Query 034397
Match_columns 96
No_of_seqs 15 out of 17
Neff 2.0
Searched_HMMs 46136
Date Fri Mar 29 02:25:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034397.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034397hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05886 yajC preprotein trans 79.8 0.76 1.6E-05 32.5 0.6 28 27-54 5-32 (109)
2 PF15141 DUF4574: Domain of un 77.0 1.4 3.1E-05 30.5 1.3 34 20-53 1-36 (84)
3 PF05057 DUF676: Putative seri 75.0 0.68 1.5E-05 33.6 -0.7 12 14-25 81-92 (217)
4 COG1862 YajC Preprotein transl 69.1 2.8 6.1E-05 29.1 1.3 33 25-57 8-40 (97)
5 TIGR00739 yajC preprotein tran 67.0 5.2 0.00011 26.5 2.2 27 28-54 5-31 (84)
6 PRK05585 yajC preprotein trans 62.3 4.1 8.9E-05 28.2 1.0 30 27-56 19-48 (106)
7 smart00318 SNc Staphylococcal 59.8 21 0.00046 23.4 4.1 24 25-48 90-113 (138)
8 PF02699 YajC: Preprotein tran 56.7 1.7 3.7E-05 28.4 -1.5 28 27-54 3-30 (82)
9 PF04612 T2SM: Type II secreti 52.0 4.8 0.0001 27.3 0.0 29 29-57 21-49 (160)
10 PRK06518 hypothetical protein; 50.4 24 0.00052 26.2 3.5 22 25-46 110-131 (177)
11 PRK06531 yajC preprotein trans 47.7 16 0.00034 25.9 2.1 26 28-54 5-30 (113)
12 PF14283 DUF4366: Domain of un 45.1 16 0.00035 28.2 1.9 18 34-51 172-190 (218)
13 cd00175 SNc Staphylococcal nuc 41.0 65 0.0014 20.7 4.1 22 26-47 83-104 (129)
14 PTZ00046 rifin; Provisional 39.4 8.2 0.00018 32.4 -0.5 36 17-54 141-176 (358)
15 PF05728 UPF0227: Uncharacteri 37.3 7.1 0.00015 28.7 -1.0 30 14-50 62-93 (187)
16 PF11760 CbiG_N: Cobalamin syn 36.0 20 0.00044 24.3 1.1 27 13-39 48-74 (84)
17 PF07819 PGAP1: PGAP1-like pro 36.0 8.7 0.00019 28.4 -0.7 12 15-26 89-100 (225)
18 PRK09697 protein secretion pro 35.9 3.6 7.7E-05 31.0 -2.8 44 33-81 45-93 (139)
19 PF13132 DUF3950: Domain of un 35.8 20 0.00044 21.0 0.9 10 25-34 13-22 (30)
20 COG3389 Uncharacterized protei 32.2 18 0.00039 29.9 0.4 24 25-48 89-112 (277)
21 PLN02965 Probable pheophorbida 32.0 12 0.00027 26.2 -0.5 11 14-24 75-85 (255)
22 PF07225 NDUF_B4: NADH-ubiquin 30.2 24 0.00052 25.5 0.7 34 48-85 23-57 (125)
23 PF09819 ABC_cobalt: ABC-type 27.3 16 0.00035 26.1 -0.5 25 29-53 44-68 (129)
24 PRK07718 fliL flagellar basal 27.1 15 0.00033 25.8 -0.7 23 30-52 14-36 (142)
25 PRK11126 2-succinyl-6-hydroxy- 27.1 12 0.00027 25.2 -1.1 10 14-23 69-78 (242)
26 PF14960 ATP_synth_reg: ATP sy 27.0 25 0.00055 22.3 0.4 25 23-47 22-48 (49)
27 PRK08775 homoserine O-acetyltr 26.8 13 0.00029 27.8 -1.1 10 14-23 141-150 (343)
28 PLN02211 methyl indole-3-aceta 26.2 16 0.00034 26.8 -0.8 11 14-24 90-100 (273)
29 PF13906 AA_permease_C: C-term 26.1 28 0.0006 21.4 0.4 15 29-43 32-46 (51)
30 KOG4040 NADH:ubiquinone oxidor 25.1 41 0.00089 26.5 1.3 41 45-90 37-77 (186)
31 COG1565 Uncharacterized conser 24.6 72 0.0016 27.1 2.7 47 40-88 111-157 (370)
32 PF13706 PepSY_TM_3: PepSY-ass 24.0 26 0.00057 19.9 0.0 18 29-49 19-36 (37)
33 PF11943 DUF3460: Protein of u 23.8 46 0.00099 21.8 1.1 26 42-68 32-57 (60)
34 PF13396 PLDc_N: Phospholipase 23.4 93 0.002 17.5 2.3 23 24-46 17-46 (46)
35 PF11167 DUF2953: Protein of u 23.2 11 0.00025 22.2 -1.7 11 76-86 6-16 (53)
36 COG1525 Micrococcal nuclease ( 22.8 2.3E+02 0.005 20.0 4.6 20 24-43 127-146 (192)
37 PHA00431 internal virion prote 21.3 53 0.0012 30.4 1.4 54 1-54 1-72 (746)
38 PRK07581 hypothetical protein; 21.0 19 0.00041 26.5 -1.2 12 14-25 127-138 (339)
39 PRK09689 prophage protein NinE 20.3 45 0.00097 22.0 0.6 12 70-81 20-31 (56)
No 1
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=79.81 E-value=0.76 Score=32.50 Aligned_cols=28 Identities=4% Similarity=0.018 Sum_probs=21.3
Q ss_pred chHHHHHHhhhheeeEEEcCchhhHHHH
Q 034397 27 ANLASWVVAGTLAYYLWVKPSQDLKREQ 54 (96)
Q Consensus 27 ~nlAaW~VAG~lAYylwvkPe~~~~~eq 54 (96)
..+.-+++..++-|||.++|.|.+++|+
T Consensus 5 ~~ll~lv~i~~i~yF~~iRPQkKr~K~~ 32 (109)
T PRK05886 5 VLFLPFLLIMGGFMYFASRRQRKAMQAT 32 (109)
T ss_pred HHHHHHHHHHHHHHHHHccHHHHHHHHH
Confidence 4566677778888999999986665554
No 2
>PF15141 DUF4574: Domain of unknown function (DUF4574)
Probab=76.99 E-value=1.4 Score=30.52 Aligned_cols=34 Identities=26% Similarity=0.513 Sum_probs=21.9
Q ss_pred ccccCCcchHHHHHHhhhheeeEEE--cCchhhHHH
Q 034397 20 MGGVRGGANLASWVVAGTLAYYLWV--KPSQDLKRE 53 (96)
Q Consensus 20 mgG~RG~~nlAaW~VAG~lAYylwv--kPe~~~~~e 53 (96)
|+++|=--+..+=+-+||++|.||+ .|..+.++|
T Consensus 1 M~~~r~~~~~~~llG~GGvG~~L~~LvtPgeerK~e 36 (84)
T PF15141_consen 1 MSSLRKALSVVALLGFGGVGYALFVLVTPGEERKQE 36 (84)
T ss_pred CchHHHHHHHHHHHHccchhheeeeEeCCcHHHHHH
Confidence 4455544555666678999999986 466654433
No 3
>PF05057 DUF676: Putative serine esterase (DUF676); InterPro: IPR007751 This domain, whose function is unknown, is found within a group of putative lipases.
Probab=74.95 E-value=0.68 Score=33.55 Aligned_cols=12 Identities=50% Similarity=1.060 Sum_probs=10.4
Q ss_pred hhhhhcccccCC
Q 034397 14 SFVGNSMGGVRG 25 (96)
Q Consensus 14 sfi~n~mgG~RG 25 (96)
||||.||||+--
T Consensus 81 sfIgHSLGGli~ 92 (217)
T PF05057_consen 81 SFIGHSLGGLIA 92 (217)
T ss_pred eEEEecccHHHH
Confidence 899999999843
No 4
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=69.14 E-value=2.8 Score=29.10 Aligned_cols=33 Identities=24% Similarity=0.403 Sum_probs=25.9
Q ss_pred CcchHHHHHHhhhheeeEEEcCchhhHHHHHHH
Q 034397 25 GGANLASWVVAGTLAYYLWVKPSQDLKREQEER 57 (96)
Q Consensus 25 G~~nlAaW~VAG~lAYylwvkPe~~~~~eqe~R 57 (96)
+.+.+.--++..++-|||.++|.|...+|.++.
T Consensus 8 ~~~~ll~~vl~~~ifyFli~RPQrKr~K~~~~m 40 (97)
T COG1862 8 GLVLLLPLVLIFAIFYFLIIRPQRKRMKEHQEL 40 (97)
T ss_pred cHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Confidence 345677788899999999999988777666554
No 5
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=67.02 E-value=5.2 Score=26.51 Aligned_cols=27 Identities=19% Similarity=0.452 Sum_probs=19.2
Q ss_pred hHHHHHHhhhheeeEEEcCchhhHHHH
Q 034397 28 NLASWVVAGTLAYYLWVKPSQDLKREQ 54 (96)
Q Consensus 28 nlAaW~VAG~lAYylwvkPe~~~~~eq 54 (96)
.|.-.++...+-|||.++|.+.+++++
T Consensus 5 ~l~~~vv~~~i~yf~~~rpqkK~~k~~ 31 (84)
T TIGR00739 5 TLLPLVLIFLIFYFLIIRPQRKRRKAH 31 (84)
T ss_pred HHHHHHHHHHHHHHheechHHHHHHHH
Confidence 345556667778999999987665555
No 6
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=62.34 E-value=4.1 Score=28.18 Aligned_cols=30 Identities=27% Similarity=0.512 Sum_probs=22.1
Q ss_pred chHHHHHHhhhheeeEEEcCchhhHHHHHH
Q 034397 27 ANLASWVVAGTLAYYLWVKPSQDLKREQEE 56 (96)
Q Consensus 27 ~nlAaW~VAG~lAYylwvkPe~~~~~eqe~ 56 (96)
..+.-+++...+-|||-++|.+.+++++++
T Consensus 19 ~~ll~lvii~~i~yf~~~RpqkK~~k~~~~ 48 (106)
T PRK05585 19 SSLLPLVVFFAIFYFLIIRPQQKRQKEHKK 48 (106)
T ss_pred HHHHHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence 456667777778899999998877766533
No 7
>smart00318 SNc Staphylococcal nuclease homologues.
Probab=59.76 E-value=21 Score=23.38 Aligned_cols=24 Identities=29% Similarity=0.295 Sum_probs=19.7
Q ss_pred CcchHHHHHHhhhheeeEEEcCch
Q 034397 25 GGANLASWVVAGTLAYYLWVKPSQ 48 (96)
Q Consensus 25 G~~nlAaW~VAG~lAYylwvkPe~ 48 (96)
++.|++.++|.-|+|+.....+..
T Consensus 90 ~~~~l~~~Lv~~G~A~~~~~~~~~ 113 (138)
T smart00318 90 GGNNIAEELVKEGLAKVYRYADKD 113 (138)
T ss_pred CCCcHHHHHHhcCCEEEEEecCcc
Confidence 457899999999999988776553
No 8
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=56.69 E-value=1.7 Score=28.38 Aligned_cols=28 Identities=21% Similarity=0.497 Sum_probs=20.3
Q ss_pred chHHHHHHhhhheeeEEEcCchhhHHHH
Q 034397 27 ANLASWVVAGTLAYYLWVKPSQDLKREQ 54 (96)
Q Consensus 27 ~nlAaW~VAG~lAYylwvkPe~~~~~eq 54 (96)
..+.-.++...+-|||.++|.+.+++|+
T Consensus 3 ~~li~lv~~~~i~yf~~~rpqkk~~k~~ 30 (82)
T PF02699_consen 3 SMLIPLVIIFVIFYFLMIRPQKKQQKEH 30 (82)
T ss_dssp HHHHHHHHHHHHHHHHTHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhheecHHHHHHHHH
Confidence 3566677778888999999987555544
No 9
>PF04612 T2SM: Type II secretion system (T2SS), protein M; InterPro: IPR007690 General secretion pathway (GSP) protein M is a membrane protein involved in the export of proteins in bacteria. It consists of a short cytosolic N-terminal domain, a transmembrane domain, and a C-terminal periplasmic domain. The precise function of this protein is unknown, though in Vibrio cholerae, the EpsM protein interacts with the EpsL protein, and also forms homodimers [],; GO: 0006858 extracellular transport; PDB: 1UV7_A.
Probab=52.04 E-value=4.8 Score=27.32 Aligned_cols=29 Identities=17% Similarity=0.268 Sum_probs=0.0
Q ss_pred HHHHHHhhhheeeEEEcCchhhHHHHHHH
Q 034397 29 LASWVVAGTLAYYLWVKPSQDLKREQEER 57 (96)
Q Consensus 29 lAaW~VAG~lAYylwvkPe~~~~~eqe~R 57 (96)
+++.+++..+.|++.+.|-.+..+..+++
T Consensus 21 ~~~~~l~~~l~~~~~~~P~~~~~~~~~~~ 49 (160)
T PF04612_consen 21 VLGVVLLLALLYLLLWQPLLERRDQLQQQ 49 (160)
T ss_dssp -----------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35678888999999999988777665443
No 10
>PRK06518 hypothetical protein; Provisional
Probab=50.38 E-value=24 Score=26.24 Aligned_cols=22 Identities=18% Similarity=0.133 Sum_probs=18.1
Q ss_pred CcchHHHHHHhhhheeeEEEcC
Q 034397 25 GGANLASWVVAGTLAYYLWVKP 46 (96)
Q Consensus 25 G~~nlAaW~VAG~lAYylwvkP 46 (96)
++.+|..++|.-|+|+.....+
T Consensus 110 ~g~dln~~mV~~G~A~ay~~~~ 131 (177)
T PRK06518 110 DGVDIAALGLAEGMAVLSKDDH 131 (177)
T ss_pred CCEEHHHHHHhCCCEEEEeecc
Confidence 4679999999999998766544
No 11
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=47.71 E-value=16 Score=25.94 Aligned_cols=26 Identities=15% Similarity=0.289 Sum_probs=15.3
Q ss_pred hHHHHHHhhhheeeEEEcCchhhHHHH
Q 034397 28 NLASWVVAGTLAYYLWVKPSQDLKREQ 54 (96)
Q Consensus 28 nlAaW~VAG~lAYylwvkPe~~~~~eq 54 (96)
.+.-.++..++-| |.++|.|.+++++
T Consensus 5 ~il~~vv~~~i~y-f~iRPQkKr~Ke~ 30 (113)
T PRK06531 5 TIIMFVVMLGLIF-FMQRQQKKQAQER 30 (113)
T ss_pred HHHHHHHHHHHHH-heechHHHHHHHH
Confidence 3444455555655 4689976665554
No 12
>PF14283 DUF4366: Domain of unknown function (DUF4366)
Probab=45.09 E-value=16 Score=28.18 Aligned_cols=18 Identities=39% Similarity=0.787 Sum_probs=10.7
Q ss_pred HhhhheeeE-EEcCchhhH
Q 034397 34 VAGTLAYYL-WVKPSQDLK 51 (96)
Q Consensus 34 VAG~lAYyl-wvkPe~~~~ 51 (96)
.+||.+||| ++||-++.+
T Consensus 172 ~gGGa~yYfK~~K~K~~~~ 190 (218)
T PF14283_consen 172 IGGGAYYYFKFYKPKQEEK 190 (218)
T ss_pred hhcceEEEEEEeccccccc
Confidence 445555555 778866544
No 13
>cd00175 SNc Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.
Probab=40.97 E-value=65 Score=20.74 Aligned_cols=22 Identities=32% Similarity=0.323 Sum_probs=19.2
Q ss_pred cchHHHHHHhhhheeeEEEcCc
Q 034397 26 GANLASWVVAGTLAYYLWVKPS 47 (96)
Q Consensus 26 ~~nlAaW~VAG~lAYylwvkPe 47 (96)
+.|++.++|.-|+|...-..+.
T Consensus 83 ~~~v~~~Lv~~G~A~~~~~~~~ 104 (129)
T cd00175 83 GENIAEELVKEGLARVYRYYPD 104 (129)
T ss_pred CCcHHHHHHhcCCEEEEEECCC
Confidence 5799999999999998877764
No 14
>PTZ00046 rifin; Provisional
Probab=39.39 E-value=8.2 Score=32.37 Aligned_cols=36 Identities=22% Similarity=0.337 Sum_probs=25.5
Q ss_pred hhcccccCCcchHHHHHHhhhheeeEEEcCchhhHHHH
Q 034397 17 GNSMGGVRGGANLASWVVAGTLAYYLWVKPSQDLKREQ 54 (96)
Q Consensus 17 ~n~mgG~RG~~nlAaW~VAG~lAYylwvkPe~~~~~eq 54 (96)
-++-+|| | .=..+|++-||+||+-|..-......+.
T Consensus 141 LkCG~~L-G-gVaP~~Gliggi~~~~Wk~~a~~aA~~a 176 (358)
T PTZ00046 141 LRCGCGL-G-GVAPSWGLIGGIAVNAWKKAALAAAIKA 176 (358)
T ss_pred HhcCCcc-c-cccccccccchHHHHHHHHHHHHHHHHH
Confidence 3555666 5 4678999999999999976555544443
No 15
>PF05728 UPF0227: Uncharacterised protein family (UPF0227); InterPro: IPR008886 Despite being classed as uncharacterised proteins, the members of this family are almost certainly enzymes in that they contain a domain distantly related to IPR000073 from INTERPRO. One of the members of this family YqiA has been shown to be a esterase []. Other members, which include the Escherichia coli (strain K12) YcfP protein are uncharacterised.
Probab=37.31 E-value=7.1 Score=28.66 Aligned_cols=30 Identities=27% Similarity=0.609 Sum_probs=17.6
Q ss_pred hhhhhcccccCCcchHHHHHHh--hhheeeEEEcCchhh
Q 034397 14 SFVGNSMGGVRGGANLASWVVA--GTLAYYLWVKPSQDL 50 (96)
Q Consensus 14 sfi~n~mgG~RG~~nlAaW~VA--G~lAYylwvkPe~~~ 50 (96)
-+||.||||+ +|.|.-. |.=+ +.+-|.-.-
T Consensus 62 ~liGSSlGG~-----~A~~La~~~~~~a--vLiNPav~p 93 (187)
T PF05728_consen 62 VLIGSSLGGF-----YATYLAERYGLPA--VLINPAVRP 93 (187)
T ss_pred EEEEEChHHH-----HHHHHHHHhCCCE--EEEcCCCCH
Confidence 5799999998 4444421 2223 556665543
No 16
>PF11760 CbiG_N: Cobalamin synthesis G N-terminal; InterPro: IPR021744 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 []. Within the cobalamin synthesis pathway CbiG catalyses the both the opening of the lactone ring and the extrusion of the two-carbon fragment of cobalt-precorrin-5A from C-20 and its associated methyl group (deacylation) to give cobalt-precorrin-5B. The N-terminal of the enzyme is conserved in this family, and the C-terminal and the mid-sections are conserved independently in other families, CbiG_C and CbiG_mid, although the distinct function of each region is unclear. ; PDB: 3EEQ_B.
Probab=36.00 E-value=20 Score=24.26 Aligned_cols=27 Identities=41% Similarity=0.516 Sum_probs=20.0
Q ss_pred hhhhhhcccccCCcchHHHHHHhhhhe
Q 034397 13 RSFVGNSMGGVRGGANLASWVVAGTLA 39 (96)
Q Consensus 13 rsfi~n~mgG~RG~~nlAaW~VAG~lA 39 (96)
-+|+.-.+||-+|+.|-.|.-+|-.|.
T Consensus 48 g~~vIplL~GH~GGan~lA~~iA~~lg 74 (84)
T PF11760_consen 48 GRFVIPLLGGHRGGANELARQIAELLG 74 (84)
T ss_dssp --EEEEEE-TTTT-HHHHHHHHHHHTT
T ss_pred CCEEEEeccCCcchHHHHHHHHHHHhC
Confidence 368888999999999999999887653
No 17
>PF07819 PGAP1: PGAP1-like protein; InterPro: IPR012908 The sequences found in this family are similar to PGAP1 (Q765A7 from SWISSPROT). This is an endoplasmic reticulum membrane protein with a catalytic serine-containing motif that is conserved in a number of lipases. PGAP1 functions as a GPI inositol-deacylase; this deacylation is important for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006505 GPI anchor metabolic process, 0006886 intracellular protein transport, 0031227 intrinsic to endoplasmic reticulum membrane
Probab=35.99 E-value=8.7 Score=28.41 Aligned_cols=12 Identities=50% Similarity=0.894 Sum_probs=9.7
Q ss_pred hhhhcccccCCc
Q 034397 15 FVGNSMGGVRGG 26 (96)
Q Consensus 15 fi~n~mgG~RG~ 26 (96)
+||.||||+--+
T Consensus 89 lVgHSmGGlvar 100 (225)
T PF07819_consen 89 LVGHSMGGLVAR 100 (225)
T ss_pred EEEEchhhHHHH
Confidence 789999998544
No 18
>PRK09697 protein secretion protein GspB; Provisional
Probab=35.86 E-value=3.6 Score=30.95 Aligned_cols=44 Identities=27% Similarity=0.382 Sum_probs=27.7
Q ss_pred HHhhhheeeEEEcCchhhHHHHHHHHHHHc-----cCCCcceeeccCCCCCccc
Q 034397 33 VVAGTLAYYLWVKPSQDLKREQEERAALAA-----LDPNRYVEKRKPIPDPQET 81 (96)
Q Consensus 33 ~VAG~lAYylwvkPe~~~~~eqe~RAAlA~-----~d~~rYVEkrkpipdpq~t 81 (96)
+|.||-||-||+.=--+ +++--.+. ..+-.||=|.+|.|-|.+.
T Consensus 45 ~~~GGYA~Qlwvlw~~k-----~~~T~~~~tP~~~Qs~qH~~FKKqPLPV~E~V 93 (139)
T PRK09697 45 VLVGGYARQLWVLWIVK-----AEVTVEAETPAFKQSTQHYFFKKQPLPVVESV 93 (139)
T ss_pred eeechhHHHHHHHHHHh-----hhheecCCCcchhhhhhheeeecCCCCCcccc
Confidence 56789999988753222 22222222 3345699999999988654
No 19
>PF13132 DUF3950: Domain of unknown function (DUF3950)
Probab=35.83 E-value=20 Score=21.03 Aligned_cols=10 Identities=40% Similarity=1.046 Sum_probs=8.6
Q ss_pred CcchHHHHHH
Q 034397 25 GGANLASWVV 34 (96)
Q Consensus 25 G~~nlAaW~V 34 (96)
|..|+.|||.
T Consensus 13 ~~~NFSaWV~ 22 (30)
T PF13132_consen 13 GSGNFSAWVK 22 (30)
T ss_pred cCcChHHHHH
Confidence 5789999986
No 20
>COG3389 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.22 E-value=18 Score=29.92 Aligned_cols=24 Identities=33% Similarity=0.303 Sum_probs=21.0
Q ss_pred CcchHHHHHHhhhheeeEEEcCch
Q 034397 25 GGANLASWVVAGTLAYYLWVKPSQ 48 (96)
Q Consensus 25 G~~nlAaW~VAG~lAYylwvkPe~ 48 (96)
+.-|++||.+|-++-|-|+.+||=
T Consensus 89 ~~i~~~si~~aI~~~~lL~~~peW 112 (277)
T COG3389 89 YAINIASIGLAIGLVYLLYKYPEW 112 (277)
T ss_pred HHHHHHHHHHHHHHHHhhhhccce
Confidence 346999999999999999999973
No 21
>PLN02965 Probable pheophorbidase
Probab=32.04 E-value=12 Score=26.21 Aligned_cols=11 Identities=45% Similarity=0.782 Sum_probs=9.0
Q ss_pred hhhhhcccccC
Q 034397 14 SFVGNSMGGVR 24 (96)
Q Consensus 14 sfi~n~mgG~R 24 (96)
-+||+||||.-
T Consensus 75 ~lvGhSmGG~i 85 (255)
T PLN02965 75 ILVGHSIGGGS 85 (255)
T ss_pred EEEecCcchHH
Confidence 57899999973
No 22
>PF07225 NDUF_B4: NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4); InterPro: IPR009866 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family contains human NADH-ubiquinone oxidoreductase subunit NDUFB4 and related sequences.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=30.20 E-value=24 Score=25.55 Aligned_cols=34 Identities=41% Similarity=0.635 Sum_probs=21.3
Q ss_pred hhhHHHHHHHHHHHc-cCCCcceeeccCCCCCcccceee
Q 034397 48 QDLKREQEERAALAA-LDPNRYVEKRKPIPDPQETGLIY 85 (96)
Q Consensus 48 ~~~~~eqe~RAAlA~-~d~~rYVEkrkpipdpq~tgliy 85 (96)
-+.++.+++|+|+-+ ++. |..|..-||-..|+|.
T Consensus 23 pE~r~a~~eR~a~Ra~Lk~----eYlkq~~nP~~~gli~ 57 (125)
T PF07225_consen 23 PEERRAQQERAAIRARLKR----EYLKQYNNPHRKGLIF 57 (125)
T ss_pred HHHHHHHHHHHHHHHHHHH----HHHHHcCCCCCCCccC
Confidence 355666777777766 544 4456666776666663
No 23
>PF09819 ABC_cobalt: ABC-type cobalt transport system, permease component; InterPro: IPR017195 This group represents a predicted ABC-type thiamin-related transport system, permease component 1. It is probably part of the ABC transporter complex ykoCDEF that could transport hydroxymethylpyrimidine (HMP) and/or thiamine. It could also transport other HMP-containing products. The complex is composed of two ATP-binding proteins (ykoD), two transmembrane proteins (ykoC and ykoE) and a solute-binding protein (ykoF).
Probab=27.30 E-value=16 Score=26.08 Aligned_cols=25 Identities=40% Similarity=0.667 Sum_probs=20.1
Q ss_pred HHHHHHhhhheeeEEEcCchhhHHH
Q 034397 29 LASWVVAGTLAYYLWVKPSQDLKRE 53 (96)
Q Consensus 29 lAaW~VAG~lAYylwvkPe~~~~~e 53 (96)
..-|..++.+|.|+..||--..--|
T Consensus 44 ~GlW~~a~~la~~iiRKPGaa~~~e 68 (129)
T PF09819_consen 44 YGLWFMAGPLAAYIIRKPGAALLAE 68 (129)
T ss_pred HHHHHHHHHHHHHHhCCCcHHHHHH
Confidence 4579999999999999997655433
No 24
>PRK07718 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=27.11 E-value=15 Score=25.81 Aligned_cols=23 Identities=26% Similarity=0.161 Sum_probs=17.3
Q ss_pred HHHHHhhhheeeEEEcCchhhHH
Q 034397 30 ASWVVAGTLAYYLWVKPSQDLKR 52 (96)
Q Consensus 30 AaW~VAG~lAYylwvkPe~~~~~ 52 (96)
.+=+++|+.||||+.++..+.+.
T Consensus 14 ~~l~~~g~~~~~~~~~~~~~~~~ 36 (142)
T PRK07718 14 IVIALIGTAALVLVMGFSEAKKQ 36 (142)
T ss_pred HHHHHHHHHHHhhhcccCCcccc
Confidence 34567889999999988766654
No 25
>PRK11126 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase; Provisional
Probab=27.07 E-value=12 Score=25.21 Aligned_cols=10 Identities=50% Similarity=0.783 Sum_probs=7.9
Q ss_pred hhhhhccccc
Q 034397 14 SFVGNSMGGV 23 (96)
Q Consensus 14 sfi~n~mgG~ 23 (96)
.+||+||||.
T Consensus 69 ~lvG~S~Gg~ 78 (242)
T PRK11126 69 WLVGYSLGGR 78 (242)
T ss_pred EEEEECHHHH
Confidence 3689999985
No 26
>PF14960 ATP_synth_reg: ATP synthase regulation
Probab=27.01 E-value=25 Score=22.26 Aligned_cols=25 Identities=28% Similarity=0.601 Sum_probs=16.9
Q ss_pred cCCcchH--HHHHHhhhheeeEEEcCc
Q 034397 23 VRGGANL--ASWVVAGTLAYYLWVKPS 47 (96)
Q Consensus 23 ~RG~~nl--AaW~VAG~lAYylwvkPe 47 (96)
++|+.|. |.|+.-|.+..|+..+|.
T Consensus 22 ~~GR~N~~~ATya~i~li~~~~k~~~k 48 (49)
T PF14960_consen 22 IRGRANVAKATYASIGLIILYFKLRRK 48 (49)
T ss_pred ccchhhhHHHHHHHHHHHHHHHhcccC
Confidence 6899996 567666666666666553
No 27
>PRK08775 homoserine O-acetyltransferase; Provisional
Probab=26.76 E-value=13 Score=27.76 Aligned_cols=10 Identities=50% Similarity=0.919 Sum_probs=8.7
Q ss_pred hhhhhccccc
Q 034397 14 SFVGNSMGGV 23 (96)
Q Consensus 14 sfi~n~mgG~ 23 (96)
.+||+||||.
T Consensus 141 ~lvG~SmGG~ 150 (343)
T PRK08775 141 AFVGYSYGAL 150 (343)
T ss_pred EEEEECHHHH
Confidence 5899999995
No 28
>PLN02211 methyl indole-3-acetate methyltransferase
Probab=26.22 E-value=16 Score=26.82 Aligned_cols=11 Identities=45% Similarity=0.839 Sum_probs=9.0
Q ss_pred hhhhhcccccC
Q 034397 14 SFVGNSMGGVR 24 (96)
Q Consensus 14 sfi~n~mgG~R 24 (96)
.+||+||||+-
T Consensus 90 ~lvGhS~GG~v 100 (273)
T PLN02211 90 ILVGHSAGGLS 100 (273)
T ss_pred EEEEECchHHH
Confidence 37899999984
No 29
>PF13906 AA_permease_C: C-terminus of AA_permease
Probab=26.07 E-value=28 Score=21.43 Aligned_cols=15 Identities=20% Similarity=0.775 Sum_probs=12.3
Q ss_pred HHHHHHhhhheeeEE
Q 034397 29 LASWVVAGTLAYYLW 43 (96)
Q Consensus 29 lAaW~VAG~lAYylw 43 (96)
+..|+++|.+.|+.+
T Consensus 32 f~iWl~iGl~iYf~Y 46 (51)
T PF13906_consen 32 FGIWLAIGLVIYFGY 46 (51)
T ss_pred HHHHHHHHHHHHHhe
Confidence 568999999988764
No 30
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=25.06 E-value=41 Score=26.48 Aligned_cols=41 Identities=34% Similarity=0.400 Sum_probs=22.6
Q ss_pred cCchhhHHHHHHHHHHHccCCCcceeeccCCCCCcccceeeecCCC
Q 034397 45 KPSQDLKREQEERAALAALDPNRYVEKRKPIPDPQETGLIYGNKNR 90 (96)
Q Consensus 45 kPe~~~~~eqe~RAAlA~~d~~rYVEkrkpipdpq~tgliyg~~~~ 90 (96)
||.---.-| |||+|-| -|-+-=+|..+|-+| .|++||.--+
T Consensus 37 kPgpyP~te-eER~AAA-kKY~lrpEdY~py~d---Dg~gyGDYPk 77 (186)
T KOG4040|consen 37 KPGPYPTTE-EERRAAA-KKYGLRPEDYQPYDD---DGVGYGDYPK 77 (186)
T ss_pred CCCCCCCCH-HHHHHHH-HHhCCCHhhcCcCCc---CCcccCCCCc
Confidence 444333333 3444434 333334688888776 5888996443
No 31
>COG1565 Uncharacterized conserved protein [Function unknown]
Probab=24.63 E-value=72 Score=27.08 Aligned_cols=47 Identities=28% Similarity=0.469 Sum_probs=37.9
Q ss_pred eeEEEcCchhhHHHHHHHHHHHccCCCcceeeccCCCCCcccceeeecC
Q 034397 40 YYLWVKPSQDLKREQEERAALAALDPNRYVEKRKPIPDPQETGLIYGNK 88 (96)
Q Consensus 40 YylwvkPe~~~~~eqe~RAAlA~~d~~rYVEkrkpipdpq~tgliyg~~ 88 (96)
=|..|-|+.++++.|.+...-.. +.-+.+|..--+|+- .+|+|.+|.
T Consensus 111 ~~~iiE~s~~L~~~Qk~~L~~~~-~~~~~~~~~e~~p~~-~~~i~~~NE 157 (370)
T COG1565 111 SYYIIEPSPELRARQKETLKATE-DLIRWVEWVEDLPKK-FPGIVVSNE 157 (370)
T ss_pred eEEEEecCHHHHHHHHHHHhccc-cchhHHHHHHhcccc-CceEEEech
Confidence 45678999999999988766554 888899998887765 689998874
No 32
>PF13706 PepSY_TM_3: PepSY-associated TM helix
Probab=23.96 E-value=26 Score=19.89 Aligned_cols=18 Identities=17% Similarity=0.348 Sum_probs=13.7
Q ss_pred HHHHHHhhhheeeEEEcCchh
Q 034397 29 LASWVVAGTLAYYLWVKPSQD 49 (96)
Q Consensus 29 lAaW~VAG~lAYylwvkPe~~ 49 (96)
+..|.++|+++.| +||.|
T Consensus 19 l~~~~~tG~~~~f---~~ei~ 36 (37)
T PF13706_consen 19 LFVIFLTGAVMVF---RDEID 36 (37)
T ss_pred HHHHHHHhHHHHH---HHhhc
Confidence 6789999999887 55543
No 33
>PF11943 DUF3460: Protein of unknown function (DUF3460); InterPro: IPR021853 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 70 amino acids in length. This protein has a conserved WDK sequence motif.
Probab=23.75 E-value=46 Score=21.79 Aligned_cols=26 Identities=42% Similarity=0.622 Sum_probs=17.1
Q ss_pred EEEcCchhhHHHHHHHHHHHccCCCcc
Q 034397 42 LWVKPSQDLKREQEERAALAALDPNRY 68 (96)
Q Consensus 42 lwvkPe~~~~~eqe~RAAlA~~d~~rY 68 (96)
||-| .+++.+..+.+||--..+||-|
T Consensus 32 lWDk-~~d~e~~~~~~~arV~qkpYvY 57 (60)
T PF11943_consen 32 LWDK-PQDLEEQARFRAARVPQKPYVY 57 (60)
T ss_pred hcCC-CCCHHHHHHHHhccCCCCCCCC
Confidence 6777 5666665566666555778666
No 34
>PF13396 PLDc_N: Phospholipase_D-nuclease N-terminal
Probab=23.43 E-value=93 Score=17.49 Aligned_cols=23 Identities=17% Similarity=0.582 Sum_probs=16.7
Q ss_pred CCcchHHHHHH-------hhhheeeEEEcC
Q 034397 24 RGGANLASWVV-------AGTLAYYLWVKP 46 (96)
Q Consensus 24 RG~~nlAaW~V-------AG~lAYylwvkP 46 (96)
|..++-.+|++ .|.++|+++-++
T Consensus 17 ~~~~~k~~W~~~i~~~P~iG~i~Yl~~gr~ 46 (46)
T PF13396_consen 17 RSPSSKILWLIVILFFPIIGPILYLIFGRK 46 (46)
T ss_pred CCCchhhHHHHHHHHHHHHHHhheEEEeCC
Confidence 55678889985 477888887553
No 35
>PF11167 DUF2953: Protein of unknown function (DUF2953); InterPro: IPR021338 This family of proteins has no known function.
Probab=23.15 E-value=11 Score=22.18 Aligned_cols=11 Identities=45% Similarity=1.060 Sum_probs=9.4
Q ss_pred CCCcccceeee
Q 034397 76 PDPQETGLIYG 86 (96)
Q Consensus 76 pdpq~tgliyg 86 (96)
.||-.||++||
T Consensus 6 ~Daa~Tgi~~G 16 (53)
T PF11167_consen 6 GDAADTGILYG 16 (53)
T ss_pred cCHHHHHHHHH
Confidence 58889999887
No 36
>COG1525 Micrococcal nuclease (thermonuclease) homologs [DNA replication, recombination, and repair]
Probab=22.80 E-value=2.3e+02 Score=20.01 Aligned_cols=20 Identities=20% Similarity=0.220 Sum_probs=17.1
Q ss_pred CCcchHHHHHHhhhheeeEE
Q 034397 24 RGGANLASWVVAGTLAYYLW 43 (96)
Q Consensus 24 RG~~nlAaW~VAG~lAYylw 43 (96)
.+++|++.|+|.=|+|.-+.
T Consensus 127 ~~~~~v~~~lV~~G~A~~~~ 146 (192)
T COG1525 127 VDGTDVNLELVKEGLARVYY 146 (192)
T ss_pred ECCEEHHHHHHhCCCEEEec
Confidence 57899999999999976655
No 37
>PHA00431 internal virion protein C
Probab=21.29 E-value=53 Score=30.40 Aligned_cols=54 Identities=28% Similarity=0.407 Sum_probs=38.5
Q ss_pred Ccchhhhhhhchhhh-hhhcccccCCc-------------c----hHHHHHHhhhheeeEEEcCchhhHHHH
Q 034397 1 MASSWRRTIGNLRSF-VGNSMGGVRGG-------------A----NLASWVVAGTLAYYLWVKPSQDLKREQ 54 (96)
Q Consensus 1 ma~~wrrt~gn~rsf-i~n~mgG~RG~-------------~----nlAaW~VAG~lAYylwvkPe~~~~~eq 54 (96)
|||.-.+.||++|.- ..-+=||.+|- + .|+-|+-||+-||-.+..-.+++..|+
T Consensus 1 MaSkl~~aL~q~~~~g~~rlrg~~~~~~yqA~~v~a~~~~s~ll~sl~~f~~aG~~ay~~y~~~~k~~AdER 72 (746)
T PHA00431 1 MASKLEQALGQMRAPGTERLRGGTGGMQYQAATVQAEVGQSNLLESLGKFAKAGADAYGAYDERRKDKADER 72 (746)
T ss_pred CcchHHHHHhcccCCcccccccccccceeehhhhccccCCchHHHHHHHHHHHhHHHHHHHHHHHHHhHhhh
Confidence 788888888888753 22233444442 2 456799999999999988888777775
No 38
>PRK07581 hypothetical protein; Validated
Probab=20.99 E-value=19 Score=26.54 Aligned_cols=12 Identities=42% Similarity=0.471 Sum_probs=9.5
Q ss_pred hhhhhcccccCC
Q 034397 14 SFVGNSMGGVRG 25 (96)
Q Consensus 14 sfi~n~mgG~RG 25 (96)
.+||+||||.-+
T Consensus 127 ~lvG~S~GG~va 138 (339)
T PRK07581 127 LVVGWSMGAQQT 138 (339)
T ss_pred EEEEeCHHHHHH
Confidence 368999999754
No 39
>PRK09689 prophage protein NinE; Provisional
Probab=20.31 E-value=45 Score=21.95 Aligned_cols=12 Identities=50% Similarity=0.706 Sum_probs=9.6
Q ss_pred eeccCCCCCccc
Q 034397 70 EKRKPIPDPQET 81 (96)
Q Consensus 70 Ekrkpipdpq~t 81 (96)
.|+||||.|.++
T Consensus 20 rkrKP~~k~Sdv 31 (56)
T PRK09689 20 RKRKPELKPSEI 31 (56)
T ss_pred cCCCCCCChhhc
Confidence 478999988765
Done!