Query psy8036
Match_columns 194
No_of_seqs 141 out of 737
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 16:47:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8036.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8036hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK03822 lplA lipoate-protein 100.0 1.5E-35 3.2E-40 256.2 11.9 164 1-192 162-331 (338)
2 PRK14061 unknown domain/lipoat 100.0 9.7E-34 2.1E-38 256.2 11.7 150 1-177 386-541 (562)
3 TIGR00545 lipoyltrans lipoyltr 100.0 3.5E-33 7.5E-38 240.4 12.0 158 1-188 160-323 (324)
4 PF10437 Lip_prot_lig_C: Bacte 99.8 4.4E-18 9.4E-23 120.0 9.5 80 98-192 1-84 (86)
5 KOG3159|consensus 99.7 4E-17 8.7E-22 136.6 4.8 148 1-174 169-319 (336)
6 COG0095 LplA Lipoate-protein l 99.3 3.2E-13 7E-18 112.6 2.5 83 1-98 165-248 (248)
7 PF03450 CO_deh_flav_C: CO deh 89.3 2.9 6.3E-05 29.6 7.5 55 119-176 17-72 (103)
8 cd06664 IscU_like Iron-sulfur 85.5 10 0.00022 27.7 8.7 67 95-173 15-85 (123)
9 TIGR01994 SUF_scaf_2 SUF syste 84.3 3.3 7.1E-05 31.4 5.6 67 87-164 11-81 (137)
10 TIGR03419 NifU_clost FeS clust 78.1 7.9 0.00017 28.6 5.7 61 95-165 14-78 (121)
11 PF01592 NifU_N: NifU-like N t 70.1 13 0.00028 27.5 5.2 69 87-166 8-83 (126)
12 TIGR01999 iscU FeS cluster ass 64.4 22 0.00049 26.2 5.5 41 118-165 37-82 (124)
13 TIGR02963 xanthine_xdhA xanthi 62.6 34 0.00075 31.2 7.4 52 122-176 385-436 (467)
14 TIGR01352 tonB_Cterm TonB fami 62.4 21 0.00046 23.0 4.6 21 118-138 10-31 (74)
15 PF03544 TonB_C: Gram-negative 61.5 17 0.00037 23.8 4.0 22 118-139 16-38 (79)
16 PRK09971 xanthine dehydrogenas 60.5 45 0.00098 28.3 7.4 53 121-176 200-252 (291)
17 TIGR03853 matur_matur probable 58.2 19 0.00042 24.7 3.8 40 153-192 6-52 (77)
18 PRK11325 scaffold protein; Pro 56.2 38 0.00082 25.2 5.5 40 118-164 39-83 (127)
19 TIGR03199 pucC xanthine dehydr 55.8 62 0.0013 27.0 7.3 52 122-176 186-238 (264)
20 COG3976 Uncharacterized protei 55.6 22 0.00047 26.8 4.0 21 118-138 62-82 (135)
21 TIGR02000 NifU_proper Fe-S clu 55.0 55 0.0012 28.0 7.0 41 95-138 17-59 (290)
22 smart00089 PKD Repeats in poly 54.8 19 0.00041 23.6 3.4 37 89-129 29-66 (79)
23 PRK10819 transport protein Ton 54.7 25 0.00055 29.4 4.7 43 118-165 181-224 (246)
24 PF04205 FMN_bind: FMN-binding 51.5 30 0.00064 23.0 4.0 21 118-138 4-25 (81)
25 COG4630 XdhA Xanthine dehydrog 50.2 38 0.00082 30.5 5.2 50 121-177 395-448 (493)
26 PRK11251 DNA-binding transcrip 49.5 15 0.00033 26.9 2.3 16 89-104 63-78 (109)
27 PF00801 PKD: PKD domain; Int 49.4 17 0.00037 23.5 2.4 37 88-129 24-63 (69)
28 PF10678 DUF2492: Protein of u 48.9 33 0.00072 23.6 3.8 41 152-192 7-54 (78)
29 PF02593 dTMP_synthase: Thymid 44.2 58 0.0013 26.8 5.2 47 118-170 131-177 (217)
30 PF08479 POTRA_2: POTRA domain 42.5 78 0.0017 20.8 4.9 43 130-176 2-44 (76)
31 PF07499 RuvA_C: RuvA, C-termi 41.7 39 0.00085 20.4 3.0 37 152-192 4-40 (47)
32 COG0822 IscU NifU homolog invo 39.4 49 0.0011 25.5 3.9 41 118-165 41-85 (150)
33 PRK14342 lipoate-protein ligas 38.7 29 0.00062 28.5 2.6 30 22-51 174-203 (213)
34 PF11006 DUF2845: Protein of u 37.9 57 0.0012 22.5 3.7 14 123-136 72-85 (87)
35 COG3811 Uncharacterized protei 37.5 53 0.0011 22.6 3.3 45 118-164 18-69 (85)
36 PRK14349 lipoate-protein ligas 35.9 35 0.00076 28.1 2.7 30 22-51 175-204 (220)
37 TIGR02969 mam_aldehyde_ox alde 35.4 1.1E+02 0.0024 31.8 6.7 53 122-177 441-495 (1330)
38 PF13103 TonB_2: TonB C termin 35.1 82 0.0018 20.9 4.1 24 118-141 26-50 (85)
39 TIGR03195 4hydrxCoA_B 4-hydrox 34.4 1.9E+02 0.0041 25.1 7.1 54 119-176 235-288 (321)
40 COG1433 Uncharacterized conser 34.2 48 0.001 24.7 3.0 25 95-138 19-43 (121)
41 cd00146 PKD polycystic kidney 33.1 65 0.0014 21.1 3.3 36 90-129 30-68 (81)
42 PF07244 Surf_Ag_VNR: Surface 31.6 1.4E+02 0.003 19.1 4.7 39 130-176 2-45 (78)
43 COG2831 FhaC Hemolysin activat 31.0 1.2E+02 0.0027 28.3 5.8 53 118-176 139-191 (554)
44 PRK14343 lipoate-protein ligas 30.3 44 0.00095 27.8 2.4 29 23-51 190-218 (235)
45 PF00374 NiFeSe_Hases: Nickel- 28.4 1.1E+02 0.0025 28.3 5.0 47 118-164 435-483 (507)
46 TIGR03303 OM_YaeT outer membra 26.6 2.3E+02 0.005 26.7 6.9 51 118-175 136-201 (741)
47 PF02845 CUE: CUE domain; Int 26.1 39 0.00085 19.8 1.1 23 23-45 4-26 (42)
48 PRK10170 hydrogenase 1 large s 26.0 93 0.002 29.5 4.0 46 118-163 510-557 (597)
49 COG0810 TonB Periplasmic prote 25.0 1.2E+02 0.0027 24.8 4.3 24 118-141 180-204 (244)
50 PRK13687 hypothetical protein; 24.8 1.3E+02 0.0028 20.9 3.6 45 118-164 18-69 (85)
51 PF10055 DUF2292: Uncharacteri 23.7 1.4E+02 0.0031 17.5 3.2 15 122-136 18-32 (38)
52 COG0321 LipB Lipoate-protein l 22.6 80 0.0017 26.0 2.6 29 22-50 181-209 (221)
53 TIGR03303 OM_YaeT outer membra 22.2 3.3E+02 0.0071 25.7 7.0 48 121-175 60-112 (741)
54 PF14814 UB2H: Bifunctional tr 21.5 1.5E+02 0.0033 20.2 3.5 31 104-136 43-73 (85)
55 PRK10467 hydrogenase 2 large s 21.2 1.5E+02 0.0032 28.0 4.4 21 118-138 15-35 (567)
56 COG3938 Proline racemase [Amin 20.5 1.9E+02 0.0042 25.2 4.5 21 118-138 124-144 (341)
57 PF11888 DUF3408: Protein of u 20.2 80 0.0017 23.7 2.0 32 19-50 88-121 (136)
No 1
>PRK03822 lplA lipoate-protein ligase A; Provisional
Probab=100.00 E-value=1.5e-35 Score=256.17 Aligned_cols=164 Identities=19% Similarity=0.266 Sum_probs=139.6
Q ss_pred CccccCCCccccccccccccccccccccccCCCCCHHHHHHHHHHHHHhhccccccCCCccccccccceeecCCCCCchh
Q psy8036 1 MRIATGASMKGIISNATASTPAPTLNLQEVCPEVSMDRLIKSLGYEYLRTKAITMEDGGEGQIAKQRGFQTINPTDDWFP 80 (194)
Q Consensus 1 m~~~L~~~~~Kl~sKgV~SVrsrVtNL~~~~~~i~~e~f~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~i~~~~e~~~ 80 (194)
|.++|+|+++|+.||||+|||||||||++++|.+++++|+++|+++|.+.|+... +.+.+ +.+++ +
T Consensus 162 l~~~L~~~~~k~~skgv~Sv~srVtnl~~~~~~~~~e~~~~~l~~~f~~~~~~~~-----------~~~~l--t~~e~-~ 227 (338)
T PRK03822 162 LANYLNPDKKKLQAKGITSVRSRVTNLTELLPGITHEQVCEAITEAFFAHYGERV-----------EAEVI--SPDKT-P 227 (338)
T ss_pred HHHHhCCChhhhhhccccchHhhhccHHHhCCCCCHHHHHHHHHHHHHHHhCCCC-----------Ccccc--CHHHH-H
Confidence 4689999999999999999999999999999889999999999999998753211 11223 45555 5
Q ss_pred hHHHHH---hhhCCcceecCCCCCceeeeeecCCCCCCCCceEEEEEEEeCCeEEEEEEEcCCCCCCcccccc---HHHH
Q psy8036 81 GLAKIQ---SEYQSWEWRYGSTPKFTISQSFDIPDEHGAPGQLVISLEIVKGLIESVCFKIPPALVNDEHFLQ---DAEL 154 (194)
Q Consensus 81 ~i~~~~---~k~~sweW~yGktP~F~~~~~~~~~~~~~~~G~i~v~l~v~~G~I~~i~i~~~~~~~~~~df~~---~~~l 154 (194)
.+.++. ++|+||||+||+||+|++..+.+|+| |.++|+++|++|+|++|+|+| ||+. +.++
T Consensus 228 ~i~~l~~~~~ky~s~eW~yg~sP~f~~~~~~~f~~-----G~v~i~~~v~~g~I~~~~i~g--------D~~~~~~~~~l 294 (338)
T PRK03822 228 DLPGFAETFARQSSWEWNFGQAPAFSHLLDERFTW-----GGVELHFDVEKGHITRAQIFT--------DSLNPAPLEAL 294 (338)
T ss_pred HHHHHHHHHHHhCCcchhcCCCCCccEeeeccccC-----CcEEEEEEEECCEEEEEEEEC--------CCCCcccHHHH
Confidence 555555 48999999999999999999999998 899999999999999999999 8876 5799
Q ss_pred HhhcCCCCCCHHHHHHHHHHHhhcCcccCCCchhhhhh
Q psy8036 155 LCSVQGRKFTETALDDLKEALTSRGQTYLGTSLDRLVT 192 (194)
Q Consensus 155 ~~~L~G~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~ 192 (194)
+++|+|++|+.++|.++|..+....+.|+ .+++||+.
T Consensus 295 ~~~L~G~~~~~~~i~~~l~~~~~~~~~~~-~~~~e~~~ 331 (338)
T PRK03822 295 AGRLQGCLYRADALQQECEALIVDFPEQE-KELRELSA 331 (338)
T ss_pred HHHhCCCCCCHHHHHHHHHHHHhhhhhhh-ccHHHHHH
Confidence 99999999999999999998843337777 77777764
No 2
>PRK14061 unknown domain/lipoate-protein ligase A fusion protein; Provisional
Probab=100.00 E-value=9.7e-34 Score=256.24 Aligned_cols=150 Identities=19% Similarity=0.286 Sum_probs=130.4
Q ss_pred CccccCCCccccccccccccccccccccccCCCCCHHHHHHHHHHHHHhhccccccCCCccccccccceeecCCCCCchh
Q psy8036 1 MRIATGASMKGIISNATASTPAPTLNLQEVCPEVSMDRLIKSLGYEYLRTKAITMEDGGEGQIAKQRGFQTINPTDDWFP 80 (194)
Q Consensus 1 m~~~L~~~~~Kl~sKgV~SVrsrVtNL~~~~~~i~~e~f~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~i~~~~e~~~ 80 (194)
|.++|+|+++|+.||||+||||||+||++++|++++++|+++|.++|.+.|+... +.+.+ +.+++ .
T Consensus 386 L~~~L~~~~~Kl~sKgvkSVrsRVtNL~e~l~~it~e~f~~~L~~~f~~~~g~~~-----------~~~~L--t~~e~-~ 451 (562)
T PRK14061 386 LANYLNPDKKKLAAKGITSVRSRVTNLTELLPGIPHEQVCEAITEAFFAHYGERV-----------EAEII--SPDKT-P 451 (562)
T ss_pred HHHHhCCCchhhhhhhhhhHHhhceeHHHhCCCCCHHHHHHHHHHHHHHHcCCCC-----------ccccC--CHHHH-H
Confidence 4689999999999999999999999999999889999999999999998743211 11223 45555 4
Q ss_pred hH---HHHHhhhCCcceecCCCCCceeeeeecCCCCCCCCceEEEEEEEeCCeEEEEEEEcCCCCCCcccccc---HHHH
Q psy8036 81 GL---AKIQSEYQSWEWRYGSTPKFTISQSFDIPDEHGAPGQLVISLEIVKGLIESVCFKIPPALVNDEHFLQ---DAEL 154 (194)
Q Consensus 81 ~i---~~~~~k~~sweW~yGktP~F~~~~~~~~~~~~~~~G~i~v~l~v~~G~I~~i~i~~~~~~~~~~df~~---~~~l 154 (194)
.+ .+.+++|+||||+||+||+|++..+.+|+| |.++|+++|++|+|++|+|+| ||+. +.+|
T Consensus 452 ~i~~l~~~~~ky~sweW~yG~sP~f~~~~~~rf~~-----G~vei~l~V~~G~I~~~ki~g--------Df~~~~~i~~l 518 (562)
T PRK14061 452 DLPNFAETFARQSSWEWNFGQAPAFSHLLDERFSW-----GGVELHFDVEKGHITRAQVFT--------DSLNPAPLEAL 518 (562)
T ss_pred HHHHHHHHHHHcCChhhhCCCCCCCcEEeeeeccc-----ccEEEEEEEeCCEEEEEEEEC--------CCCCcccHHHH
Confidence 44 444469999999999999999999999999 999999999999999999999 9987 5799
Q ss_pred HhhcCCCCCCHHHHHHHHHHHhh
Q psy8036 155 LCSVQGRKFTETALDDLKEALTS 177 (194)
Q Consensus 155 ~~~L~G~~~~~~~i~~~l~~~~~ 177 (194)
++.|+|++|+.++|.++|..+..
T Consensus 519 e~~L~G~~y~~~~i~~~l~~~~~ 541 (562)
T PRK14061 519 AGRLQGCLYRADMLQQECEALLV 541 (562)
T ss_pred HHHhCCCCcCHHHHHHHHHHHHh
Confidence 99999999999999999988865
No 3
>TIGR00545 lipoyltrans lipoyltransferase and lipoate-protein ligase. One member of this group of proteins is bovine lipoyltransferase, which transfers the lipoyl group from lipoyl-AMP to the specific Lys of lipoate-dependent enzymes. However, it does not first activate lipoic acid with ATP to create lipoyl-AMP and pyrophosphate. Another member of this group, lipoate-protein ligase A from E. coli, catalyzes both the activation and the transfer of lipoate. Homology between the two is full-length, except for the bovine mitochondrial targeting signal, but is strongest toward the N-terminus.
Probab=100.00 E-value=3.5e-33 Score=240.45 Aligned_cols=158 Identities=20% Similarity=0.388 Sum_probs=138.2
Q ss_pred CccccCCCccccccccccccccccccccccCCCCCHHHHHHHHHHHHHhhccccccCCCccccccccceeecCCCCCchh
Q psy8036 1 MRIATGASMKGIISNATASTPAPTLNLQEVCPEVSMDRLIKSLGYEYLRTKAITMEDGGEGQIAKQRGFQTINPTDDWFP 80 (194)
Q Consensus 1 m~~~L~~~~~Kl~sKgV~SVrsrVtNL~~~~~~i~~e~f~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~i~~~~e~~~ 80 (194)
|.++|+|+++|+.+||++||||||+||++++|.+++++|+++|+++|.+. +... +.+.+ +++++ +
T Consensus 160 l~~~L~~~~~k~~skgv~sv~~rv~nl~~~l~~~~~e~~~~~l~~~f~~~-~~~~-----------~~~~l--t~~e~-~ 224 (324)
T TIGR00545 160 LAKYLNVDKTKIESKGITSVRSRVVNVKEYLPNITTEQFLEEMTQAFFTY-TERV-----------ETYIL--DENKT-P 224 (324)
T ss_pred HHHhcCCChhhhHhhcccchhhhcccHHHhCCCCCHHHHHHHHHHHHHhh-CCCC-----------ceEec--CHHHH-H
Confidence 56899999999999999999999999999998899999999999999862 1100 12233 55666 7
Q ss_pred hHHHHH-hhhCCcceecCCCCCceeeeeecCCCCCCCCceEEEEEEEeCCeEEEEEEEcCCCCCCcccccc---HHHHHh
Q psy8036 81 GLAKIQ-SEYQSWEWRYGSTPKFTISQSFDIPDEHGAPGQLVISLEIVKGLIESVCFKIPPALVNDEHFLQ---DAELLC 156 (194)
Q Consensus 81 ~i~~~~-~k~~sweW~yGktP~F~~~~~~~~~~~~~~~G~i~v~l~v~~G~I~~i~i~~~~~~~~~~df~~---~~~l~~ 156 (194)
.++++. ++|+||||+||++|+|++..+.+|+| |.++++++|++|+|++|+|+| ||+. +.+|++
T Consensus 225 ~~~~l~~~ky~s~eW~yg~sp~f~~~~~~r~~~-----G~v~i~l~v~~g~I~~~~i~g--------Df~~~~~~~~l~~ 291 (324)
T TIGR00545 225 DVEKRAKERFQSWEWNFGKTPKFNFKNKKRFTA-----GGFELHVQVEKGKIVDCKFFG--------DFLSVADITPVTN 291 (324)
T ss_pred HHHHHHHHhcCCccccCCCCCCCceeeeEecCC-----CcEEEEEEEeCCEEEEEEEEC--------CCCCcccHHHHHH
Confidence 888877 59999999999999999999999998 899999999999999999999 9987 579999
Q ss_pred hcCCCCCCHHHHHHHHHHHh-hcCcccCC-Cchh
Q psy8036 157 SVQGRKFTETALDDLKEALT-SRGQTYLG-TSLD 188 (194)
Q Consensus 157 ~L~G~~~~~~~i~~~l~~~~-~~~~~~~~-~~~~ 188 (194)
+|+|++|+.++|.++|..++ . ..||+ .+++
T Consensus 292 ~L~G~~~~~~~i~~~l~~~~~~--~~~~~~~~~~ 323 (324)
T TIGR00545 292 RLIGQKYDYDTFAKELENLDVF--KEYFGELTPE 323 (324)
T ss_pred HhCCCccCHHHHHHHHHhhhhh--hhhhccCCcC
Confidence 99999999999999999998 7 78885 4544
No 4
>PF10437 Lip_prot_lig_C: Bacterial lipoate protein ligase C-terminus; InterPro: IPR019491 This is the C-terminal domain of a bacterial lipoate protein ligase. There is no conservation between this C terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with IPR004143 from INTERPRO, further upstream. This C-terminal domain is more stable than IPR004143 from INTERPRO and the hypothesis is that the C-terminal domain has a role in recognising the lipoyl domain and/or transferring the lipoyl group onto it from the lipoyl-AMP intermediate. C-terminal fragments of length 172 to 193 amino acid residues are observed in the eubacterial enzymes whereas in their archaeal counterparts the C-terminal segment is significantly smaller, ranging in size from 87 to 107 amino acid residues. ; PDB: 1X2G_A 3A7R_A 3A7A_A 1X2H_C 1VQZ_A 3R07_C.
Probab=99.76 E-value=4.4e-18 Score=119.98 Aligned_cols=80 Identities=23% Similarity=0.443 Sum_probs=73.6
Q ss_pred CCCCceeeeeecCCCCCCCCceEEEEEEEeCCeEEEEEEEcCCCCCCcccccc---HHHHHhhcCCCCCCHHHHHHHHHH
Q psy8036 98 STPKFTISQSFDIPDEHGAPGQLVISLEIVKGLIESVCFKIPPALVNDEHFLQ---DAELLCSVQGRKFTETALDDLKEA 174 (194)
Q Consensus 98 ktP~F~~~~~~~~~~~~~~~G~i~v~l~v~~G~I~~i~i~~~~~~~~~~df~~---~~~l~~~L~G~~~~~~~i~~~l~~ 174 (194)
|||+|+++.+.||+| |.|+|+++|++|+|++|+|+| ||+. +.+|+++|+|++|+.++|.++|+.
T Consensus 1 ksP~f~~~~~~rf~~-----G~v~v~~~V~~G~I~~i~i~g--------Df~~~~~i~~le~~L~G~~~~~~~i~~~l~~ 67 (86)
T PF10437_consen 1 KSPEFTFSKERRFPW-----GTVEVHLNVKNGIIKDIKIYG--------DFFGPEDIEELEEALIGCPYDREAIKEALNS 67 (86)
T ss_dssp TS-CESEEEEEEETT-----EEEEEEEEEETTEEEEEEEEE--------CBS-CCCHHHHHHHHTTCBSSHHHHHHHHHH
T ss_pred CcCCCcEeeeeEcCC-----ceEEEEEEEECCEEEEEEEEC--------CCCCchHHHHHHHHHHhcCCCHHHHHHHHHH
Confidence 799999999999999 999999999999999999999 9987 689999999999999999999999
Q ss_pred HhhcCcccCC-Cchhhhhh
Q psy8036 175 LTSRGQTYLG-TSLDRLVT 192 (194)
Q Consensus 175 ~~~~~~~~~~-~~~~~~~~ 192 (194)
++. ..|++ .+.+||+.
T Consensus 68 ~~~--~~~~~~~~~~el~~ 84 (86)
T PF10437_consen 68 VDL--EDYFGNISVEELIE 84 (86)
T ss_dssp CHG--GGTCCTHHHHHHHH
T ss_pred hCH--hhccccCCHHHHHH
Confidence 999 99996 58888875
No 5
>KOG3159|consensus
Probab=99.67 E-value=4e-17 Score=136.64 Aligned_cols=148 Identities=28% Similarity=0.417 Sum_probs=113.4
Q ss_pred CccccCCCcccccccccccccc-ccccccccCCCCCHHHHHHHHHHHHHhhccccccCCCccccccccceeecCCCCCc-
Q psy8036 1 MRIATGASMKGIISNATASTPA-PTLNLQEVCPEVSMDRLIKSLGYEYLRTKAITMEDGGEGQIAKQRGFQTINPTDDW- 78 (194)
Q Consensus 1 m~~~L~~~~~Kl~sKgV~SVrs-rVtNL~~~~~~i~~e~f~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~i~~~~e~- 78 (194)
|+.+|+++...+.|+++.|||| ||.|+.+-.+.++.+.++-++..+|.+++. +++ ++..+++.+++
T Consensus 169 ls~lL~sp~~~~~s~at~sv~sp~vk~lie~~~~v~~~q~~~av~~~y~~t~~---~d~---------~i~svn~~e~~~ 236 (336)
T KOG3159|consen 169 LSELLKSPRVNIRSKATSSVRSPRVKNLIEKDDFVNVEQSAVAVQEEYKKTFK---EDG---------EIKSVNPTEELK 236 (336)
T ss_pred HHhhccCCCCCccccccccccchhhhhhhhhcCcccHhHHHHHHHHHHHHHhc---ccC---------Ccceeccccccc
Confidence 5678999988899999999999 899999877779999999999999998621 122 34566677765
Q ss_pred -hhhHHHHHhhhCCcceecCCCCCceeeeeecCCCCCCCCceEEEEEEEeCCeEEEEEEEcCCCCCCccccccHHHHHhh
Q psy8036 79 -FPGLAKIQSEYQSWEWRYGSTPKFTISQSFDIPDEHGAPGQLVISLEIVKGLIESVCFKIPPALVNDEHFLQDAELLCS 157 (194)
Q Consensus 79 -~~~i~~~~~k~~sweW~yGktP~F~~~~~~~~~~~~~~~G~i~v~l~v~~G~I~~i~i~~~~~~~~~~df~~~~~l~~~ 157 (194)
.++|.+...+|+||||+||+||+|++..+.. . -.+++.++|++|.|++|.|..|.. + +..-+-.-
T Consensus 237 ~~~~I~~~~~elqswdWiygktPkF~~~~~~~--~-----l~~~~~i~v~~g~i~~c~i~~P~~-----~--~~~~v~~~ 302 (336)
T KOG3159|consen 237 TNPEITKAENELQSWDWIYGKTPKFSVKIEDK--H-----LTLKLSIDVEKGMIEDCDIQTPQP-----N--QLELVGTP 302 (336)
T ss_pred cCHhHHHHHHHhhhhhhhcCCCCceEEEeecc--C-----ceeeeeeEeecCceEEeccCCCCc-----c--hhcccccc
Confidence 3689999999999999999999999955432 1 378899999999999999998743 2 11122355
Q ss_pred cCCCCCCHHHHHHHHHH
Q psy8036 158 VQGRKFTETALDDLKEA 174 (194)
Q Consensus 158 L~G~~~~~~~i~~~l~~ 174 (194)
|+|.+|..+.....|.+
T Consensus 303 l~g~~~~~~~~n~~l~~ 319 (336)
T KOG3159|consen 303 LKGFLYNIDTENTILGA 319 (336)
T ss_pred ceeeeecCCccceeeee
Confidence 88888865544444433
No 6
>COG0095 LplA Lipoate-protein ligase A [Coenzyme metabolism]
Probab=99.35 E-value=3.2e-13 Score=112.61 Aligned_cols=83 Identities=18% Similarity=0.433 Sum_probs=67.7
Q ss_pred CccccCCCccccccccccccccccccccccCCCCCHHHHHHHHHHHHHhhccccccCCCccccccccceeecCCCCCchh
Q psy8036 1 MRIATGASMKGIISNATASTPAPTLNLQEVCPEVSMDRLIKSLGYEYLRTKAITMEDGGEGQIAKQRGFQTINPTDDWFP 80 (194)
Q Consensus 1 m~~~L~~~~~Kl~sKgV~SVrsrVtNL~~~~~~i~~e~f~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~i~~~~e~~~ 80 (194)
|.++|+++++|+++||++|+|+||+||.+. .++++++|++++.++|.+.++... +.+++ +.+++ .
T Consensus 165 l~~~l~~~~~k~~~k~~~s~~~rv~~l~~~-~~~~~~e~~~~l~~~f~~~~~~~~-----------~~~~l--t~~e~-~ 229 (248)
T COG0095 165 LARVLRVPKEKIKSKGIKSVRERVANLEEL-LKISVEEFLEALLEAFFKVLGVEL-----------EEYEL--TPEEL-E 229 (248)
T ss_pred HHHHhCCChhhhhhcccccHHHhCcchhhc-cCCCHHHHHHHHHHHHHHhhCCCc-----------cccCC--CHHHH-H
Confidence 468999999999999999999999999998 679999999999999998632111 22233 55666 6
Q ss_pred hHHHHH-hhhCCcceecCC
Q psy8036 81 GLAKIQ-SEYQSWEWRYGS 98 (194)
Q Consensus 81 ~i~~~~-~k~~sweW~yGk 98 (194)
.+.+++ ++|++|+|+||+
T Consensus 230 ~~~~~~~~~~~~~~w~~~~ 248 (248)
T COG0095 230 LAEKLAEEKYSSWEWNFGK 248 (248)
T ss_pred HHHHHHHHHhcchhhhccC
Confidence 777777 599999999996
No 7
>PF03450 CO_deh_flav_C: CO dehydrogenase flavoprotein C-terminal domain; InterPro: IPR005107 Proteins containing this domain form structural complexes with other known families, such as IPR008274 from INTERPRO and IPR001041 from INTERPRO]. The carbon monoxide (CO) dehydrogenase of Oligotropha carboxidovorans is a heterotrimeric complex composed of a apoflavoprotein, a molybdoprotein, and an iron-sulphur protein. It can be dissociated with sodium dodecylsulphate []. CO dehydrogenase catalyzes the oxidation of CO according to the following equation []: CO + H2O = CO2 + 2e + 2H+ Subunit S represents the iron-sulphur protein of CO dehydrogenase and is clearly divided into a C- and an N-terminal domain, each binding a [2Fe-2S] cluster [].; PDB: 3EUB_K 3NS1_K 3NVV_B 1FO4_B 3AM9_A 3AX7_B 3BDJ_A 3ETR_B 3UNI_A 3AMZ_A ....
Probab=89.34 E-value=2.9 Score=29.64 Aligned_cols=55 Identities=16% Similarity=0.297 Sum_probs=39.4
Q ss_pred eEEEEEEEeCC-eEEEEEEEcCCCCCCccccccHHHHHhhcCCCCCCHHHHHHHHHHHh
Q psy8036 119 QLVISLEIVKG-LIESVCFKIPPALVNDEHFLQDAELLCSVQGRKFTETALDDLKEALT 176 (194)
Q Consensus 119 ~i~v~l~v~~G-~I~~i~i~~~~~~~~~~df~~~~~l~~~L~G~~~~~~~i~~~l~~~~ 176 (194)
.+-+.+.+++| +|+++++.- |-+.+ -..-..++++.|.|.+.+.+.++++...+.
T Consensus 17 ~~a~~~~~~~~~~i~~~ria~--g~v~~-~p~r~~~~E~~L~g~~~~~~~~~~~~~~~~ 72 (103)
T PF03450_consen 17 NVAVLVSVDDDGRIEDARIAV--GGVAP-TPVRAEEVEAALIGKPLSEETLEEAAEAVS 72 (103)
T ss_dssp EEEEEEEEETTSEEEEEEEEE--ESSSS-STEE-HHHHHHTTTSBSSHHHHHHHHHHHH
T ss_pred hhhheEEEecCceEEEEEEEE--ecccc-ceeehHHHHHHHhhcchhhhhHHHHHHHHH
Confidence 45566777766 999999984 22222 111146899999999999999999887664
No 8
>cd06664 IscU_like Iron-sulfur cluster scaffold-like proteins. IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.
Probab=85.50 E-value=10 Score=27.73 Aligned_cols=67 Identities=16% Similarity=0.127 Sum_probs=43.2
Q ss_pred ecCCCCCceeeeeecCCCCCCCCceEEEEEEEeCCeEEEEEEEcCCCCCCcccccc----HHHHHhhcCCCCCCHHHHHH
Q psy8036 95 RYGSTPKFTISQSFDIPDEHGAPGQLVISLEIVKGLIESVCFKIPPALVNDEHFLQ----DAELLCSVQGRKFTETALDD 170 (194)
Q Consensus 95 ~yGktP~F~~~~~~~~~~~~~~~G~i~v~l~v~~G~I~~i~i~~~~~~~~~~df~~----~~~l~~~L~G~~~~~~~i~~ 170 (194)
++|.-+.++......-|. +| ..+++.+.+++|+|+++.|.+- -+.. ..-+.+.+.|. +-+++..
T Consensus 15 ~~g~l~~~~~~~~~~n~~-CG--D~v~l~l~i~~~~I~d~~f~~~-------GC~i~~Asas~~~~~~~Gk--~~~ea~~ 82 (123)
T cd06664 15 NVGRLEDADGTGEVGNPL-CG--DEITLYLKVEDGRITDAKFQGF-------GCAISIASASLLTELIKGK--TLDEALK 82 (123)
T ss_pred CCCCCCCCCeEEEcCCCC-CC--ceEEEEEEEcCCEEEEEEEEec-------CcHHHHHHHHHHHHHHcCC--cHHHHHH
Confidence 556666666655555442 12 5899999999999999999971 2221 23455888898 4444444
Q ss_pred HHH
Q psy8036 171 LKE 173 (194)
Q Consensus 171 ~l~ 173 (194)
++.
T Consensus 83 i~~ 85 (123)
T cd06664 83 LLN 85 (123)
T ss_pred HHH
Confidence 443
No 9
>TIGR01994 SUF_scaf_2 SUF system FeS assembly protein, NifU family. Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred.
Probab=84.25 E-value=3.3 Score=31.36 Aligned_cols=67 Identities=13% Similarity=0.235 Sum_probs=43.5
Q ss_pred hhhCCcceecCCCCCceeeeeecCCCCCCCCceEEEEEEEeCCeEEEEEEEcCCCCCCcccccc----HHHHHhhcCCCC
Q psy8036 87 SEYQSWEWRYGSTPKFTISQSFDIPDEHGAPGQLVISLEIVKGLIESVCFKIPPALVNDEHFLQ----DAELLCSVQGRK 162 (194)
Q Consensus 87 ~k~~sweW~yGktP~F~~~~~~~~~~~~~~~G~i~v~l~v~~G~I~~i~i~~~~~~~~~~df~~----~~~l~~~L~G~~ 162 (194)
+.|+.+. ++|..+.++......-|.. | ..|.+.+.|++|+|+++.|.+. -+.. ..-+.+.++|..
T Consensus 11 eh~~~p~-n~g~l~~~~~~~~~~np~C-G--D~i~l~l~v~~~~I~d~~f~~~-------GCais~Asas~~~e~i~Gk~ 79 (137)
T TIGR01994 11 DHYKNPR-HRGKLEDATVQERGHNPTC-G--DEITLTVKLEGDRIEDIAFEGE-------GCSISQASASMMTELIKGKT 79 (137)
T ss_pred HHHhCCC-CCCCCCCCCeeEEeCCCCC-C--cEEEEEEEEcCCeEEEEEEEec-------ccHHHHHHHHHHHHHHcCCC
Confidence 3444442 5787777765554433321 2 4899999999999999999972 2321 134458888987
Q ss_pred CC
Q psy8036 163 FT 164 (194)
Q Consensus 163 ~~ 164 (194)
.+
T Consensus 80 ~~ 81 (137)
T TIGR01994 80 VE 81 (137)
T ss_pred HH
Confidence 65
No 10
>TIGR03419 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not.
Probab=78.07 E-value=7.9 Score=28.60 Aligned_cols=61 Identities=18% Similarity=0.197 Sum_probs=39.4
Q ss_pred ecCCCCCceeeeeecCCCCCCCCceEEEEEEEeCCeEEEEEEEcCCCCCCcccccc----HHHHHhhcCCCCCCH
Q psy8036 95 RYGSTPKFTISQSFDIPDEHGAPGQLVISLEIVKGLIESVCFKIPPALVNDEHFLQ----DAELLCSVQGRKFTE 165 (194)
Q Consensus 95 ~yGktP~F~~~~~~~~~~~~~~~G~i~v~l~v~~G~I~~i~i~~~~~~~~~~df~~----~~~l~~~L~G~~~~~ 165 (194)
++|+-+.++......-|. +| ..|++.+.+++|+|++++|.+. -+.. ..-+.+.+.|..++.
T Consensus 14 ~~g~l~~~~~~~~~~np~-CG--D~i~l~l~i~~~~I~d~~f~~~-------GC~is~Asas~~~e~i~Gk~l~e 78 (121)
T TIGR03419 14 NVGEIENADGVGEVGNPK-CG--DIMKIFLKVEDDIIKDVKFKTF-------GCGAAIASSSMATEMIKGKTLEE 78 (121)
T ss_pred CCCCCCCCCeEEEeCCCC-Cc--cEEEEEEEEcCCEEEEEEEEEe-------ccHHHHHHHHHHHHHHcCCCHHH
Confidence 466655555444444331 11 4899999999999999999972 2211 134457888887765
No 11
>PF01592 NifU_N: NifU-like N terminal domain; InterPro: IPR002871 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the N-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal and a C-terminal domain (IPR001075 from INTERPRO) []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 3LVL_A 4EB5_C 4EB7_C 1WFZ_A 2Z7E_C 2AZH_A 1XJS_A 1Q48_A 1R9P_A 2KQK_A ....
Probab=70.10 E-value=13 Score=27.51 Aligned_cols=69 Identities=19% Similarity=0.259 Sum_probs=44.0
Q ss_pred hhhCCcceecCCCCCcee-eeeecCCCCCCCCceEEEEEEEeC--CeEEEEEEEcCCCCCCcccccc----HHHHHhhcC
Q psy8036 87 SEYQSWEWRYGSTPKFTI-SQSFDIPDEHGAPGQLVISLEIVK--GLIESVCFKIPPALVNDEHFLQ----DAELLCSVQ 159 (194)
Q Consensus 87 ~k~~sweW~yGktP~F~~-~~~~~~~~~~~~~G~i~v~l~v~~--G~I~~i~i~~~~~~~~~~df~~----~~~l~~~L~ 159 (194)
+.|.++. ++|.-+.++. .....-|.. | ..+++.+.|++ |+|++++|.+- -+.. ..-+.+.+.
T Consensus 8 ~~~~nP~-~~g~l~~~~~~~~~~~n~~C-G--D~i~i~l~i~~~~~~I~d~~f~~~-------GC~~~~Asas~~~~~i~ 76 (126)
T PF01592_consen 8 DHYRNPR-NYGKLEDADAGTGEAGNPSC-G--DEIRIYLKIDDDGGRIKDAKFQGF-------GCAISIASASMMCELIK 76 (126)
T ss_dssp HHHHSTS-SBSSSTTTSSEEEEEEETTT-T--EEEEEEEEESSSTSBEEEEEEEEE-------SSHHHHHHHHHHHHHHT
T ss_pred HHHhCCC-CCCCCCCCCcceeeecCCCC-C--CEEEEEEEEecCCCeEEEEEEEee-------cChHHHHHHHHHHHHHc
Confidence 3444443 4788777774 444443322 1 48999999998 89999999971 1111 234558888
Q ss_pred CCCCCHH
Q psy8036 160 GRKFTET 166 (194)
Q Consensus 160 G~~~~~~ 166 (194)
|.+++..
T Consensus 77 gk~l~ea 83 (126)
T PF01592_consen 77 GKTLEEA 83 (126)
T ss_dssp TSBHHHH
T ss_pred CCCHHHH
Confidence 9886544
No 12
>TIGR01999 iscU FeS cluster assembly scaffold IscU. This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms.
Probab=64.37 E-value=22 Score=26.23 Aligned_cols=41 Identities=17% Similarity=0.270 Sum_probs=28.7
Q ss_pred ceEEEEEEEeC-CeEEEEEEEcCCCCCCcccccc----HHHHHhhcCCCCCCH
Q psy8036 118 GQLVISLEIVK-GLIESVCFKIPPALVNDEHFLQ----DAELLCSVQGRKFTE 165 (194)
Q Consensus 118 G~i~v~l~v~~-G~I~~i~i~~~~~~~~~~df~~----~~~l~~~L~G~~~~~ 165 (194)
..+++.+.|++ |+|++++|.+- -+.. ..-+.+.+.|..++.
T Consensus 37 D~i~l~l~v~~~~~I~d~~f~~~-------GC~~s~Asas~~~e~i~Gktl~e 82 (124)
T TIGR01999 37 DVMKLQIKVNDDGIIEDAKFKTF-------GCGSAIASSSLATELIKGKSLEE 82 (124)
T ss_pred cEEEEEEEECCCCeEEEEEEEec-------CcHHHHHHHHHHHHHHcCCCHHH
Confidence 58899999975 89999999971 2211 134457788886653
No 13
>TIGR02963 xanthine_xdhA xanthine dehydrogenase, small subunit. Members of this protein family are the small subunit (or, in eukaryotes, the N-terminal domain) of xanthine dehydrogenase, an enzyme of purine catabolism via urate. The small subunit contains both an FAD and a 2Fe-2S cofactor. Aldehyde oxidase (retinal oxidase) appears to have arisen as a neofunctionalization among xanthine dehydrogenases in eukaryotes and
Probab=62.60 E-value=34 Score=31.24 Aligned_cols=52 Identities=15% Similarity=0.264 Sum_probs=38.1
Q ss_pred EEEEEeCCeEEEEEEEcCCCCCCccccccHHHHHhhcCCCCCCHHHHHHHHHHHh
Q psy8036 122 ISLEIVKGLIESVCFKIPPALVNDEHFLQDAELLCSVQGRKFTETALDDLKEALT 176 (194)
Q Consensus 122 v~l~v~~G~I~~i~i~~~~~~~~~~df~~~~~l~~~L~G~~~~~~~i~~~l~~~~ 176 (194)
+.+.+++|+|++++|.- |-+.+ ...-..+.++.|.|.+++.+.++++.+.+.
T Consensus 385 ~~v~~~~~~i~~~ria~--Ggva~-~p~r~~~~E~~L~G~~~~~~~l~~a~~~l~ 436 (467)
T TIGR02963 385 FNLELDGGVVAEIRIAF--GGMAA-TPKRAAATEAALLGKPWNEATVEAAMAALA 436 (467)
T ss_pred EEEEEcCCeEeEEEEEE--ecCCC-CceehHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence 55566689999999985 22222 222246888999999999999999887664
No 14
>TIGR01352 tonB_Cterm TonB family C-terminal domain. This model represents the C-terminal of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to help span the periplasm.
Probab=62.39 E-value=21 Score=22.98 Aligned_cols=21 Identities=24% Similarity=0.419 Sum_probs=18.9
Q ss_pred ceEEEEEEEe-CCeEEEEEEEc
Q psy8036 118 GQLVISLEIV-KGLIESVCFKI 138 (194)
Q Consensus 118 G~i~v~l~v~-~G~I~~i~i~~ 138 (194)
|.+.|.+.|. +|.|.++++..
T Consensus 10 G~v~v~~~i~~~G~v~~~~i~~ 31 (74)
T TIGR01352 10 GTVVVRFTVDADGRVTSVSVLK 31 (74)
T ss_pred eEEEEEEEECCCCCEEEEEEEE
Confidence 8999999995 99999999985
No 15
>PF03544 TonB_C: Gram-negative bacterial TonB protein C-terminal; InterPro: IPR006260 The sequences in this set all contain a conserved C-terminal domain which is characteristic of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria []. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetitive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to span the periplasm. Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins []. The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis ezymes, and receptors that recognise iron-bound siderophores []. An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin []. To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors. B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016020 membrane, 0030288 outer membrane-bounded periplasmic space; PDB: 1U07_B 1IHR_A 2GRX_C 2GSK_B 1QXX_A 1XX3_A 2K9K_A.
Probab=61.49 E-value=17 Score=23.78 Aligned_cols=22 Identities=23% Similarity=0.389 Sum_probs=19.8
Q ss_pred ceEEEEEEE-eCCeEEEEEEEcC
Q psy8036 118 GQLVISLEI-VKGLIESVCFKIP 139 (194)
Q Consensus 118 G~i~v~l~v-~~G~I~~i~i~~~ 139 (194)
|.+.+.+.| .+|.|.++++...
T Consensus 16 G~v~v~~~I~~~G~v~~~~v~~s 38 (79)
T PF03544_consen 16 GTVVVEFTIDPDGRVSDVRVIQS 38 (79)
T ss_dssp EEEEEEEEEETTTEEEEEEEEEE
T ss_pred EEEEEEEEEeCCCCEEEEEEEEc
Confidence 899999999 7999999999963
No 16
>PRK09971 xanthine dehydrogenase subunit XdhB; Provisional
Probab=60.49 E-value=45 Score=28.31 Aligned_cols=53 Identities=9% Similarity=0.150 Sum_probs=37.5
Q ss_pred EEEEEEeCCeEEEEEEEcCCCCCCccccccHHHHHhhcCCCCCCHHHHHHHHHHHh
Q psy8036 121 VISLEIVKGLIESVCFKIPPALVNDEHFLQDAELLCSVQGRKFTETALDDLKEALT 176 (194)
Q Consensus 121 ~v~l~v~~G~I~~i~i~~~~~~~~~~df~~~~~l~~~L~G~~~~~~~i~~~l~~~~ 176 (194)
-+.+.+++|+|.+++|.- |.+.+ -..-..+.++.|.|.+++.+.+.++...+.
T Consensus 200 a~~~~~~~g~i~~~ria~--G~v~~-~p~r~~~~E~~L~G~~~~~~~~~~a~~~~~ 252 (291)
T PRK09971 200 AVLCRLDNGNFEDLRLAF--GVAAP-TPIRCQHAEQTAKGAPLNLETLEAIGELVL 252 (291)
T ss_pred EEEEEEcCCEEEEEEEEE--EcccC-ceeeHHHHHHHhCCCCCCHHHHHHHHHHHH
Confidence 355556789999999985 22222 111146889999999999999988876554
No 17
>TIGR03853 matur_matur probable metal-binding protein. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems.
Probab=58.22 E-value=19 Score=24.66 Aligned_cols=40 Identities=23% Similarity=0.365 Sum_probs=28.9
Q ss_pred HHHhhc--CCCCCCHHHHHHHHHHHhhcCcccC-----CCchhhhhh
Q psy8036 153 ELLCSV--QGRKFTETALDDLKEALTSRGQTYL-----GTSLDRLVT 192 (194)
Q Consensus 153 ~l~~~L--~G~~~~~~~i~~~l~~~~~~~~~~~-----~~~~~~~~~ 192 (194)
++.+.| .|.+|+++++..++.+---+...|- +++.++||.
T Consensus 6 eVL~mml~~~~~~t~~~L~~~i~~~FG~~arFhTCSa~~m~a~~Li~ 52 (77)
T TIGR03853 6 EVLNLMLASGEPYTRESLKAAIEQKFGEDARFHTCSAEGMTADELLQ 52 (77)
T ss_pred HHHHHHHHcCCCcCHHHHHHHHHHHhCCCceEeecccccCCHHHHHH
Confidence 566778 8999999999999865433334443 578888875
No 18
>PRK11325 scaffold protein; Provisional
Probab=56.23 E-value=38 Score=25.16 Aligned_cols=40 Identities=18% Similarity=0.276 Sum_probs=28.1
Q ss_pred ceEEEEEEEe-CCeEEEEEEEcCCCCCCcccccc----HHHHHhhcCCCCCC
Q psy8036 118 GQLVISLEIV-KGLIESVCFKIPPALVNDEHFLQ----DAELLCSVQGRKFT 164 (194)
Q Consensus 118 G~i~v~l~v~-~G~I~~i~i~~~~~~~~~~df~~----~~~l~~~L~G~~~~ 164 (194)
..++|.+.|. +|+|++++|.+- -+.. ..-+.+.+.|..++
T Consensus 39 D~i~l~l~v~~~~~I~d~~f~~~-------GC~is~Asas~~~e~~~Gktl~ 83 (127)
T PRK11325 39 DVMKLQIKVNDEGIIEDAKFKTY-------GCGSAIASSSLVTEWVKGKTLD 83 (127)
T ss_pred cEEEEEEEECCCCeEEEEEEEee-------CCHHHHHHHHHHHHHHcCCCHH
Confidence 5899999996 799999999971 2221 12344777787654
No 19
>TIGR03199 pucC xanthine dehydrogenase C subunit. This gene has been characterized in B. subtilis as the FAD binding-subunit of xanthine dehydrogenase (pucC), acting in conjunction with pucD, the molybdopterin-binding subunit and pucE, the FeS-binding subunit.
Probab=55.76 E-value=62 Score=26.99 Aligned_cols=52 Identities=6% Similarity=0.002 Sum_probs=36.2
Q ss_pred EEEEEe-CCeEEEEEEEcCCCCCCccccccHHHHHhhcCCCCCCHHHHHHHHHHHh
Q psy8036 122 ISLEIV-KGLIESVCFKIPPALVNDEHFLQDAELLCSVQGRKFTETALDDLKEALT 176 (194)
Q Consensus 122 v~l~v~-~G~I~~i~i~~~~~~~~~~df~~~~~l~~~L~G~~~~~~~i~~~l~~~~ 176 (194)
+.+.+. +|.|++++|.- |-+.+ -..-..+.|+.|.|.+++.+.++++.+.+.
T Consensus 186 ~~~~~~~~~~i~~~ria~--Ggv~~-~p~r~~~~E~~L~G~~~~~~~~~~a~~~~~ 238 (264)
T TIGR03199 186 GRFLLDGSQTIKEIRLAV--GGADI-TPRRLLDSEAKLMAPPWDPHLLAELYKTII 238 (264)
T ss_pred EEEEEcCCCeEEEEEEEe--ecCCC-ceeeHHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence 334554 48999999985 22222 122256889999999999999988876553
No 20
>COG3976 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.60 E-value=22 Score=26.82 Aligned_cols=21 Identities=24% Similarity=0.303 Sum_probs=20.1
Q ss_pred ceEEEEEEEeCCeEEEEEEEc
Q psy8036 118 GQLVISLEIVKGLIESVCFKI 138 (194)
Q Consensus 118 G~i~v~l~v~~G~I~~i~i~~ 138 (194)
|.++|++.++.|+|+.|++-+
T Consensus 62 g~lqv~vtIk~grItaikvl~ 82 (135)
T COG3976 62 GILQVQVTIKGGRITAIKVLK 82 (135)
T ss_pred ceEEEEEEEecCcEEEEEEec
Confidence 799999999999999999997
No 21
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.
Probab=55.00 E-value=55 Score=28.01 Aligned_cols=41 Identities=15% Similarity=0.121 Sum_probs=27.1
Q ss_pred ecCCCCCceeeeeecCCCCCCCCceEEEEEEEe--CCeEEEEEEEc
Q psy8036 95 RYGSTPKFTISQSFDIPDEHGAPGQLVISLEIV--KGLIESVCFKI 138 (194)
Q Consensus 95 ~yGktP~F~~~~~~~~~~~~~~~G~i~v~l~v~--~G~I~~i~i~~ 138 (194)
++|.-+.++......-|.. | -.+.+.+.|+ +|+|++++|.+
T Consensus 17 n~G~L~~~~~~g~~~np~C-G--D~i~l~l~vd~~~~~I~d~~F~~ 59 (290)
T TIGR02000 17 NAGVVEDANAVGEVGSISC-G--DALRLMLKVDPESDKIVDAGFQT 59 (290)
T ss_pred CCCCCCCCCcEEEeCCCCC-c--ceEEEEEEEcCCCCeEEEEEEEe
Confidence 5566555554443332211 1 4888999996 79999999997
No 22
>smart00089 PKD Repeats in polycystic kidney disease 1 (PKD1) and other proteins. Polycystic kidney disease 1 protein contains 14 repeats, present elsewhere such as in microbial collagenases.
Probab=54.81 E-value=19 Score=23.63 Aligned_cols=37 Identities=19% Similarity=0.494 Sum_probs=22.8
Q ss_pred hCCcceecCCCCCce-eeeeecCCCCCCCCceEEEEEEEeCC
Q psy8036 89 YQSWEWRYGSTPKFT-ISQSFDIPDEHGAPGQLVISLEIVKG 129 (194)
Q Consensus 89 ~~sweW~yGktP~F~-~~~~~~~~~~~~~~G~i~v~l~v~~G 129 (194)
-.+|+|.||...... ....+.|+. .|...|.+.+.+.
T Consensus 29 ~~~~~W~fgdg~~~~~~~~~~~y~~----~G~y~v~l~v~n~ 66 (79)
T smart00089 29 IVSYTWDFGDGTSSTGPTVTHTYTK----PGTYTVTLTVTNA 66 (79)
T ss_pred eEEEEEEeCCCCccCCCCEEEEeCC----CcEEEEEEEEEcC
Confidence 467889998764333 233334433 2788888888653
No 23
>PRK10819 transport protein TonB; Provisional
Probab=54.74 E-value=25 Score=29.35 Aligned_cols=43 Identities=12% Similarity=0.344 Sum_probs=28.5
Q ss_pred ceEEEEEEEe-CCeEEEEEEEcCCCCCCccccccHHHHHhhcCCCCCCH
Q psy8036 118 GQLVISLEIV-KGLIESVCFKIPPALVNDEHFLQDAELLCSVQGRKFTE 165 (194)
Q Consensus 118 G~i~v~l~v~-~G~I~~i~i~~~~~~~~~~df~~~~~l~~~L~G~~~~~ 165 (194)
|.+.|+|+|. +|+|.+|+|....| . +.| +.+..++++..+|..
T Consensus 181 G~V~V~f~I~~~G~V~~v~V~~Ssg---~-~~f-D~aal~Avr~wr~~p 224 (246)
T PRK10819 181 GQVKVKFDVDEDGRVDNVRILSAEP---R-NMF-EREVKQAMRKWRYEA 224 (246)
T ss_pred eEEEEEEEECCCCCEEEEEEeccCC---h-HHH-HHHHHHHHHhcCCCC
Confidence 8999999996 89999999976322 1 222 234445555556653
No 24
>PF04205 FMN_bind: FMN-binding domain; InterPro: IPR007329 This conserved region includes the FMN-binding site of the NqrC protein [] as well as the NosR and NirI regulatory proteins.; GO: 0010181 FMN binding, 0016020 membrane; PDB: 3LWX_A 2KZX_A 3DCZ_A 3O6U_D.
Probab=51.52 E-value=30 Score=23.00 Aligned_cols=21 Identities=29% Similarity=0.406 Sum_probs=19.3
Q ss_pred ceEEEEEEEeC-CeEEEEEEEc
Q psy8036 118 GQLVISLEIVK-GLIESVCFKI 138 (194)
Q Consensus 118 G~i~v~l~v~~-G~I~~i~i~~ 138 (194)
|.+.+.+.+++ |+|.+|++..
T Consensus 4 g~i~v~v~i~~dg~I~~v~~~~ 25 (81)
T PF04205_consen 4 GPITVTVTIDKDGKITDVKILE 25 (81)
T ss_dssp EEEEEEEEEETTTEEEEEEEEE
T ss_pred ceEEEEEEEeCCCEEEEEEEee
Confidence 78999999987 9999999997
No 25
>COG4630 XdhA Xanthine dehydrogenase, iron-sulfur cluster and FAD-binding subunit A [Nucleotide transport and metabolism]
Probab=50.17 E-value=38 Score=30.49 Aligned_cols=50 Identities=16% Similarity=0.330 Sum_probs=40.1
Q ss_pred EEEEEEeCCeEEEEEEEcCCCCCCcccccc----HHHHHhhcCCCCCCHHHHHHHHHHHhh
Q psy8036 121 VISLEIVKGLIESVCFKIPPALVNDEHFLQ----DAELLCSVQGRKFTETALDDLKEALTS 177 (194)
Q Consensus 121 ~v~l~v~~G~I~~i~i~~~~~~~~~~df~~----~~~l~~~L~G~~~~~~~i~~~l~~~~~ 177 (194)
-+.+++..|+|.+++|-- | -+-. ..+.|++|.|.|.+.+.++.+.+++.-
T Consensus 395 Af~l~Ldg~~V~~arIa~--G-----GmAaTPkRA~~~EaAL~Gk~wteatve~A~aAl~~ 448 (493)
T COG4630 395 AFALDLDGGRVADARIAF--G-----GMAATPKRASEVEAALLGKPWTEATVEAAAAALAG 448 (493)
T ss_pred HheeeecCCeeeeeeeec--C-----ccccCccchHHHHHHHcCCCccHHHHHHHHHHHhc
Confidence 377888999999999974 1 2211 468999999999999999999988754
No 26
>PRK11251 DNA-binding transcriptional activator OsmE; Provisional
Probab=49.53 E-value=15 Score=26.85 Aligned_cols=16 Identities=6% Similarity=-0.083 Sum_probs=11.7
Q ss_pred hCCcceecCCCCCcee
Q psy8036 89 YQSWEWRYGSTPKFTI 104 (194)
Q Consensus 89 ~~sweW~yGktP~F~~ 104 (194)
...|+|+|++.|.-..
T Consensus 63 ~t~w~Yv~~~~~g~~~ 78 (109)
T PRK11251 63 GTCQTYILGNRDGKAQ 78 (109)
T ss_pred CcceeEEEecCCCceE
Confidence 4469999988877433
No 27
>PF00801 PKD: PKD domain; InterPro: IPR000601 The PKD (Polycystic Kidney Disease) domain was first identified in the Polycystic Kidney Disease protein, polycystin-1 (PDK1 gene), and contains an Ig-like fold consisting of a beta-sandwich of seven strands in two sheets with a Greek key topology, although some members have additional strands []. Polycystin-1 is a large cell-surface glycoprotein involved in adhesive protein-protein and protein-carbohydrate interactions; however it is not clear if the PKD domain mediates any of these interactions. PKD domains are also found in other proteins, usually in the extracellular parts of proteins involved in interactions with other proteins. For example, domains with a PKD-type fold are found in archaeal surface layer proteins that protect the cell from extreme environments [], and in the human VPS10 domain-containing receptor SorCS2 [].; PDB: 1B4R_A 2KZW_A 2C4X_A 2C26_A 2Y72_B 3JQU_A 3JS7_B 1WGO_A 1L0Q_A.
Probab=49.42 E-value=17 Score=23.46 Aligned_cols=37 Identities=19% Similarity=0.514 Sum_probs=21.8
Q ss_pred hhCCcceecCCCCCce---eeeeecCCCCCCCCceEEEEEEEeCC
Q psy8036 88 EYQSWEWRYGSTPKFT---ISQSFDIPDEHGAPGQLVISLEIVKG 129 (194)
Q Consensus 88 k~~sweW~yGktP~F~---~~~~~~~~~~~~~~G~i~v~l~v~~G 129 (194)
.=-+|.|.||- +... ....+.|.. .|...|.+.|.++
T Consensus 24 ~~~~y~W~fgd-~~~~~~~~~~t~ty~~----~G~y~V~ltv~n~ 63 (69)
T PF00801_consen 24 SPVTYSWDFGD-NGTVSTGSSVTHTYSS----PGTYTVTLTVTNG 63 (69)
T ss_dssp SECEEEEE-SS-ESEEECSSEEEEEESS----SEEEEEEEEEEET
T ss_pred CCeEEEEEECC-CCccccCCCEEEEcCC----CeEEEEEEEEEEC
Confidence 34567899998 2221 233333433 2899999998765
No 28
>PF10678 DUF2492: Protein of unknown function (DUF2492); InterPro: IPR019620 This entry describes a family of small cytosolic proteins, about 80 amino acids in length, in which the eight invariant residues include three His residues and two Cys residues. Two pairs of these invariant residues occur in motifs HxH (where x is A or G) and CxH, both of which suggest metal-binding activity. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulphatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulphur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulphatase/maturase systems.
Probab=48.93 E-value=33 Score=23.59 Aligned_cols=41 Identities=22% Similarity=0.315 Sum_probs=29.0
Q ss_pred HHHHhhc--CCCCCCHHHHHHHHHHHhhcCcccC-----CCchhhhhh
Q psy8036 152 AELLCSV--QGRKFTETALDDLKEALTSRGQTYL-----GTSLDRLVT 192 (194)
Q Consensus 152 ~~l~~~L--~G~~~~~~~i~~~l~~~~~~~~~~~-----~~~~~~~~~ 192 (194)
.++.+.| .|.+|+++++.+++.+---+...|- +++.++||.
T Consensus 7 HeVL~mmi~~~~~~t~~~L~~ai~~~FG~~arFhTCSae~m~a~eLv~ 54 (78)
T PF10678_consen 7 HEVLNMMIESGNPYTKEELKAAIIEKFGEDARFHTCSAEGMTADELVD 54 (78)
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHHHHhCCCceEEecCCCCCCHHHHHH
Confidence 4677788 8999999999988855432223333 478888874
No 29
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=44.22 E-value=58 Score=26.77 Aligned_cols=47 Identities=13% Similarity=0.132 Sum_probs=35.6
Q ss_pred ceEEEEEEEeCCeEEEEEEEcCCCCCCccccccHHHHHhhcCCCCCCHHHHHH
Q psy8036 118 GQLVISLEIVKGLIESVCFKIPPALVNDEHFLQDAELLCSVQGRKFTETALDD 170 (194)
Q Consensus 118 G~i~v~l~v~~G~I~~i~i~~~~~~~~~~df~~~~~l~~~L~G~~~~~~~i~~ 170 (194)
|.-++.+.|++|+|++|++--.+ -+-...-..+.|+|.+++......
T Consensus 131 GkP~~ei~v~~~~I~~V~VlR~a------PCGsT~~vAk~l~G~~~~d~~~~~ 177 (217)
T PF02593_consen 131 GKPKVEIEVENGKIKDVKVLRSA------PCGSTWFVAKRLIGKEVEDAPEKA 177 (217)
T ss_pred CCceEEEEecCCcEEEEEEEecC------CCccHHHHHHHhcCCccchhhhhh
Confidence 67778888899999999988410 233345677899999999877666
No 30
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=42.48 E-value=78 Score=20.82 Aligned_cols=43 Identities=28% Similarity=0.359 Sum_probs=28.0
Q ss_pred eEEEEEEEcCCCCCCccccccHHHHHhhcCCCCCCHHHHHHHHHHHh
Q psy8036 130 LIESVCFKIPPALVNDEHFLQDAELLCSVQGRKFTETALDDLKEALT 176 (194)
Q Consensus 130 ~I~~i~i~~~~~~~~~~df~~~~~l~~~L~G~~~~~~~i~~~l~~~~ 176 (194)
.|.+|.|.|. ..++. ....++.+.+.|.+++...+..+.+++.
T Consensus 2 ~i~~i~~~G~-~~~~~---~~l~~~~~~~~g~~l~~~~l~~~~~~l~ 44 (76)
T PF08479_consen 2 PIKGIRFEGN-TLLPE---EELQAILAPYIGRCLTLADLQQLADALT 44 (76)
T ss_dssp ---EEEEES--TSSSC---CHHHHHHGGGTTSBB-HHHHHHHHHHHH
T ss_pred CeEEEEEECC-CcCCH---HHHHHHHHHhcCCCcCHHHHHHHHHHHH
Confidence 3778899982 21221 1146777889999999999999988764
No 31
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=41.71 E-value=39 Score=20.44 Aligned_cols=37 Identities=11% Similarity=0.243 Sum_probs=27.0
Q ss_pred HHHHhhcCCCCCCHHHHHHHHHHHhhcCcccCCCchhhhhh
Q psy8036 152 AELLCSVQGRKFTETALDDLKEALTSRGQTYLGTSLDRLVT 192 (194)
Q Consensus 152 ~~l~~~L~G~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~ 192 (194)
.++.++|.+.-|++.++.+++..+.. . -+.+.+++|+
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~~~~--~--~~~~~e~~ik 40 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSKLLE--K--PGMDVEELIK 40 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHHHHH--S--TTS-HHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhhc--C--CCCCHHHHHH
Confidence 46778899999999999999998864 1 2345666664
No 32
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=39.44 E-value=49 Score=25.47 Aligned_cols=41 Identities=22% Similarity=0.284 Sum_probs=29.6
Q ss_pred ceEEEEEEEeCCeEEEEEEEcCCCCCCcccccc----HHHHHhhcCCCCCCH
Q psy8036 118 GQLVISLEIVKGLIESVCFKIPPALVNDEHFLQ----DAELLCSVQGRKFTE 165 (194)
Q Consensus 118 G~i~v~l~v~~G~I~~i~i~~~~~~~~~~df~~----~~~l~~~L~G~~~~~ 165 (194)
-.+.+.+.+++|+|++++|.|- -+.. ..-+.+.++|..+++
T Consensus 41 D~i~l~lkv~~~~I~d~~F~~~-------GC~is~ASss~~te~v~Gkti~E 85 (150)
T COG0822 41 DVITLYLKVDNGVIEDAKFKGF-------GCAISIASSSMMTELVKGKTLDE 85 (150)
T ss_pred ceEEEEEEEcCCEEEEEEeeec-------CcHHHHHHHHHHHHHHcCCCHHH
Confidence 3788999999999999999971 2221 123447888988763
No 33
>PRK14342 lipoate-protein ligase B; Provisional
Probab=38.67 E-value=29 Score=28.47 Aligned_cols=30 Identities=17% Similarity=0.127 Sum_probs=26.4
Q ss_pred cccccccccCCCCCHHHHHHHHHHHHHhhc
Q psy8036 22 APTLNLQEVCPEVSMDRLIKSLGYEYLRTK 51 (194)
Q Consensus 22 srVtNL~~~~~~i~~e~f~~~l~~~f~~~~ 51 (194)
.+||+|+++...++++++.+.+.++|.+.+
T Consensus 174 ~~vTSl~~~~~~~~~~~v~~~~~~~f~~~f 203 (213)
T PRK14342 174 LEMTQLSDLGGPATVDEVAPRLLAELLALL 203 (213)
T ss_pred CcEeeHHHhCCCCCHHHHHHHHHHHHHHHh
Confidence 679999887777999999999999999873
No 34
>PF11006 DUF2845: Protein of unknown function (DUF2845); InterPro: IPR021268 This bacterial family of proteins has no known function.
Probab=37.93 E-value=57 Score=22.47 Aligned_cols=14 Identities=14% Similarity=0.109 Sum_probs=9.5
Q ss_pred EEEEeCCeEEEEEE
Q psy8036 123 SLEIVKGLIESVCF 136 (194)
Q Consensus 123 ~l~v~~G~I~~i~i 136 (194)
.+..++|++.+|+-
T Consensus 72 ~l~f~~Gkl~~I~~ 85 (87)
T PF11006_consen 72 ILTFENGKLVRIES 85 (87)
T ss_pred EEEEECCEEEEEEe
Confidence 35557888888763
No 35
>COG3811 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.49 E-value=53 Score=22.58 Aligned_cols=45 Identities=22% Similarity=0.243 Sum_probs=30.6
Q ss_pred ceEEEEEEEeCCeEEEEEEEcCCCCCCcccccc-------HHHHHhhcCCCCCC
Q psy8036 118 GQLVISLEIVKGLIESVCFKIPPALVNDEHFLQ-------DAELLCSVQGRKFT 164 (194)
Q Consensus 118 G~i~v~l~v~~G~I~~i~i~~~~~~~~~~df~~-------~~~l~~~L~G~~~~ 164 (194)
|.|++.=+ ..|+|..++.++.-||+-. |+.- -..+.+.-.|.||.
T Consensus 18 GrIe~~rd-~~grI~~v~C~tRdGw~l~-dctlavF~kLKrK~li~S~~G~PYR 69 (85)
T COG3811 18 GRIEIERD-ASGRITSVECYTRDGWLLP-DCTLAVFRKLKRKKLIKSSQGGPYR 69 (85)
T ss_pred CeEEEEec-CCCcEEEEEEecccccccC-CccHHHHHHHHhccceeccCCCceE
Confidence 66665443 6889999999998899887 7632 12233444577775
No 36
>PRK14349 lipoate-protein ligase B; Provisional
Probab=35.88 E-value=35 Score=28.11 Aligned_cols=30 Identities=20% Similarity=0.203 Sum_probs=24.2
Q ss_pred cccccccccCCCCCHHHHHHHHHHHHHhhc
Q psy8036 22 APTLNLQEVCPEVSMDRLIKSLGYEYLRTK 51 (194)
Q Consensus 22 srVtNL~~~~~~i~~e~f~~~l~~~f~~~~ 51 (194)
..||+|++...+++++++.+.+.++|.+.+
T Consensus 175 ~~vTSl~~~g~~~~~~~v~~~l~~~f~~~f 204 (220)
T PRK14349 175 LRTVDLAACGVRTSVERAGELLAAQLARAH 204 (220)
T ss_pred CcEeeHHHhCCCCCHHHHHHHHHHHHHHHh
Confidence 356777666667999999999999999874
No 37
>TIGR02969 mam_aldehyde_ox aldehyde oxidase. Members of this family are mammalian aldehyde oxidase (EC 1.2.3.1) isozymes, closely related to xanthine dehydrogenase/oxidase.
Probab=35.42 E-value=1.1e+02 Score=31.82 Aligned_cols=53 Identities=15% Similarity=0.187 Sum_probs=38.4
Q ss_pred EEEEE--eCCeEEEEEEEcCCCCCCccccccHHHHHhhcCCCCCCHHHHHHHHHHHhh
Q psy8036 122 ISLEI--VKGLIESVCFKIPPALVNDEHFLQDAELLCSVQGRKFTETALDDLKEALTS 177 (194)
Q Consensus 122 v~l~v--~~G~I~~i~i~~~~~~~~~~df~~~~~l~~~L~G~~~~~~~i~~~l~~~~~ 177 (194)
+.+.+ ++|+|++++|.- |-+.+ ...-..+.++.|.|.+++.+.++++.+.+..
T Consensus 441 ~~v~l~~~~~~i~~aria~--Ggvap-~p~ra~~~E~~L~Gk~~~~~~~~~A~~~l~~ 495 (1330)
T TIGR02969 441 MRVFFGEGDGIIRELSISY--GGVGP-TTICAKNSCQKLIGRPWNEEMLDTACRLILD 495 (1330)
T ss_pred EEEEEEcCCCEEeEEEEEE--EcCcC-ceecHHHHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 44555 478999999985 32222 2222468899999999999999999877653
No 38
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=35.08 E-value=82 Score=20.92 Aligned_cols=24 Identities=17% Similarity=0.177 Sum_probs=16.7
Q ss_pred ceEEEEEEE-eCCeEEEEEEEcCCC
Q psy8036 118 GQLVISLEI-VKGLIESVCFKIPPA 141 (194)
Q Consensus 118 G~i~v~l~v-~~G~I~~i~i~~~~~ 141 (194)
+.+.|.|.+ .+|.|.+++|..+.|
T Consensus 26 ~~~~V~i~i~~dG~v~~~~i~~sSG 50 (85)
T PF13103_consen 26 LSVTVRITIDPDGRVISVRIVKSSG 50 (85)
T ss_dssp --EEEEEEE-TTSBEEEEEEEE--S
T ss_pred cEEEEEEEECCCCCEEEEEEecCCC
Confidence 577777777 689999999997555
No 39
>TIGR03195 4hydrxCoA_B 4-hydroxybenzoyl-CoA reductase, beta subunit. This model represents the second largest chain, beta, of the enzyme 4-hydroxybenzoyl-CoA reductase. In species capable of degrading various aromatic compounds by way of benzoyl-CoA, this enzyme can convert 4-hydroxybenzoyl-CoA to benzoyl-CoA.
Probab=34.36 E-value=1.9e+02 Score=25.13 Aligned_cols=54 Identities=13% Similarity=0.185 Sum_probs=36.2
Q ss_pred eEEEEEEEeCCeEEEEEEEcCCCCCCccccccHHHHHhhcCCCCCCHHHHHHHHHHHh
Q psy8036 119 QLVISLEIVKGLIESVCFKIPPALVNDEHFLQDAELLCSVQGRKFTETALDDLKEALT 176 (194)
Q Consensus 119 ~i~v~l~v~~G~I~~i~i~~~~~~~~~~df~~~~~l~~~L~G~~~~~~~i~~~l~~~~ 176 (194)
.+-+.++..+|+|.+++|.- |-+.+ -..-..+. +.|.|.+++.+.++++.+.+.
T Consensus 235 ~vav~l~~~~~~i~~~ria~--Ggva~-~p~r~~~~-e~l~G~~~~~~~~~~a~~~~~ 288 (321)
T TIGR03195 235 GVAVALQRDGDRIAGLRVAL--TGTNS-RPLMVPGT-DALAGRPLDDAAAEEIARLVR 288 (321)
T ss_pred EEEEEEEeCCCeEEEEEEEE--ECccC-ceeehHHH-HHhcCCCCCHHHHHHHHHHHH
Confidence 34556667788999999984 22222 11113343 668999999999988877654
No 40
>COG1433 Uncharacterized conserved protein [Function unknown]
Probab=34.18 E-value=48 Score=24.66 Aligned_cols=25 Identities=32% Similarity=0.543 Sum_probs=18.1
Q ss_pred ecCCCCCceeeeeecCCCCCCCCceEEEEEEEeCCeEEEEEEEc
Q psy8036 95 RYGSTPKFTISQSFDIPDEHGAPGQLVISLEIVKGLIESVCFKI 138 (194)
Q Consensus 95 ~yGktP~F~~~~~~~~~~~~~~~G~i~v~l~v~~G~I~~i~i~~ 138 (194)
-||++|.|.+. ++++|.|..+.+..
T Consensus 19 hFgrap~F~Iv-------------------d~e~g~i~~vev~~ 43 (121)
T COG1433 19 HFGRAPYFTIV-------------------DVEDGEIKNVEVIE 43 (121)
T ss_pred CccCCceEEEE-------------------EecCCcEEEEEEee
Confidence 46777777763 45678888888886
No 41
>cd00146 PKD polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases.
Probab=33.06 E-value=65 Score=21.06 Aligned_cols=36 Identities=14% Similarity=0.424 Sum_probs=21.3
Q ss_pred CCcceecCCC-CCce--eeeeecCCCCCCCCceEEEEEEEeCC
Q psy8036 90 QSWEWRYGST-PKFT--ISQSFDIPDEHGAPGQLVISLEIVKG 129 (194)
Q Consensus 90 ~sweW~yGkt-P~F~--~~~~~~~~~~~~~~G~i~v~l~v~~G 129 (194)
.++.|.||-. .... ....+.|+.. |...|.+.+.++
T Consensus 30 ~~~~W~fgdg~~~~~~~~~~~~~y~~~----G~y~v~l~v~d~ 68 (81)
T cd00146 30 VSYKWDFGDGEVSSSGEPTVTHTYTKP----GTYTVTLTVTNA 68 (81)
T ss_pred EEEEEEeCCCCccccCCCceEEEcCCC----cEEEEEEEEEeC
Confidence 4677888774 1111 2233334332 799999998775
No 42
>PF07244 Surf_Ag_VNR: Surface antigen variable number repeat; InterPro: IPR010827 This motif is found primarily in bacterial surface antigens, normally as variable number repeats at the N terminus. The C terminus of these proteins is normally represented by IPR000184 from INTERPRO. There may also be a relationship to haemolysin activator HlyB (IPR005565 from INTERPRO). The alignment centres on a -GY- or -GF- motif. Some members of this family are found in the mitochondria. It is predicted to have a mixed alpha/beta secondary structure.; GO: 0019867 outer membrane; PDB: 2X8X_X 3MC8_A 3OG5_A 3MC9_B 2QCZ_B 3EFC_A 3Q6B_A 2QDF_A 2V9H_A.
Probab=31.58 E-value=1.4e+02 Score=19.13 Aligned_cols=39 Identities=21% Similarity=0.220 Sum_probs=27.6
Q ss_pred eEEEEEEEcCCCCCCccc--cccHHHHHh---hcCCCCCCHHHHHHHHHHHh
Q psy8036 130 LIESVCFKIPPALVNDEH--FLQDAELLC---SVQGRKFTETALDDLKEALT 176 (194)
Q Consensus 130 ~I~~i~i~~~~~~~~~~d--f~~~~~l~~---~L~G~~~~~~~i~~~l~~~~ 176 (194)
+|.+|.|.| . .+....|.. .-.|.+|+...+.+....+.
T Consensus 2 ~i~~I~i~G--------n~~~~~~~~l~~~l~~~~G~~~~~~~i~~~~~~l~ 45 (78)
T PF07244_consen 2 RIGEINIEG--------NLKKFSDEELRRELGLKPGDPFNPEKIEEDIERLQ 45 (78)
T ss_dssp EEEEEEEES--------E-SSSHHHHHHHCHSS-TTSBECHHHHHHHHHHHH
T ss_pred EEEEEEEEc--------CceEeCHHHHHhhcCCCCCCEeCHHHHHHHHHHHH
Confidence 578999998 3 122334444 44599999999999988876
No 43
>COG2831 FhaC Hemolysin activation/secretion protein [Intracellular trafficking and secretion]
Probab=31.04 E-value=1.2e+02 Score=28.31 Aligned_cols=53 Identities=25% Similarity=0.307 Sum_probs=37.0
Q ss_pred ceEEEEEEEeCCeEEEEEEEcCCCCCCccccccHHHHHhhcCCCCCCHHHHHHHHHHHh
Q psy8036 118 GQLVISLEIVKGLIESVCFKIPPALVNDEHFLQDAELLCSVQGRKFTETALDDLKEALT 176 (194)
Q Consensus 118 G~i~v~l~v~~G~I~~i~i~~~~~~~~~~df~~~~~l~~~L~G~~~~~~~i~~~l~~~~ 176 (194)
|.+ .|.|-.|+|++|+|.+.... ..-....+.....|.+.+...|+..+..++
T Consensus 139 G~l--~l~VveG~i~~i~i~g~~~~----~~~~~~~~~p~~~g~~Ln~~~lEq~l~~l~ 191 (554)
T COG2831 139 GTL--RLQVVEGRIEDIRITGDSDL----RSVALRSLFPAHRGDPLNLRDLEQGLELLN 191 (554)
T ss_pred CeE--EEEEeceEeeeEEEcCCCcc----chhhHHhhccccCCCCCCHHHHHHHHHHhh
Confidence 564 57789999999999983210 000022334557899999999999998765
No 44
>PRK14343 lipoate-protein ligase B; Provisional
Probab=30.32 E-value=44 Score=27.83 Aligned_cols=29 Identities=7% Similarity=0.157 Sum_probs=23.8
Q ss_pred ccccccccCCCCCHHHHHHHHHHHHHhhc
Q psy8036 23 PTLNLQEVCPEVSMDRLIKSLGYEYLRTK 51 (194)
Q Consensus 23 rVtNL~~~~~~i~~e~f~~~l~~~f~~~~ 51 (194)
.||+|+++..+++++++.+.|+++|.+.+
T Consensus 190 ~vTSL~~lg~~~~~~~v~~~l~~~f~~~f 218 (235)
T PRK14343 190 ETVDMASLGVAADWADVAQTLARRLIANL 218 (235)
T ss_pred cEeeHHHhCCCCCHHHHHHHHHHHHHHHh
Confidence 56777666667899999999999999863
No 45
>PF00374 NiFeSe_Hases: Nickel-dependent hydrogenase; InterPro: IPR001501 Hydrogenases are enzymes that catalyze the reversible activation of hydrogen and which occur widely in prokaryotes as well as in some eukaryotes. There are various types of hydrogenases, but all of them seem to contain at least one iron-sulphur cluster. They can be broadly divided into two groups: hydrogenases containing nickel and, in some cases, also selenium (the [NiFe] and [NiFeSe] hydrogenases) and those lacking nickel (the [Fe] hydrogenases). The [NiFe] and [NiFeSe] hydrogenases are heterodimer that consist of a small subunit that contains a signal peptide and a large subunit. All the known large subunits seem to be evolutionary related []; they contain two Cys-x-x-Cys motifs; one at their N-terminal end; the other at their C-terminal end. These four cysteines are involved in the binding of nickel []. In the [NiFeSe] hydrogenases the first cysteine of the C-terminal motif is a selenocysteine which has experimentally been shown to be a nickel ligand [].; GO: 0016151 nickel ion binding; PDB: 1E3D_D 3USC_M 3USE_L 3UQY_M 3RGW_L 1CC1_L 1YQ9_I 2FRV_D 1FRV_B 3MYR_F ....
Probab=28.43 E-value=1.1e+02 Score=28.26 Aligned_cols=47 Identities=15% Similarity=0.120 Sum_probs=30.1
Q ss_pred ceEEEEEEEeCCeEEEEEEEcCCCC-CCcccccc-HHHHHhhcCCCCCC
Q psy8036 118 GQLVISLEIVKGLIESVCFKIPPAL-VNDEHFLQ-DAELLCSVQGRKFT 164 (194)
Q Consensus 118 G~i~v~l~v~~G~I~~i~i~~~~~~-~~~~df~~-~~~l~~~L~G~~~~ 164 (194)
|.+--.+.+++|+|++.++..|-.| .++-|... .-.++++|+|++..
T Consensus 435 G~L~H~~~i~~G~I~nyqiIvPTtwN~~Prd~~g~~g~~E~aLig~~v~ 483 (507)
T PF00374_consen 435 GALGHWIVIEDGKIKNYQIIVPTTWNASPRDENGQPGPYEQALIGTPVA 483 (507)
T ss_dssp EEEEEEEEEETTEEEEEEEEEHHHHHHS---TT----HHHHHHTT-B-S
T ss_pred cceEEEEEECCCeEEEEEEeCCCccchhhhhhccccHHHHHHhcCCCcc
Confidence 7888889999999999999976221 00002222 34789999999884
No 46
>TIGR03303 OM_YaeT outer membrane protein assembly complex, YaeT protein. Members of this protein family are the YaeT protein of the YaeT/YfiO complex for assembling proteins into the outer membrane of Gram-negative bacteria. This protein is similar in sequence and function to a non-essential paralog, YtfM, that is also in the Omp85 family. Members of this family typically have five tandem copies of the surface antigen variable number repeat (pfam07244), followed by an outer membrane beta-barrel domain (pfam01103), while the YtfM family typically has a single pfam07244 repeat.
Probab=26.65 E-value=2.3e+02 Score=26.70 Aligned_cols=51 Identities=22% Similarity=0.295 Sum_probs=35.5
Q ss_pred ceEEEEEEEeCC---eEEEEEEEcCCCCCCccccccHHHHHhhc------------CCCCCCHHHHHHHHHHH
Q psy8036 118 GQLVISLEIVKG---LIESVCFKIPPALVNDEHFLQDAELLCSV------------QGRKFTETALDDLKEAL 175 (194)
Q Consensus 118 G~i~v~l~v~~G---~I~~i~i~~~~~~~~~~df~~~~~l~~~L------------~G~~~~~~~i~~~l~~~ 175 (194)
+.+.|.+.|+.| +|.+|.|.|. ..+...+|.+.+ .|.+|+.+.+.+....+
T Consensus 136 ~~~~v~~~v~eg~~~~i~~i~~~Gn-------~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~i 201 (741)
T TIGR03303 136 NRVDLEFNIKEGKKAKIKKINFVGN-------KAFSDSELRDVFALKESNFWSWFTGDDKYSKQKLEADLELL 201 (741)
T ss_pred CeEEEEEEEecCCEEEEEEEEEECC-------CcCCHHHHHHHHhcCcchhHHhccCCCeECHHHHhhhHHHH
Confidence 578899999999 7999999983 222222333322 25789999998777665
No 47
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=26.11 E-value=39 Score=19.77 Aligned_cols=23 Identities=22% Similarity=0.275 Sum_probs=17.3
Q ss_pred ccccccccCCCCCHHHHHHHHHH
Q psy8036 23 PTLNLQEVCPEVSMDRLIKSLGY 45 (194)
Q Consensus 23 rVtNL~~~~~~i~~e~f~~~l~~ 45 (194)
-|..|++.+|+++.+.+..+|.+
T Consensus 4 ~v~~L~~mFP~~~~~~I~~~L~~ 26 (42)
T PF02845_consen 4 MVQQLQEMFPDLDREVIEAVLQA 26 (42)
T ss_dssp HHHHHHHHSSSS-HHHHHHHHHH
T ss_pred HHHHHHHHCCCCCHHHHHHHHHH
Confidence 35678899999999988887654
No 48
>PRK10170 hydrogenase 1 large subunit; Provisional
Probab=25.99 E-value=93 Score=29.55 Aligned_cols=46 Identities=15% Similarity=0.091 Sum_probs=34.4
Q ss_pred ceEEEEEEEeCCeEEEEEEEcCCCC-CCcccccc-HHHHHhhcCCCCC
Q psy8036 118 GQLVISLEIVKGLIESVCFKIPPAL-VNDEHFLQ-DAELLCSVQGRKF 163 (194)
Q Consensus 118 G~i~v~l~v~~G~I~~i~i~~~~~~-~~~~df~~-~~~l~~~L~G~~~ 163 (194)
|.+.--+.+++|+|++-++..|..| +++-|-.. .-.+|++|+|++.
T Consensus 510 GaL~HWi~Ie~gkI~nYQiVvPTTWN~sPRD~~g~~Gp~E~aLiGt~v 557 (597)
T PRK10170 510 GALGHWAAIRDGKIDLYQCVVPTTWNASPRDPKGQIGAYEAALMNTKM 557 (597)
T ss_pred ccceeeEEEeCCeEecceEeCCCCCCCCCCCCCCCcCHHHHHhcCCCc
Confidence 7888889999999999999988554 11112222 3588999999996
No 49
>COG0810 TonB Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]
Probab=24.97 E-value=1.2e+02 Score=24.83 Aligned_cols=24 Identities=17% Similarity=0.285 Sum_probs=20.9
Q ss_pred ceEEEEEEE-eCCeEEEEEEEcCCC
Q psy8036 118 GQLVISLEI-VKGLIESVCFKIPPA 141 (194)
Q Consensus 118 G~i~v~l~v-~~G~I~~i~i~~~~~ 141 (194)
|.+.|.|+| .+|.|.+++|....|
T Consensus 180 G~V~V~f~i~~~G~v~~v~v~~SSg 204 (244)
T COG0810 180 GTVKVKFTIDPDGNVTNVRVLKSSG 204 (244)
T ss_pred ceEEEEEEECCCCCEeeeEEeecCC
Confidence 899999999 688999999997554
No 50
>PRK13687 hypothetical protein; Provisional
Probab=24.78 E-value=1.3e+02 Score=20.93 Aligned_cols=45 Identities=18% Similarity=0.175 Sum_probs=30.1
Q ss_pred ceEEEEEEEeCCeEEEEEEEcCCCCCCcccccc-----H--HHHHhhcCCCCCC
Q psy8036 118 GQLVISLEIVKGLIESVCFKIPPALVNDEHFLQ-----D--AELLCSVQGRKFT 164 (194)
Q Consensus 118 G~i~v~l~v~~G~I~~i~i~~~~~~~~~~df~~-----~--~~l~~~L~G~~~~ 164 (194)
|.|.+.=+ .+|+|.++..++.-||+=. |+.- + ..|.+.-.|.||.
T Consensus 18 GrI~~~rd-~~gri~~v~C~TReG~~l~-dctl~vF~kLK~krlI~S~~G~PYR 69 (85)
T PRK13687 18 GRIEHERD-DSGRITAVECYTREGWLLA-DCTLAVFKKLKRKRLIKSVNGQPYR 69 (85)
T ss_pred CeEEEEEC-CCCcEEEEEEEccCCcccC-CCCHHHHHHHHhhcceecCCCCCeE
Confidence 56555443 7899999999998888776 6642 1 2333444588885
No 51
>PF10055 DUF2292: Uncharacterized small protein (DUF2292); InterPro: IPR018743 Members of this family of hypothetical bacterial proteins have no known function.
Probab=23.68 E-value=1.4e+02 Score=17.51 Aligned_cols=15 Identities=13% Similarity=0.231 Sum_probs=11.7
Q ss_pred EEEEEeCCeEEEEEE
Q psy8036 122 ISLEIVKGLIESVCF 136 (194)
Q Consensus 122 v~l~v~~G~I~~i~i 136 (194)
|.+.|++|+|..+.-
T Consensus 18 V~iiiqdG~vvQIe~ 32 (38)
T PF10055_consen 18 VTIIIQDGRVVQIEK 32 (38)
T ss_pred EEEEEECCEEEEEEh
Confidence 567789999988763
No 52
>COG0321 LipB Lipoate-protein ligase B [Coenzyme metabolism]
Probab=22.59 E-value=80 Score=26.04 Aligned_cols=29 Identities=21% Similarity=0.379 Sum_probs=26.1
Q ss_pred cccccccccCCCCCHHHHHHHHHHHHHhh
Q psy8036 22 APTLNLQEVCPEVSMDRLIKSLGYEYLRT 50 (194)
Q Consensus 22 srVtNL~~~~~~i~~e~f~~~l~~~f~~~ 50 (194)
..||.|++..+..+++++..+|.++|.+.
T Consensus 181 ~~~tsl~d~~~~v~~~~V~~~l~~~~~~~ 209 (221)
T COG0321 181 MEVTSLSDLGPPVTVDEVAKALVAAFAKL 209 (221)
T ss_pred CceeEHHHhCCCCcHHHHHHHHHHHHHHH
Confidence 56899999888899999999999999986
No 53
>TIGR03303 OM_YaeT outer membrane protein assembly complex, YaeT protein. Members of this protein family are the YaeT protein of the YaeT/YfiO complex for assembling proteins into the outer membrane of Gram-negative bacteria. This protein is similar in sequence and function to a non-essential paralog, YtfM, that is also in the Omp85 family. Members of this family typically have five tandem copies of the surface antigen variable number repeat (pfam07244), followed by an outer membrane beta-barrel domain (pfam01103), while the YtfM family typically has a single pfam07244 repeat.
Probab=22.20 E-value=3.3e+02 Score=25.68 Aligned_cols=48 Identities=21% Similarity=0.396 Sum_probs=33.6
Q ss_pred EEEEEEeCC-eEEEEEEEcCCCCCCccccccHHHHHhhc----CCCCCCHHHHHHHHHHH
Q psy8036 121 VISLEIVKG-LIESVCFKIPPALVNDEHFLQDAELLCSV----QGRKFTETALDDLKEAL 175 (194)
Q Consensus 121 ~v~l~v~~G-~I~~i~i~~~~~~~~~~df~~~~~l~~~L----~G~~~~~~~i~~~l~~~ 175 (194)
.+.+.|+.+ +|.+|+|.|. ..+...+|.+.+ .|.+|++..+++.+..+
T Consensus 60 ~l~~~v~e~~~i~~i~~~G~-------~~~~~~~l~~~~~~~~~g~~~~~~~~~~~~~~l 112 (741)
T TIGR03303 60 VLVIKVKERPIINSIVFSGN-------KEIKKDQLKKALVGIKKGEIFNRAKLEKDEKAL 112 (741)
T ss_pred EEEEEEEecceEEEEEEECC-------ccCCHHHHHHHHhhccCCCcCCHHHHHHHHHHH
Confidence 355666555 8899999983 222234555555 69999999999888776
No 54
>PF14814 UB2H: Bifunctional transglycosylase second domain; PDB: 3FWL_A 3VMA_A.
Probab=21.45 E-value=1.5e+02 Score=20.18 Aligned_cols=31 Identities=23% Similarity=0.357 Sum_probs=19.6
Q ss_pred eeeeecCCCCCCCCceEEEEEEEeCCeEEEEEE
Q psy8036 104 ISQSFDIPDEHGAPGQLVISLEIVKGLIESVCF 136 (194)
Q Consensus 104 ~~~~~~~~~~~~~~G~i~v~l~v~~G~I~~i~i 136 (194)
+...+.|+.+.. ..-.+.++..+|+|..|.-
T Consensus 43 ~~R~F~F~Dg~e--~~~~~~l~f~~~~V~~i~~ 73 (85)
T PF14814_consen 43 YTRGFDFPDGQE--PARRVRLTFSGGRVSSIQD 73 (85)
T ss_dssp EE--EEETTCEE----EEEEEEEETTEEEEEEE
T ss_pred EECCCCCCCCCc--cCEEEEEEECCCEEEEEEE
Confidence 355566665322 4566888889999999985
No 55
>PRK10467 hydrogenase 2 large subunit; Provisional
Probab=21.20 E-value=1.5e+02 Score=27.98 Aligned_cols=21 Identities=29% Similarity=0.374 Sum_probs=19.6
Q ss_pred ceEEEEEEEeCCeEEEEEEEc
Q psy8036 118 GQLVISLEIVKGLIESVCFKI 138 (194)
Q Consensus 118 G~i~v~l~v~~G~I~~i~i~~ 138 (194)
|.++|.+.+++|+|.++.+.+
T Consensus 15 G~lri~v~vd~g~V~~a~~~g 35 (567)
T PRK10467 15 GHLRIDCEIENGVVSKAWASG 35 (567)
T ss_pred eEEEEEEEEECCEEEEEEEcC
Confidence 799999999999999999876
No 56
>COG3938 Proline racemase [Amino acid transport and metabolism]
Probab=20.52 E-value=1.9e+02 Score=25.17 Aligned_cols=21 Identities=24% Similarity=0.311 Sum_probs=20.0
Q ss_pred ceEEEEEEEeCCeEEEEEEEc
Q psy8036 118 GQLVISLEIVKGLIESVCFKI 138 (194)
Q Consensus 118 G~i~v~l~v~~G~I~~i~i~~ 138 (194)
|.|++..++++|+.+.|++..
T Consensus 124 GlV~~~a~crdGk~E~V~l~N 144 (341)
T COG3938 124 GLVEATAECRDGKVERVRLRN 144 (341)
T ss_pred cEEEEEEEecCCcEEEEEEEc
Confidence 899999999999999999986
No 57
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=20.16 E-value=80 Score=23.68 Aligned_cols=32 Identities=16% Similarity=0.122 Sum_probs=20.5
Q ss_pred ccccccccccccCC--CCCHHHHHHHHHHHHHhh
Q psy8036 19 STPAPTLNLQEVCP--EVSMDRLIKSLGYEYLRT 50 (194)
Q Consensus 19 SVrsrVtNL~~~~~--~i~~e~f~~~l~~~f~~~ 50 (194)
.++.|+..|...+. .+|+-.+++.|+...++.
T Consensus 88 e~h~~l~~Iv~~ig~~~~si~~yidNIL~~Hle~ 121 (136)
T PF11888_consen 88 ETHERLSRIVRVIGERKMSISGYIDNILRHHLEE 121 (136)
T ss_pred HHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHH
Confidence 34455555555443 488888888888776654
Done!