Query 033102
Match_columns 127
No_of_seqs 93 out of 95
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 09:49:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033102.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033102hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK14624 hypothetical protein; 99.4 2.6E-13 5.7E-18 100.3 6.0 46 81-127 1-46 (115)
2 PRK14626 hypothetical protein; 99.4 1.3E-12 2.9E-17 95.3 6.2 44 83-127 2-45 (110)
3 PRK14625 hypothetical protein; 99.3 3.5E-12 7.6E-17 93.5 5.4 42 85-127 1-42 (109)
4 PRK14621 hypothetical protein; 99.3 6.3E-12 1.4E-16 92.2 6.0 42 85-127 3-44 (111)
5 TIGR00103 DNA_YbaB_EbfC DNA-bi 99.3 7.7E-12 1.7E-16 89.4 6.1 43 84-127 3-45 (102)
6 PRK14628 hypothetical protein; 99.3 1.4E-11 3.1E-16 91.2 6.6 45 83-127 15-59 (118)
7 COG0718 Uncharacterized protei 99.3 1.1E-11 2.3E-16 91.1 5.8 44 83-127 2-45 (105)
8 PRK14627 hypothetical protein; 99.2 1.5E-11 3.2E-16 88.3 5.3 40 87-127 2-41 (100)
9 PRK14623 hypothetical protein; 99.2 1.9E-11 4.2E-16 89.3 5.2 40 87-127 2-41 (106)
10 PRK14622 hypothetical protein; 99.2 2.1E-11 4.5E-16 88.1 5.3 40 87-127 2-41 (103)
11 PRK03762 hypothetical protein; 99.2 3.7E-11 8.1E-16 87.3 5.7 40 84-127 6-45 (103)
12 PRK00153 hypothetical protein; 99.2 6.1E-11 1.3E-15 84.1 5.5 42 85-127 2-43 (104)
13 PRK14629 hypothetical protein; 99.1 2.4E-10 5.3E-15 82.8 5.3 38 89-127 6-43 (99)
14 PRK00587 hypothetical protein; 99.0 5.2E-10 1.1E-14 81.0 5.6 38 88-127 3-40 (99)
15 PF02575 YbaB_DNA_bd: YbaB/Ebf 98.5 2.3E-07 4.9E-12 63.1 4.9 35 92-127 1-35 (93)
16 PRK00153 hypothetical protein; 91.0 0.53 1.1E-05 33.4 4.6 27 81-107 1-27 (104)
17 PRK14626 hypothetical protein; 88.5 0.99 2.1E-05 33.2 4.5 27 81-107 3-29 (110)
18 PRK14628 hypothetical protein; 85.9 1.6 3.5E-05 32.6 4.4 26 79-105 14-40 (118)
19 PRK14623 hypothetical protein; 84.4 2.8 6E-05 30.9 5.0 44 83-126 1-51 (106)
20 PRK14621 hypothetical protein; 82.9 3.4 7.3E-05 30.5 5.0 26 80-106 2-27 (111)
21 PRK14625 hypothetical protein; 82.3 3.2 6.9E-05 30.7 4.6 25 82-106 1-25 (109)
22 COG0718 Uncharacterized protei 72.5 6.2 0.00014 29.3 3.8 19 83-101 5-23 (105)
23 TIGR00103 DNA_YbaB_EbfC DNA-bi 69.9 5.9 0.00013 28.4 3.1 28 83-111 5-32 (102)
24 PRK14624 hypothetical protein; 69.8 6.3 0.00014 29.4 3.3 27 82-108 5-31 (115)
25 PF15047 DUF4533: Protein of u 64.1 8.2 0.00018 32.4 3.3 26 84-109 52-77 (225)
26 COG1422 Predicted membrane pro 54.1 15 0.00033 30.2 3.2 25 90-115 98-122 (201)
27 PRK00587 hypothetical protein; 46.9 14 0.00031 26.8 1.8 24 83-106 1-24 (99)
28 PF13080 DUF3926: Protein of u 42.6 28 0.00061 22.8 2.5 17 93-113 13-29 (44)
29 cd04772 HTH_TioE_rpt1 First He 34.7 70 0.0015 22.2 3.7 27 84-110 73-99 (99)
30 PF05811 DUF842: Eukaryotic pr 33.6 53 0.0011 24.4 3.1 23 90-112 57-79 (131)
31 COG1422 Predicted membrane pro 31.6 61 0.0013 26.8 3.4 9 85-93 77-85 (201)
32 PRK03762 hypothetical protein; 31.6 1.2E+02 0.0026 22.2 4.6 24 82-106 7-31 (103)
33 cd03081 TRX_Fd_NuoE_FDH_gamma 30.5 45 0.00098 22.2 2.1 31 91-126 13-43 (80)
34 cd01417 Ribosomal_L19e_E Ribos 30.1 1.2E+02 0.0026 24.3 4.7 36 77-113 124-159 (164)
35 PF03449 GreA_GreB_N: Transcri 28.7 1.4E+02 0.0031 20.3 4.3 27 89-115 48-74 (74)
36 COG5374 Uncharacterized conser 27.0 73 0.0016 26.4 3.1 19 55-73 127-145 (192)
37 PTZ00097 60S ribosomal protein 26.3 1.5E+02 0.0033 24.0 4.7 36 77-113 125-160 (175)
38 KOG3377 Uncharacterized conser 26.2 84 0.0018 24.9 3.2 21 92-112 67-87 (143)
39 PF02096 60KD_IMP: 60Kd inner 24.4 1.2E+02 0.0026 22.8 3.6 28 84-111 31-58 (198)
40 PRK01885 greB transcription el 23.3 2.4E+02 0.0051 21.5 5.1 31 89-119 49-79 (157)
41 PF11328 DUF3130: Protein of u 23.3 1.5E+02 0.0033 21.8 3.9 23 86-108 51-73 (90)
42 TIGR03592 yidC_oxa1_cterm memb 22.9 1.3E+02 0.0028 22.9 3.6 9 100-108 53-61 (181)
43 PF06305 DUF1049: Protein of u 22.7 1.4E+02 0.0031 18.6 3.3 14 100-113 54-67 (68)
44 PRK13848 conjugal transfer pro 22.6 38 0.00082 25.4 0.6 16 99-114 8-23 (98)
45 PTZ00421 coronin; Provisional 22.1 1.1E+02 0.0025 27.1 3.6 30 84-114 451-480 (493)
46 PF09932 DUF2164: Uncharacteri 20.9 1.5E+02 0.0034 20.5 3.4 25 90-114 50-74 (76)
47 PF01346 FKBP_N: Domain amino 20.7 2.9E+02 0.0063 19.1 4.8 28 83-110 65-92 (124)
48 PTZ00464 SNF-7-like protein; P 20.5 3E+02 0.0065 22.3 5.4 30 84-113 15-44 (211)
49 KOG0009 Ubiquitin-like/40S rib 20.2 75 0.0016 22.1 1.7 24 46-69 35-58 (62)
No 1
>PRK14624 hypothetical protein; Provisional
Probab=99.43 E-value=2.6e-13 Score=100.32 Aligned_cols=46 Identities=15% Similarity=0.309 Sum_probs=43.8
Q ss_pred ccCChHHHHHHHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 81 ILGNMQNLYETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 81 mlgNMqnL~e~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
||-+|+||.+++|+||++ |++|+++|+||++++|+|+||||+|+|+
T Consensus 1 ~~~~~~nm~~~mkqAq~m-Q~km~~~QeeL~~~~v~g~sGgG~VkV~ 46 (115)
T PRK14624 1 MFDKIKNMSEALSNMGNI-REKMEEVKKRIASIRVVGDAGAGMVTVT 46 (115)
T ss_pred CcchHHhHHHHHHHHHHH-HHHHHHHHHHHhccEEEEEECCcEEEEE
Confidence 567999999999999996 9999999999999999999999999986
No 2
>PRK14626 hypothetical protein; Provisional
Probab=99.36 E-value=1.3e-12 Score=95.32 Aligned_cols=44 Identities=27% Similarity=0.314 Sum_probs=41.3
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 83 GNMQNLYETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 83 gNMqnL~e~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
.+|+||.+++||||++ |++|+++|+||+.++|+|++|||+||||
T Consensus 2 ~~~gn~~~mmkqaq~m-Q~km~~~qeeL~~~~v~g~sggG~VkV~ 45 (110)
T PRK14626 2 FNFGNLAELMKQMQSI-KENVEKAKEELKKEEIVVEVGGGMVKVV 45 (110)
T ss_pred CCcHhHHHHHHHHHHH-HHHHHHHHHHHhccEEEEEecCcEEEEE
Confidence 3788999999999996 9999999999999999999999999996
No 3
>PRK14625 hypothetical protein; Provisional
Probab=99.30 E-value=3.5e-12 Score=93.53 Aligned_cols=42 Identities=29% Similarity=0.401 Sum_probs=38.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 85 MQNLYETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 85 MqnL~e~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
|+||.+++||||++ |++|+++|+||++++|+|+||||+|+|+
T Consensus 1 ~~nm~~mmkqaq~m-Q~km~~~Q~el~~~~v~g~sggG~VkV~ 42 (109)
T PRK14625 1 MKDLGGLMKQAQAM-QQKLADAQARLAETTVEGTSGGGMVTVT 42 (109)
T ss_pred CccHHHHHHHHHHH-HHHHHHHHHHHhccEEEEEECCCeEEEE
Confidence 45788888999996 9999999999999999999999999996
No 4
>PRK14621 hypothetical protein; Provisional
Probab=99.29 E-value=6.3e-12 Score=92.18 Aligned_cols=42 Identities=29% Similarity=0.330 Sum_probs=38.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 85 MQNLYETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 85 MqnL~e~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
|+||.+++|+||++ |++|+++|+||+.++|||++|||+|+||
T Consensus 3 ~~nm~~mmkqaq~m-Q~km~~~Q~eL~~~~v~g~sGgG~VkV~ 44 (111)
T PRK14621 3 MPNLGDMMKQIQQA-GEKMQDVQKQLEKLVAHGEAGGGMVKAS 44 (111)
T ss_pred chhHHHHHHHHHHH-HHHHHHHHHHHHccEEEEEECCceEEEE
Confidence 55788889999996 9999999999999999999999999996
No 5
>TIGR00103 DNA_YbaB_EbfC DNA-binding protein, YbaB/EbfC family. The function of this protein is unknown, but it has been expressed and crystallized. Its gene nearly always occurs next to recR and/or dnaX. It is restricted to Bacteria and the plant Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A member is present even in the minimal gene complement of Mycoplasm genitalium.
Probab=99.28 E-value=7.7e-12 Score=89.44 Aligned_cols=43 Identities=33% Similarity=0.371 Sum_probs=40.2
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 84 NMQNLYETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 84 NMqnL~e~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
+|+||.+++++||++ |++++++|+||++++|+|+++||+|+|+
T Consensus 3 ~~~n~~~m~kqaq~m-Q~k~~~~q~eL~~~~v~g~sggGlV~V~ 45 (102)
T TIGR00103 3 GKGNLGELMKQAQQM-QEKMKKLQEEIAQFEVTGKSGAGLVTVT 45 (102)
T ss_pred ChhhHHHHHHHHHHH-HHHHHHHHHHHhccEEEEEECCCEEEEE
Confidence 577899999999996 9999999999999999999999999996
No 6
>PRK14628 hypothetical protein; Provisional
Probab=99.25 E-value=1.4e-11 Score=91.23 Aligned_cols=45 Identities=16% Similarity=0.312 Sum_probs=40.5
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 83 GNMQNLYETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 83 gNMqnL~e~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
|+|++|+++++|+|+.+|++++++|+||++++|+|+||||+|+|+
T Consensus 15 g~~~~lm~q~~k~qq~mq~k~~elqe~l~~~~v~g~sggG~VkV~ 59 (118)
T PRK14628 15 GKQEKLLKDFAKMQEELQKKIQELEESFSQIEVEASVGGGAVRIV 59 (118)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHceEEEEEecCceEEEE
Confidence 468888877777777779999999999999999999999999996
No 7
>COG0718 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.25 E-value=1.1e-11 Score=91.08 Aligned_cols=44 Identities=34% Similarity=0.508 Sum_probs=37.2
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 83 GNMQNLYETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 83 gNMqnL~e~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
+++.+|.+++|+||++ |++++++|+||+++||+|++|||+|+|+
T Consensus 2 ~~~~~~~~l~kqaqqm-Q~~~~~~Q~ela~~ev~g~aggGlVtV~ 45 (105)
T COG0718 2 GGMMDMQKLMKQAQQM-QKKMQKMQEELAQKEVTGKAGGGLVTVT 45 (105)
T ss_pred CchhhHHHHHHHHHHH-HHHHHHHHHHHHhcEEeeecCCcEEEEE
Confidence 3455566666888885 8889999999999999999999999995
No 8
>PRK14627 hypothetical protein; Provisional
Probab=99.23 E-value=1.5e-11 Score=88.31 Aligned_cols=40 Identities=35% Similarity=0.378 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 87 NLYETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 87 nL~e~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
||.+++|+||++ |++|+++|+||+.++|||++|||+|+|+
T Consensus 2 n~~~~mkqaq~m-Q~km~~~Q~el~~~~veg~sggG~VkV~ 41 (100)
T PRK14627 2 NQRQLMQMAQQM-QRQMQKVQEELAATIVEGTAGGGAITVK 41 (100)
T ss_pred CHHHHHHHHHHH-HHHHHHHHHHHhccEEEEEEcCCeEEEE
Confidence 555667777775 8889999999999999999999999996
No 9
>PRK14623 hypothetical protein; Provisional
Probab=99.21 E-value=1.9e-11 Score=89.28 Aligned_cols=40 Identities=20% Similarity=0.234 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 87 NLYETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 87 nL~e~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
||.+++|+||++ |++|+++|+||++++|+|++|||+|+||
T Consensus 2 ~~~~~mkqaqkm-Q~km~~~Qeel~~~~v~g~sggG~VkVt 41 (106)
T PRK14623 2 DMMGMMGKLKEA-QQKVEATKKRLDTVLIDEQSSDGLLKVT 41 (106)
T ss_pred CHHHHHHHHHHH-HHHHHHHHHHHhccEEEEEECCceEEEE
Confidence 466677778885 8889999999999999999999999996
No 10
>PRK14622 hypothetical protein; Provisional
Probab=99.21 E-value=2.1e-11 Score=88.11 Aligned_cols=40 Identities=18% Similarity=0.318 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 87 NLYETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 87 nL~e~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
+|.+++|+||++ |++|+++|+||++++|+|++|||+|+||
T Consensus 2 ~~~~lmkqaq~m-Q~~m~~~q~el~~~~v~g~sggG~VkV~ 41 (103)
T PRK14622 2 DIQYLMRQAKKL-EKAMADAKEKLAEIAVEAESGGGLVKVA 41 (103)
T ss_pred CHHHHHHHHHHH-HHHHHHHHHHHhccEEEEEECCceEEEE
Confidence 466777888886 8889999999999999999999999996
No 11
>PRK03762 hypothetical protein; Provisional
Probab=99.18 E-value=3.7e-11 Score=87.28 Aligned_cols=40 Identities=28% Similarity=0.400 Sum_probs=33.7
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 84 NMQNLYETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 84 NMqnL~e~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
||++|+++++++ |++++++|+||++++|+|++|||+|+|+
T Consensus 6 ~~~~m~kqaqkm----Q~km~~~Q~el~~~~v~g~sggGlVkV~ 45 (103)
T PRK03762 6 DFSKLGEMLEQM----QKKAKQLEEENANKEFTAKSGGGLVSVS 45 (103)
T ss_pred CHHHHHHHHHHH----HHHHHHHHHHHhccEEEEEEcCceEEEE
Confidence 677776665554 5569999999999999999999999996
No 12
>PRK00153 hypothetical protein; Validated
Probab=99.16 E-value=6.1e-11 Score=84.12 Aligned_cols=42 Identities=38% Similarity=0.524 Sum_probs=36.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 85 MQNLYETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 85 MqnL~e~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
|+||.++++|||++ |++++++|+||+.++|+|+|+||+|+||
T Consensus 2 ~~~~~~m~~qaq~~-q~~~~~~q~~l~~~~~~~~s~~G~V~V~ 43 (104)
T PRK00153 2 MGNMQNLMKQAQQM-QEKMQKMQEELAQMEVEGEAGGGLVKVT 43 (104)
T ss_pred cccHHHHHHHHHHH-HHHHHHHHHHHhccEEEEEECCCeEEEE
Confidence 44566777888885 8889999999999999999999999996
No 13
>PRK14629 hypothetical protein; Provisional
Probab=99.06 E-value=2.4e-10 Score=82.78 Aligned_cols=38 Identities=13% Similarity=0.187 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 89 YETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 89 ~e~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
.+++|+||++ |++|+++|+||++++|||++|||+|+|+
T Consensus 6 ~~~mkqaq~m-Q~km~~~Q~eL~~~~veg~aggGlVkV~ 43 (99)
T PRK14629 6 LDFLKNMSSF-KDNIDNIKKEISQIVVCGRAGSDVVVVE 43 (99)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHhccEEEEEecCCEEEEE
Confidence 3688999996 9999999999999999999999999996
No 14
>PRK00587 hypothetical protein; Provisional
Probab=99.02 E-value=5.2e-10 Score=80.97 Aligned_cols=38 Identities=21% Similarity=0.202 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 88 LYETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 88 L~e~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
|.+++|+||++ |++|+++|+||++++|+|++ ||+|+|+
T Consensus 3 ~~~lmkqaqkm-Q~km~~~QeeL~~~~v~g~~-gGlVkV~ 40 (99)
T PRK00587 3 FQKLAQQLKKM-QNTMEKKQKEFEEKEFDFDY-KKYILIK 40 (99)
T ss_pred HHHHHHHHHHH-HHHHHHHHHHHhccEEEEEc-CCeEEEE
Confidence 45556667774 77799999999999999998 9999996
No 15
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=98.49 E-value=2.3e-07 Score=63.11 Aligned_cols=35 Identities=34% Similarity=0.393 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEEC
Q 033102 92 VKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVC 127 (127)
Q Consensus 92 ~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkVt 127 (127)
|+++|++ |++++++|++|++++|+|++++|+|+|+
T Consensus 1 m~~~~~~-~~~~~~~~~~l~~~~~~~~s~~g~V~V~ 35 (93)
T PF02575_consen 1 MKQAQEM-QEKMEEAQEELAEIEVTGTSGDGLVTVT 35 (93)
T ss_dssp HHHHHHH-HHHHHHHHHHHHHSEEEEEETCCTEEEE
T ss_pred ChHHHHH-HHHHHHHHHHHhcCEEEEEECCCEEEEE
Confidence 5788996 9999999999999999999999999996
No 16
>PRK00153 hypothetical protein; Validated
Probab=90.97 E-value=0.53 Score=33.42 Aligned_cols=27 Identities=30% Similarity=0.327 Sum_probs=20.2
Q ss_pred ccCChHHHHHHHHHHHHHHHHHHHHHH
Q 033102 81 ILGNMQNLYETVKKAQMVVQVEAVRVQ 107 (127)
Q Consensus 81 mlgNMqnL~e~~KKAQq~VQ~~m~klQ 107 (127)
|++||++|+++++++|+.+++--+++.
T Consensus 1 ~~~~~~~m~~qaq~~q~~~~~~q~~l~ 27 (104)
T PRK00153 1 GMGNMQNLMKQAQQMQEKMQKMQEELA 27 (104)
T ss_pred CcccHHHHHHHHHHHHHHHHHHHHHHh
Confidence 458999999999999998544434443
No 17
>PRK14626 hypothetical protein; Provisional
Probab=88.48 E-value=0.99 Score=33.16 Aligned_cols=27 Identities=15% Similarity=0.281 Sum_probs=19.9
Q ss_pred ccCChHHHHHHHHHHHHHHHHHHHHHH
Q 033102 81 ILGNMQNLYETVKKAQMVVQVEAVRVQ 107 (127)
Q Consensus 81 mlgNMqnL~e~~KKAQq~VQ~~m~klQ 107 (127)
+++||++|++++|++|+..++--+++-
T Consensus 3 ~~gn~~~mmkqaq~mQ~km~~~qeeL~ 29 (110)
T PRK14626 3 NFGNLAELMKQMQSIKENVEKAKEELK 29 (110)
T ss_pred CcHhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 457999999999999987554444443
No 18
>PRK14628 hypothetical protein; Provisional
Probab=85.93 E-value=1.6 Score=32.60 Aligned_cols=26 Identities=12% Similarity=0.093 Sum_probs=16.3
Q ss_pred cCccCC-hHHHHHHHHHHHHHHHHHHHH
Q 033102 79 AGILGN-MQNLYETVKKAQMVVQVEAVR 105 (127)
Q Consensus 79 ~gmlgN-MqnL~e~~KKAQq~VQ~~m~k 105 (127)
.|++++ |++++++.+++|+. ++++++
T Consensus 14 ~g~~~~lm~q~~k~qq~mq~k-~~elqe 40 (118)
T PRK14628 14 GGKQEKLLKDFAKMQEELQKK-IQELEE 40 (118)
T ss_pred chhHHHHHHHHHHHHHHHHHH-HHHHHH
Confidence 455555 67777777766664 666655
No 19
>PRK14623 hypothetical protein; Provisional
Probab=84.39 E-value=2.8 Score=30.86 Aligned_cols=44 Identities=20% Similarity=0.287 Sum_probs=26.8
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHH-------hhcEeeeeeCCceEEE
Q 033102 83 GNMQNLYETVKKAQMVVQVEAVRVQKEL-------AAAEFDGYCEGELIKV 126 (127)
Q Consensus 83 gNMqnL~e~~KKAQq~VQ~~m~klQeEL-------a~~EfEG~aggGlVkV 126 (127)
+||++|++++|++|+.+++--+++-+.- ....|+=+..+.+++|
T Consensus 1 ~~~~~~mkqaqkmQ~km~~~Qeel~~~~v~g~sggG~VkVt~~G~~~i~~i 51 (106)
T PRK14623 1 GDMMGMMGKLKEAQQKVEATKKRLDTVLIDEQSSDGLLKVTVTANREIKSI 51 (106)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhccEEEEEECCceEEEEEEcCccEEEE
Confidence 4899999999999988554444443332 2244444444455443
No 20
>PRK14621 hypothetical protein; Provisional
Probab=82.95 E-value=3.4 Score=30.54 Aligned_cols=26 Identities=12% Similarity=0.229 Sum_probs=19.8
Q ss_pred CccCChHHHHHHHHHHHHHHHHHHHHH
Q 033102 80 GILGNMQNLYETVKKAQMVVQVEAVRV 106 (127)
Q Consensus 80 gmlgNMqnL~e~~KKAQq~VQ~~m~kl 106 (127)
|| +||++|++++|++|+..++--+++
T Consensus 2 ~~-~nm~~mmkqaq~mQ~km~~~Q~eL 27 (111)
T PRK14621 2 AM-PNLGDMMKQIQQAGEKMQDVQKQL 27 (111)
T ss_pred Cc-hhHHHHHHHHHHHHHHHHHHHHHH
Confidence 44 799999999999998855444444
No 21
>PRK14625 hypothetical protein; Provisional
Probab=82.30 E-value=3.2 Score=30.71 Aligned_cols=25 Identities=12% Similarity=0.224 Sum_probs=18.5
Q ss_pred cCChHHHHHHHHHHHHHHHHHHHHH
Q 033102 82 LGNMQNLYETVKKAQMVVQVEAVRV 106 (127)
Q Consensus 82 lgNMqnL~e~~KKAQq~VQ~~m~kl 106 (127)
|+||++|++++|++|+.+++--+++
T Consensus 1 ~~nm~~mmkqaq~mQ~km~~~Q~el 25 (109)
T PRK14625 1 MKDLGGLMKQAQAMQQKLADAQARL 25 (109)
T ss_pred CccHHHHHHHHHHHHHHHHHHHHHH
Confidence 4699999999999998844433333
No 22
>COG0718 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.48 E-value=6.2 Score=29.28 Aligned_cols=19 Identities=26% Similarity=0.284 Sum_probs=15.8
Q ss_pred CChHHHHHHHHHHHHHHHH
Q 033102 83 GNMQNLYETVKKAQMVVQV 101 (127)
Q Consensus 83 gNMqnL~e~~KKAQq~VQ~ 101 (127)
+||++|++++|++|+..++
T Consensus 5 ~~~~~l~kqaqqmQ~~~~~ 23 (105)
T COG0718 5 MDMQKLMKQAQQMQKKMQK 23 (105)
T ss_pred hhHHHHHHHHHHHHHHHHH
Confidence 7999999999999987433
No 23
>TIGR00103 DNA_YbaB_EbfC DNA-binding protein, YbaB/EbfC family. The function of this protein is unknown, but it has been expressed and crystallized. Its gene nearly always occurs next to recR and/or dnaX. It is restricted to Bacteria and the plant Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A member is present even in the minimal gene complement of Mycoplasm genitalium.
Probab=69.86 E-value=5.9 Score=28.38 Aligned_cols=28 Identities=14% Similarity=0.183 Sum_probs=20.8
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033102 83 GNMQNLYETVKKAQMVVQVEAVRVQKELA 111 (127)
Q Consensus 83 gNMqnL~e~~KKAQq~VQ~~m~klQeELa 111 (127)
+||++|++++|++|+. -+++++--++..
T Consensus 5 ~n~~~m~kqaq~mQ~k-~~~~q~eL~~~~ 32 (102)
T TIGR00103 5 GNLGELMKQAQQMQEK-MKKLQEEIAQFE 32 (102)
T ss_pred hhHHHHHHHHHHHHHH-HHHHHHHHhccE
Confidence 6999999999999988 444555444443
No 24
>PRK14624 hypothetical protein; Provisional
Probab=69.80 E-value=6.3 Score=29.44 Aligned_cols=27 Identities=11% Similarity=0.172 Sum_probs=19.9
Q ss_pred cCChHHHHHHHHHHHHHHHHHHHHHHH
Q 033102 82 LGNMQNLYETVKKAQMVVQVEAVRVQK 108 (127)
Q Consensus 82 lgNMqnL~e~~KKAQq~VQ~~m~klQe 108 (127)
+.||++|++++|++|+.+++--+++-+
T Consensus 5 ~~nm~~~mkqAq~mQ~km~~~QeeL~~ 31 (115)
T PRK14624 5 IKNMSEALSNMGNIREKMEEVKKRIAS 31 (115)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 368999999999999886654444443
No 25
>PF15047 DUF4533: Protein of unknown function (DUF4533)
Probab=64.10 E-value=8.2 Score=32.36 Aligned_cols=26 Identities=31% Similarity=0.438 Sum_probs=24.1
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHH
Q 033102 84 NMQNLYETVKKAQMVVQVEAVRVQKE 109 (127)
Q Consensus 84 NMqnL~e~~KKAQq~VQ~~m~klQeE 109 (127)
|+..|.+.||++|.+||..-.++|+|
T Consensus 52 ~~eqmi~~~kemQ~~vd~kd~~mq~e 77 (225)
T PF15047_consen 52 NFEQMIKIFKEMQSVVDAKDKEMQKE 77 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 78999999999999999988899988
No 26
>COG1422 Predicted membrane protein [Function unknown]
Probab=54.08 E-value=15 Score=30.25 Aligned_cols=25 Identities=36% Similarity=0.438 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcEe
Q 033102 90 ETVKKAQMVVQVEAVRVQKELAAAEF 115 (127)
Q Consensus 90 e~~KKAQq~VQ~~m~klQeELa~~Ef 115 (127)
++++|.|++ |.+|...|.||=.+.|
T Consensus 98 ~~lkkLq~~-qmem~~~Q~elmk~qf 122 (201)
T COG1422 98 KKLKKLQEK-QMEMMDDQRELMKMQF 122 (201)
T ss_pred HHHHHHHHH-HHHHHHHHHHHHHHhh
Confidence 455666775 7777777777766544
No 27
>PRK00587 hypothetical protein; Provisional
Probab=46.87 E-value=14 Score=26.85 Aligned_cols=24 Identities=25% Similarity=0.256 Sum_probs=18.0
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHH
Q 033102 83 GNMQNLYETVKKAQMVVQVEAVRV 106 (127)
Q Consensus 83 gNMqnL~e~~KKAQq~VQ~~m~kl 106 (127)
|||++|++++|++|+..++-=+++
T Consensus 1 m~~~~lmkqaqkmQ~km~~~QeeL 24 (99)
T PRK00587 1 MNFQKLAQQLKKMQNTMEKKQKEF 24 (99)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 489999999999998844433333
No 28
>PF13080 DUF3926: Protein of unknown function (DUF3926)
Probab=42.59 E-value=28 Score=22.80 Aligned_cols=17 Identities=24% Similarity=0.268 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhc
Q 033102 93 KKAQMVVQVEAVRVQKELAAA 113 (127)
Q Consensus 93 KKAQq~VQ~~m~klQeELa~~ 113 (127)
+.|++| .--+||||++-
T Consensus 13 QsAkqm----lnILQEELssy 29 (44)
T PF13080_consen 13 QSAKQM----LNILQEELSSY 29 (44)
T ss_pred HHHHHH----HHHHHHHHHhc
Confidence 456666 77899999863
No 29
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=34.72 E-value=70 Score=22.18 Aligned_cols=27 Identities=19% Similarity=0.202 Sum_probs=17.9
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033102 84 NMQNLYETVKKAQMVVQVEAVRVQKEL 110 (127)
Q Consensus 84 NMqnL~e~~KKAQq~VQ~~m~klQeEL 110 (127)
+.....+.+.+-++.|+++++++|+||
T Consensus 73 ~~~~~~~ll~~~~~~l~~~i~~L~~~~ 99 (99)
T cd04772 73 IVASALALVDAAHALLQRYRQQLDQEL 99 (99)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 344556666666666777777777764
No 30
>PF05811 DUF842: Eukaryotic protein of unknown function (DUF842); InterPro: IPR008560 This family consists of a number of conserved eukaryotic proteins of unknown function. The sequences carry three sets of CxxxC motifs, which might suggest a type of zinc-finger formation.
Probab=33.61 E-value=53 Score=24.42 Aligned_cols=23 Identities=30% Similarity=0.313 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Q 033102 90 ETVKKAQMVVQVEAVRVQKELAA 112 (127)
Q Consensus 90 e~~KKAQq~VQ~~m~klQeELa~ 112 (127)
.-+.+||..||.++.+.|+-|..
T Consensus 57 ~pl~~aq~~vq~El~~FQ~rlqr 79 (131)
T PF05811_consen 57 QPLQQAQNYVQNELEQFQNRLQR 79 (131)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHH
Confidence 34788999999999999998853
No 31
>COG1422 Predicted membrane protein [Function unknown]
Probab=31.61 E-value=61 Score=26.75 Aligned_cols=9 Identities=11% Similarity=0.431 Sum_probs=3.4
Q ss_pred hHHHHHHHH
Q 033102 85 MQNLYETVK 93 (127)
Q Consensus 85 MqnL~e~~K 93 (127)
+|++++.+|
T Consensus 77 ~qk~m~efq 85 (201)
T COG1422 77 LQKMMKEFQ 85 (201)
T ss_pred HHHHHHHHH
Confidence 333333333
No 32
>PRK03762 hypothetical protein; Provisional
Probab=31.56 E-value=1.2e+02 Score=22.19 Aligned_cols=24 Identities=17% Similarity=0.350 Sum_probs=12.2
Q ss_pred cCChHHHHHHHH-HHHHHHHHHHHHH
Q 033102 82 LGNMQNLYETVK-KAQMVVQVEAVRV 106 (127)
Q Consensus 82 lgNMqnL~e~~K-KAQq~VQ~~m~kl 106 (127)
|+||..+++.+| |+++ +|++++..
T Consensus 7 ~~~m~kqaqkmQ~km~~-~Q~el~~~ 31 (103)
T PRK03762 7 FSKLGEMLEQMQKKAKQ-LEEENANK 31 (103)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHhcc
Confidence 355555444443 4455 36666643
No 33
>cd03081 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidat
Probab=30.51 E-value=45 Score=22.23 Aligned_cols=31 Identities=13% Similarity=0.252 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcEeeeeeCCceEEE
Q 033102 91 TVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKV 126 (127)
Q Consensus 91 ~~KKAQq~VQ~~m~klQeELa~~EfEG~aggGlVkV 126 (127)
.++-++++ .+.++++|. +++-++..+|.|++
T Consensus 13 ~~~G~~~l----l~~l~~~l~-~~~g~~~~dg~~~l 43 (80)
T cd03081 13 QAMGAEAL----AAHIKARLG-IDFHETTADGSVTL 43 (80)
T ss_pred HhCCHHHH----HHHHHHHhC-CCCCCcCCCCeEEE
Confidence 34557777 788888885 44455677777775
No 34
>cd01417 Ribosomal_L19e_E Ribosomal protein L19e, eukaryotic. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits.
Probab=30.06 E-value=1.2e+02 Score=24.35 Aligned_cols=36 Identities=19% Similarity=0.291 Sum_probs=29.9
Q ss_pred CccCccCChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033102 77 SKAGILGNMQNLYETVKKAQMVVQVEAVRVQKELAAA 113 (127)
Q Consensus 77 ~k~gmlgNMqnL~e~~KKAQq~VQ~~m~klQeELa~~ 113 (127)
.|||.|-|--.|++.+.+++.. ..-...+++++++.
T Consensus 124 aKGn~Fknk~~L~~~I~~~kae-~~r~k~l~~q~~a~ 159 (164)
T cd01417 124 AKGNVFKNKRVLMEHIHKAKAE-KAREKELADQAEAR 159 (164)
T ss_pred hcCCCcCcHHHHHHHHHHHHHH-HHHHHHHHHHHHHH
Confidence 5899999999999999999886 66777777777664
No 35
>PF03449 GreA_GreB_N: Transcription elongation factor, N-terminal; InterPro: IPR022691 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A 2ETN_C 2P4V_B.
Probab=28.67 E-value=1.4e+02 Score=20.32 Aligned_cols=27 Identities=26% Similarity=0.414 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcEe
Q 033102 89 YETVKKAQMVVQVEAVRVQKELAAAEF 115 (127)
Q Consensus 89 ~e~~KKAQq~VQ~~m~klQeELa~~Ef 115 (127)
+.+.|..|..++..+..+++.|+..+|
T Consensus 48 Y~aAke~q~~le~rI~~Le~~l~~a~V 74 (74)
T PF03449_consen 48 YHAAKERQAFLEARIRELEERLARAEV 74 (74)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHEEE
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhCcC
Confidence 478888898899999999999998775
No 36
>COG5374 Uncharacterized conserved protein [Function unknown]
Probab=26.99 E-value=73 Score=26.35 Aligned_cols=19 Identities=32% Similarity=0.286 Sum_probs=12.2
Q ss_pred eeEEEeeeccccCCCCCCC
Q 033102 55 SLRVYGLFGGKKDNNEKGD 73 (127)
Q Consensus 55 ~~~~~~lfgg~k~~~e~~~ 73 (127)
-+--.++.|||+|..|.++
T Consensus 127 ml~~~~~~~~k~D~~eA~~ 145 (192)
T COG5374 127 MLEENAKKGGKIDKMEADS 145 (192)
T ss_pred HHHHhhhcccchhhhhcch
Confidence 3444677889988765443
No 37
>PTZ00097 60S ribosomal protein L19; Provisional
Probab=26.27 E-value=1.5e+02 Score=24.04 Aligned_cols=36 Identities=28% Similarity=0.374 Sum_probs=29.7
Q ss_pred CccCccCChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033102 77 SKAGILGNMQNLYETVKKAQMVVQVEAVRVQKELAAA 113 (127)
Q Consensus 77 ~k~gmlgNMqnL~e~~KKAQq~VQ~~m~klQeELa~~ 113 (127)
.|||.|-|--.|++.+.+++.. ..-...+++++++.
T Consensus 125 aKGn~Fknk~~L~~~I~~~kae-~~r~k~l~~q~~a~ 160 (175)
T PTZ00097 125 SKGNQFKNKRVLIEAIHKTKNE-KVKEKKIQDQLEAR 160 (175)
T ss_pred hcCCCcCcHHHHHHHHHHHHHH-HHHHHHHHHHHHHH
Confidence 6899999999999999999886 67777777777654
No 38
>KOG3377 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.22 E-value=84 Score=24.88 Aligned_cols=21 Identities=38% Similarity=0.347 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhh
Q 033102 92 VKKAQMVVQVEAVRVQKELAA 112 (127)
Q Consensus 92 ~KKAQq~VQ~~m~klQeELa~ 112 (127)
+.+||+-||.++.+.|+-|+.
T Consensus 67 l~~aQ~~~~~El~~FQ~RL~R 87 (143)
T KOG3377|consen 67 LTKAQQYVQSELGKFQDRLNR 87 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 679999999999999999874
No 39
>PF02096 60KD_IMP: 60Kd inner membrane protein; InterPro: IPR001708 This family of proteins is required for the insertion of integral membrane proteins into cellular membranes. Many of these integral membrane proteins are associated with respiratory chain complexes, for example a large number of members of this family play an essential role in the activity and assembly of cytochrome c oxidase. Stage III sporulation protein J (SP3J) is a probable lipoprotein, rich in basic and hydrophobic amino acids. Mutations in the protein abolish the transcription of prespore-specific genes transcribed by the sigma G form of RNA polymerase []. SP3J could be involved in a signal transduction pathway coupling gene expression in the prespore to events in the mother cell, or it may be necessary for essential metabolic interactions between the two cells []. The protein shows a high degree of similarity to Bacillus subtilis YQJG, to yeast OXA1 and also to bacterial 60 kDa inner-membrane proteins [, , , ]. ; GO: 0051205 protein insertion into membrane, 0016021 integral to membrane
Probab=24.42 E-value=1.2e+02 Score=22.83 Aligned_cols=28 Identities=25% Similarity=0.347 Sum_probs=13.2
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033102 84 NMQNLYETVKKAQMVVQVEAVRVQKELA 111 (127)
Q Consensus 84 NMqnL~e~~KKAQq~VQ~~m~klQeELa 111 (127)
+|+++...+++.|+..+++.++.|+|..
T Consensus 31 k~~~~~P~l~~i~~k~~~~~~~~~~~~~ 58 (198)
T PF02096_consen 31 KMQELQPELKEIQEKYKEDQQKMQQEMQ 58 (198)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence 3445555555544444444444555443
No 40
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=23.34 E-value=2.4e+02 Score=21.53 Aligned_cols=31 Identities=19% Similarity=0.132 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcEeeeee
Q 033102 89 YETVKKAQMVVQVEAVRVQKELAAAEFDGYC 119 (127)
Q Consensus 89 ~e~~KKAQq~VQ~~m~klQeELa~~EfEG~a 119 (127)
+.+.|..|..++..+..++.+|+..+|.-.+
T Consensus 49 Y~aAk~~~~~~e~rI~~L~~~L~~A~iid~~ 79 (157)
T PRK01885 49 YIYGKKRLREIDRRVRFLTKRLENLKVVDYS 79 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCEEECCC
Confidence 4678999999999999999999999987543
No 41
>PF11328 DUF3130: Protein of unknown function (DUF3130; InterPro: IPR021477 This bacterial family of proteins has no known function.
Probab=23.26 E-value=1.5e+02 Score=21.84 Aligned_cols=23 Identities=35% Similarity=0.473 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 033102 86 QNLYETVKKAQMVVQVEAVRVQK 108 (127)
Q Consensus 86 qnL~e~~KKAQq~VQ~~m~klQe 108 (127)
=.|.+.+...|+++|..+.++++
T Consensus 51 ~dLv~~Ve~fq~v~~~DA~Rlkk 73 (90)
T PF11328_consen 51 IDLVDVVENFQQVVKKDASRLKK 73 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 36778899999999999999986
No 42
>TIGR03592 yidC_oxa1_cterm membrane protein insertase, YidC/Oxa1 family, C-terminal domain. This model describes full-length from some species, and the C-terminal region only from other species, of the YidC/Oxa1 family of proteins. This domain appears to be univeral among bacteria (although absent from Archaea). The well-characterized YidC protein from Escherichia coli and its close homologs contain a large N-terminal periplasmic domain in addition to the region modeled here.
Probab=22.85 E-value=1.3e+02 Score=22.90 Aligned_cols=9 Identities=33% Similarity=0.434 Sum_probs=3.4
Q ss_pred HHHHHHHHH
Q 033102 100 QVEAVRVQK 108 (127)
Q Consensus 100 Q~~m~klQe 108 (127)
|+++.++++
T Consensus 53 ~~e~~~l~k 61 (181)
T TIGR03592 53 QQEMMKLYK 61 (181)
T ss_pred HHHHHHHHH
Confidence 333333333
No 43
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=22.66 E-value=1.4e+02 Score=18.65 Aligned_cols=14 Identities=29% Similarity=0.385 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHhhc
Q 033102 100 QVEAVRVQKELAAA 113 (127)
Q Consensus 100 Q~~m~klQeELa~~ 113 (127)
+.+++++|+|+++.
T Consensus 54 ~k~l~~le~e~~~l 67 (68)
T PF06305_consen 54 RKELKKLEKELEQL 67 (68)
T ss_pred HHHHHHHHHHHHhc
Confidence 44588888888764
No 44
>PRK13848 conjugal transfer protein TraC; Provisional
Probab=22.59 E-value=38 Score=25.38 Aligned_cols=16 Identities=31% Similarity=0.524 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHhhcE
Q 033102 99 VQVEAVRVQKELAAAE 114 (127)
Q Consensus 99 VQ~~m~klQeELa~~E 114 (127)
|..++++||++|.+.+
T Consensus 8 I~~eI~kLqe~lk~~e 23 (98)
T PRK13848 8 IREEIAKLQEQLKQAE 23 (98)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5677777777776654
No 45
>PTZ00421 coronin; Provisional
Probab=22.10 E-value=1.1e+02 Score=27.05 Aligned_cols=30 Identities=20% Similarity=0.217 Sum_probs=23.2
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHhhcE
Q 033102 84 NMQNLYETVKKAQMVVQVEAVRVQKELAAAE 114 (127)
Q Consensus 84 NMqnL~e~~KKAQq~VQ~~m~klQeELa~~E 114 (127)
..+.|++..-|.++. ++++++++|+|.+.|
T Consensus 451 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~ 480 (493)
T PTZ00421 451 RLGRLQALSEKLRTQ-HEEIKRCREALQKKE 480 (493)
T ss_pred HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence 345677777778886 888999999998754
No 46
>PF09932 DUF2164: Uncharacterized conserved protein (DUF2164); InterPro: IPR018680 This family of various hypothetical prokaryotic proteins has no known function.
Probab=20.87 E-value=1.5e+02 Score=20.51 Aligned_cols=25 Identities=28% Similarity=0.340 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcE
Q 033102 90 ETVKKAQMVVQVEAVRVQKELAAAE 114 (127)
Q Consensus 90 e~~KKAQq~VQ~~m~klQeELa~~E 114 (127)
..+..||+.+++.++.+.++|-+.|
T Consensus 50 qgv~DA~~~~~~r~~~l~~~ly~lE 74 (76)
T PF09932_consen 50 QGVQDAQAVLEERMEDLEEELYELE 74 (76)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHhh
Confidence 6789999999999999999987654
No 47
>PF01346 FKBP_N: Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; InterPro: IPR000774 Peptidyl-prolyl cis-trans isomerase (PPIase) catalyses the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides [, ]. This alpha helical domain is found at the N terminus of proteins belonging to the FKBP-type peptidyl-prolyl cis-trans isomerase(IPR001179 from INTERPRO) family. Peptidyl-prolyl cis-trans isomerase has been shown to accelerate the refolding of several proteins in vitro [, , ]; the FKPB-type enzymes probably act in the folding of extracytoplasmic proteins.; GO: 0006457 protein folding; PDB: 1FD9_A 2VCD_A 3OE2_A 2UZ5_A 3B09_A 1Q6H_B 1Q6I_B 1Q6U_A.
Probab=20.70 E-value=2.9e+02 Score=19.12 Aligned_cols=28 Identities=11% Similarity=-0.007 Sum_probs=19.3
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033102 83 GNMQNLYETVKKAQMVVQVEAVRVQKEL 110 (127)
Q Consensus 83 gNMqnL~e~~KKAQq~VQ~~m~klQeEL 110 (127)
++..++.+.+++.++.+|+..++..+++
T Consensus 65 l~~~e~~~~l~~~~~~~~~~~~~~~~~~ 92 (124)
T PF01346_consen 65 LSDEEAQEALQAFQQKMQAKQQEKMAKA 92 (124)
T ss_dssp S-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHhhcchhhh
Confidence 5788888888888887776665554444
No 48
>PTZ00464 SNF-7-like protein; Provisional
Probab=20.54 E-value=3e+02 Score=22.27 Aligned_cols=30 Identities=13% Similarity=0.228 Sum_probs=16.0
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 033102 84 NMQNLYETVKKAQMVVQVEAVRVQKELAAA 113 (127)
Q Consensus 84 NMqnL~e~~KKAQq~VQ~~m~klQeELa~~ 113 (127)
..+.-.+.+.+-..+++....++.+||+..
T Consensus 15 t~~d~~~~l~~r~~~l~kKi~~ld~E~~~a 44 (211)
T PTZ00464 15 TLEDASKRIGGRSEVVDARINKIDAELMKL 44 (211)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444455544455555566666665543
No 49
>KOG0009 consensus Ubiquitin-like/40S ribosomal S30 protein fusion [Translation, ribosomal structure and biogenesis; Posttranslational modification, protein turnover, chaperones]
Probab=20.19 E-value=75 Score=22.14 Aligned_cols=24 Identities=25% Similarity=0.235 Sum_probs=18.6
Q ss_pred ccccccccceeEEEeeeccccCCC
Q 033102 46 QQKSGHQFRSLRVYGLFGGKKDNN 69 (127)
Q Consensus 46 ~~k~~~~~~~~~~~~lfgg~k~~~ 69 (127)
+++-.+.+|...|+..||||.--|
T Consensus 35 ~~Rlqy~rR~vn~~~~~g~Kr~~N 58 (62)
T KOG0009|consen 35 KKRLQYNRRFVNVVFGVGGKRGPN 58 (62)
T ss_pred HHHhhhheeeEEeeeccccccCCC
Confidence 344556789999999999987754
Done!