ss_pred HHHHHHHH-Hhhcccccccccc----------CCCChHHHHHHH
Q psy5244 14 ELQQSVRL-SSCGPSTKDTKTK----------ADQTDSTLRLWV 46 (90)
Q Consensus 14 gFedsVR~-fi~~v~Tfq~I~~----------~~l~d~~L~~~i 46 (90)
.|||.|-. -=|+ =-|+.++. |..+|.+|++||
T Consensus 16 d~Ed~igd~~p~R-FkYr~V~p~~fGLt~~eIL~adDkeLNq~v 58 (93)
T PF12936_consen 16 DYEDIIGDDMPTR-FKYREVPPNSFGLTTEEILMADDKELNQWV 58 (93)
T ss_pred cHHHHcCCCCCCc-eeeeecCcccCCCCHHHHHhCCHHHHHHHh
Confidence 88888733 1111 22333333 777899999999
No 80
>KOG1348|consensus
Probab=20.18 E-value=54 Score=27.62 Aligned_cols=33 Identities=24% Similarity=0.258 Sum_probs=22.7
Q ss_pred ccccccccCCCChHHHHHHHHHhCceEcCCeEEE----ecCCCCccccccee
Q psy5244 27 STKDTKTKADQTDSTLRLWVKKYGWKELDNGYIF----IANQDENIKTKNIT 74 (90)
Q Consensus 27 ~Tfq~I~~~~l~d~~L~~~i~~~gW~~~~~g~i~----~~N~dn~iKtk~I~ 74 (90)
.+||.+.+|||.++ |.++| |+|.+++..+..|-
T Consensus 68 HAYqiLrkgGikeE---------------nIvv~MYDDIA~~~~NPrpG~ii 104 (477)
T KOG1348|consen 68 HAYQILRKGGIKEE---------------NIVVMMYDDIANNEENPRPGVII 104 (477)
T ss_pred HHHHHHHhcCCCch---------------hEEEEEehhhhcCCCCCCCceee
Confidence 45776666666554 66666 78888888877653
Done!