Query psy7992
Match_columns 131
No_of_seqs 138 out of 925
Neff 5.2
Searched_HMMs 46136
Date Sat Aug 17 00:02:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7992.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7992hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01018 rpsD_arch ribosomal 100.0 2E-52 4.3E-57 321.1 12.9 123 7-131 4-131 (162)
2 PLN00189 40S ribosomal protein 100.0 2.3E-52 5E-57 328.3 11.2 131 1-131 1-136 (194)
3 PTZ00155 40S ribosomal protein 100.0 1.2E-50 2.5E-55 316.0 11.6 128 4-131 2-134 (181)
4 PRK04051 rps4p 30S ribosomal p 100.0 1.3E-48 2.8E-53 303.6 13.0 124 7-131 4-130 (177)
5 KOG3301|consensus 100.0 4.6E-37 9.9E-42 236.4 8.1 119 11-131 1-124 (183)
6 KOG4655|consensus 100.0 1.8E-35 4E-40 227.7 5.5 116 15-131 14-134 (181)
7 COG0522 RpsD Ribosomal protein 99.9 1.6E-26 3.4E-31 183.3 9.3 113 10-131 7-121 (205)
8 PF00163 Ribosomal_S4: Ribosom 98.6 2.8E-10 6.2E-15 79.4 -6.6 89 8-103 2-94 (94)
9 CHL00113 rps4 ribosomal protei 97.7 3.5E-05 7.6E-10 61.3 3.0 34 98-131 83-116 (201)
10 TIGR01017 rpsD_bact ribosomal 97.4 0.00011 2.3E-09 58.1 3.1 33 99-131 85-117 (200)
11 PRK05327 rpsD 30S ribosomal pr 97.4 0.00012 2.5E-09 58.1 3.1 33 99-131 88-120 (203)
12 PF01479 S4: S4 domain; Inter 97.4 0.00012 2.7E-09 44.5 2.0 28 104-131 1-28 (48)
13 cd00165 S4 S4/Hsp/ tRNA synthe 88.4 0.38 8.3E-06 29.1 2.0 27 105-131 2-28 (70)
14 smart00363 S4 S4 RNA-binding d 83.6 0.98 2.1E-05 26.5 2.0 27 105-131 2-28 (60)
15 TIGR02988 YaaA_near_RecF S4 do 74.9 2.8 6.1E-05 26.3 2.2 28 104-131 9-36 (59)
16 PF15467 SGIII: Secretogranin- 61.6 9.2 0.0002 33.7 3.3 35 53-87 136-170 (453)
17 PF08656 DASH_Dad3: DASH compl 55.9 22 0.00047 24.6 3.7 35 43-77 8-43 (78)
18 COG1188 Ribosome-associated he 50.1 7.8 0.00017 28.0 0.9 29 103-131 8-36 (100)
19 PRK05912 tyrosyl-tRNA syntheta 39.8 1E+02 0.0023 26.8 6.4 27 105-131 344-370 (408)
20 COG0162 TyrS Tyrosyl-tRNA synt 39.8 1.8E+02 0.0038 25.7 7.8 54 71-131 310-363 (401)
21 PF12659 Stn1_C: Telomere capp 39.6 28 0.00061 26.0 2.5 42 70-111 12-55 (126)
22 PRK12899 secA preprotein trans 37.6 2.3E+02 0.0049 28.0 8.7 34 36-69 9-42 (970)
23 TIGR03069 PS_II_S4 photosystem 35.8 19 0.00042 29.4 1.2 27 104-131 184-210 (257)
24 KOG4603|consensus 33.9 57 0.0012 26.1 3.5 23 41-63 158-180 (201)
25 PF06777 DUF1227: Protein of u 33.0 1.2E+02 0.0027 23.1 5.1 65 42-117 54-123 (146)
26 PRK12906 secA preprotein trans 32.0 2.5E+02 0.0055 27.0 8.0 42 36-78 9-53 (796)
27 PRK13354 tyrosyl-tRNA syntheta 31.5 35 0.00076 29.8 2.1 28 104-131 343-370 (410)
28 TIGR03879 near_KaiC_dom probab 30.8 1.2E+02 0.0025 20.6 4.2 47 50-100 2-48 (73)
29 PF02829 3H: 3H domain; Inter 29.1 1.9E+02 0.0042 20.4 5.3 59 23-83 7-97 (98)
30 PRK12904 preprotein translocas 28.8 2.4E+02 0.0052 27.3 7.3 43 36-78 9-54 (830)
31 PRK13103 secA preprotein trans 28.8 2.8E+02 0.006 27.3 7.7 33 36-68 10-42 (913)
32 PF06417 DUF1077: Protein of u 27.0 41 0.0009 25.0 1.6 14 71-84 97-110 (124)
33 PRK06771 hypothetical protein; 26.1 64 0.0014 23.0 2.3 29 101-129 34-66 (93)
34 PRK13104 secA preprotein trans 26.0 3.3E+02 0.0072 26.7 7.7 52 36-94 10-64 (896)
35 PF12617 LdpA_C: Iron-Sulfur b 25.8 69 0.0015 25.5 2.7 57 71-127 113-181 (183)
36 PF09851 SHOCT: Short C-termin 25.2 45 0.00098 18.6 1.2 13 73-85 7-19 (31)
37 PF07899 Frigida: Frigida-like 24.6 3.5E+02 0.0076 22.6 6.9 58 71-130 131-189 (290)
38 PF04614 Pex19: Pex19 protein 24.6 2E+02 0.0042 23.4 5.2 45 40-84 164-215 (248)
39 PF13309 HTH_22: HTH domain 23.2 1.6E+02 0.0035 18.8 3.7 23 70-93 26-48 (64)
40 PF10862 FcoT: FcoT-like thioe 23.0 58 0.0013 25.4 1.7 33 72-111 66-98 (157)
41 PRK13107 preprotein translocas 22.6 2.7E+02 0.0059 27.3 6.4 43 36-78 10-55 (908)
42 PRK09200 preprotein translocas 22.3 3.7E+02 0.008 25.9 7.2 43 36-78 6-51 (790)
43 PRK14136 recX recombination re 22.2 1.3E+02 0.0029 25.7 3.9 63 56-119 181-244 (309)
44 COG2302 Uncharacterized conser 21.0 49 0.0011 27.7 1.1 35 93-131 173-207 (257)
No 1
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=100.00 E-value=2e-52 Score=321.11 Aligned_cols=123 Identities=63% Similarity=1.012 Sum_probs=119.4
Q ss_pred CCCCCccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH-----HHHHHHHHHcc
Q psy7992 7 PSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR-----NALLRRLVRIG 81 (131)
Q Consensus 7 ~~~~~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~-----~~LL~kL~~~G 81 (131)
|++++|+|+||++||++|++++|+++|++|||+||+|||+||++|++||++|+.|++++ ||+ ++||+|||+||
T Consensus 4 p~~~~k~~~~P~~pw~ker~~~E~~l~~kYgLknk~E~wk~~~~~~kiR~~Ar~L~~l~--d~~r~~~~~~LL~kL~~~G 81 (162)
T TIGR01018 4 PRKPRKKYETPRHPWIKERLDRELKLVGKYGLRNKKEVWKAETTLRKYRRAARELLGLD--DEQRLFEGNQLLRRLVRLG 81 (162)
T ss_pred CCCCCcccCCCCCChhhhhCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHcCC--cHHHHHHHHHHHHHHHHcC
Confidence 68999999999999999999999999999999999999999999999999999999999 665 89999999999
Q ss_pred ccCcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 82 VLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 82 ll~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
||+|++.+||+|++|||++|||||||+|||++|||+|++||||||+||||
T Consensus 82 ll~e~~~~Ld~vl~Ltv~~~leRRL~~vv~r~g~a~s~~~ArqlI~hgHI 131 (162)
T TIGR01018 82 ILDEENAKLDDVLGLTVEDFLERRLQTQVFKKGLARTIHQARQLIVHGHI 131 (162)
T ss_pred CCccccCCHHHHHhccHHHHHHHhHhhHhhhccCcCCHHHHHHHhhCCCe
Confidence 99876789999999999999999999999999999999999999999998
No 2
>PLN00189 40S ribosomal protein S9; Provisional
Probab=100.00 E-value=2.3e-52 Score=328.31 Aligned_cols=131 Identities=70% Similarity=1.062 Sum_probs=126.9
Q ss_pred CCCCCCCCCCCccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH-----HHHHH
Q psy7992 1 MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR-----NALLR 75 (131)
Q Consensus 1 ~~~~~~~~~~~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~-----~~LL~ 75 (131)
|+-+.++++++|+|+||++||+++|+++|+++|++|||+||+|||+|+++|++||++|+.|++++++||+ .+||+
T Consensus 1 ~~~~~~~~~~~K~y~tP~~P~ek~Rl~~E~kli~kYgLknK~E~wky~~ll~kiRk~Ar~Ll~l~~~d~~r~~~~~~LL~ 80 (194)
T PLN00189 1 MVHVSFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRNKRELWRVQYALSRIRNAARMLLTLDEKNPRRIFEGEALLR 80 (194)
T ss_pred CCcccCCCCCCcccCCCCCchhhHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHccCCCccHhHHHHHHHHH
Confidence 6777789999999999999999999999999999999999999999999999999999999999999996 89999
Q ss_pred HHHHccccCcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 76 RLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 76 kL~~~Gll~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
|||+||||++++.+||+|++|+|++|||||||+|||++|||+|+++|||||+||||
T Consensus 81 kL~~~GlL~~~~~~Ld~vl~Ltvs~~leRRL~~vv~r~g~a~si~~ARqlI~hgHI 136 (194)
T PLN00189 81 RMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHI 136 (194)
T ss_pred HHHHhCCccccccCHHHHhhccHHHHHHhhhceeeeecCCcCCHHHHHHheeCCCE
Confidence 99999999767889999999999999999999999999999999999999999998
No 3
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=100.00 E-value=1.2e-50 Score=315.97 Aligned_cols=128 Identities=75% Similarity=1.148 Sum_probs=123.9
Q ss_pred CCCCCCCCccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH-----HHHHHHHH
Q psy7992 4 NRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR-----NALLRRLV 78 (131)
Q Consensus 4 ~~~~~~~~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~-----~~LL~kL~ 78 (131)
.++|++++|+|+||++||+++|+++|+++|++|||+||+|||+|+++|++||++|+.|++++++||+ ++||+||+
T Consensus 2 ~~~~~~~~k~y~~P~~P~~k~rl~~E~~li~kYgLknk~E~wk~~~~~~kiR~~Ar~L~~l~~~d~~r~~~~~~LL~kL~ 81 (181)
T PTZ00155 2 GRNYRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMH 81 (181)
T ss_pred CCCCCCCCcccCCCCCchhHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHH
Confidence 3568999999999999999999999999999999999999999999999999999999999999996 89999999
Q ss_pred HccccCcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 79 RIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 79 ~~Gll~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
+||++.+++++|++|++|++++|||||||+|||++|||+|+++|||||+||||
T Consensus 82 ~~Gi~~~~k~~l~~~~~l~~~~~leRRL~~iv~r~g~A~ti~~ARqlI~HGHI 134 (181)
T PTZ00155 82 RLGLLDEDERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHI 134 (181)
T ss_pred HhCCcchhhccHHHHHCccHHHHHHHhhhhHHHhccCcCCHHHhhhheeCCCE
Confidence 99999766789999999999999999999999999999999999999999998
No 4
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=100.00 E-value=1.3e-48 Score=303.58 Aligned_cols=124 Identities=45% Similarity=0.767 Sum_probs=117.3
Q ss_pred CCCCCccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH---HHHHHHHHHcccc
Q psy7992 7 PSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR---NALLRRLVRIGVL 83 (131)
Q Consensus 7 ~~~~~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~---~~LL~kL~~~Gll 83 (131)
|++++|+|+||++||++||+++|+++|++|||+||+|||+||++|++||++|+.|++.++.... ++||+|||+||||
T Consensus 4 p~~~~k~~~~P~~pw~~~r~~~E~~l~~~YgLknk~E~wk~~~~~~~iR~~Ar~Ll~~~~~~r~~~~~~Ll~kL~~~Gil 83 (177)
T PRK04051 4 PKKPRKKYETPNHPWQKERIAEERELLGKYGLRNKRELWKAQSILRKYRRQARSLLALPPEERAKEEEQLLGKLKRYGIL 83 (177)
T ss_pred CCCCCcCcCCCCCchhhhhcHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHcCCC
Confidence 7999999999999999999999999999999999999999999999999999999995432211 8999999999999
Q ss_pred CcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 84 DESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 84 ~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
+ ++.+||+|++|||++|||||||++|++.|||+|+++|+|||.||||
T Consensus 84 ~-~~~~L~~vl~L~v~~~lerRLd~il~r~gla~S~~~Ar~lI~hGhV 130 (177)
T PRK04051 84 K-ENATLDDVLSLTVEDILERRLQTIVYRKGLARTPKQARQFIVHGHI 130 (177)
T ss_pred C-CCCCHHHHHhccHHHHHHhHHHHHHHHccCcCCHHHHHHHHHcCCE
Confidence 8 4889999999999999999999999999999999999999999997
No 5
>KOG3301|consensus
Probab=100.00 E-value=4.6e-37 Score=236.39 Aligned_cols=119 Identities=80% Similarity=1.190 Sum_probs=114.8
Q ss_pred CccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH-----HHHHHHHHHccccCc
Q psy7992 11 SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR-----NALLRRLVRIGVLDE 85 (131)
Q Consensus 11 ~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~-----~~LL~kL~~~Gll~e 85 (131)
+|+|++|+.|||++|++.|+++++.|||+|++|+|+....+.++|+.||.| |+++||. .+|+++|.+.|+++|
T Consensus 1 ~k~y~~PRrpfek~Rld~elkl~g~yglknk~elwr~~~~l~K~r~aaR~l--l~~k~p~rlf~g~allrrLvr~g~l~e 78 (183)
T KOG3301|consen 1 SKTYKTPRRPFEKERLDAELKLVGEYGLKNKRELWRVSRSLSKIRYAAREL--LDEKDPKRLFEGNALLRRLVRYGVLDE 78 (183)
T ss_pred CCccCCCCChHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHHHHH--hccccHHHHhcchHHHHHHHHHhhhhc
Confidence 589999999999999999999999999999999999999999999999999 6677774 899999999999999
Q ss_pred CccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 86 SKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 86 ~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
++.+||+|+.+++++||||||||+||++|||.||+|||++|.|+||
T Consensus 79 ~~~Kldyvl~l~ie~fLErRLqt~vFklGlAkSIhhARvLi~~rhI 124 (183)
T KOG3301|consen 79 RKNKLDYVLALTVEDFLERRLQTIVFKLGLAKSIHHARVLIRQRHI 124 (183)
T ss_pred cccchhHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHhcCccE
Confidence 9999999999999999999999999999999999999999999998
No 6
>KOG4655|consensus
Probab=100.00 E-value=1.8e-35 Score=227.73 Aligned_cols=116 Identities=24% Similarity=0.370 Sum_probs=113.7
Q ss_pred cCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH-----HHHHHHHHHccccCcCccc
Q psy7992 15 VTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR-----NALLRRLVRIGVLDESKMK 89 (131)
Q Consensus 15 ~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~-----~~LL~kL~~~Gll~e~~~~ 89 (131)
++.|.+|+.+..++|..++++|||+++|||.+||.+++++|++|+.|..+++.||| ..||+|||.||+++ +.++
T Consensus 14 kVdFLnWkv~d~~re~~v~rrY~l~~REdY~kyn~l~~~~r~la~~l~~l~~sDpfR~~~t~~LL~kly~~Gvip-Tr~~ 92 (181)
T KOG4655|consen 14 KVDFLNWKVTDHHRELCVLRRYHLKKREDYTKYNRLAGKVRKLANRLALLDESDPFRLQYTLLLLEKLYAMGVIP-TRKS 92 (181)
T ss_pred hcccceeeecCchhhHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHHHhhccccccceec-chhh
Confidence 67899999999999999999999999999999999999999999999999999998 79999999999999 8999
Q ss_pred hhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 90 LDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 90 L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
++++.++|+|+||+||||+|+.+++||+|+++|..||+||||
T Consensus 93 l~~~~kvtvssfCrRRLP~Vm~~l~m~~~~k~A~~~vEqGHV 134 (181)
T KOG4655|consen 93 LELTEKVTVSSFCRRRLPVVMGRLRMAESVKEAVRFVEQGHV 134 (181)
T ss_pred hhhcccchhHHHhhhccceeeeechhhhhHHHHHHHHHcCce
Confidence 999999999999999999999999999999999999999997
No 7
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=1.6e-26 Score=183.34 Aligned_cols=113 Identities=29% Similarity=0.385 Sum_probs=105.5
Q ss_pred CCcc--ccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHccccCcCc
Q psy7992 10 HSKT--YVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVRIGVLDESK 87 (131)
Q Consensus 10 ~~k~--~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~~~LL~kL~~~Gll~e~~ 87 (131)
++++ |++|++||.+++...|.+.+..|| +++.+.|+-.+.++..++.+++|..... ....+|+++|+++|++++
T Consensus 7 ~~~K~~rr~g~~~~~~~~~~~~~~~~~~pG-qhk~~~~~k~s~yg~qL~ekqkl~~~yg-~~ekqf~~~l~~a~~l~g-- 82 (205)
T COG0522 7 PKKKLSRRLGFNPWLKERLCKERKLPYKPG-QHGQERWKKLSDYGLQLREKQKLRAFYG-VLEKQFRRYLKEAGRLKG-- 82 (205)
T ss_pred cccceeeecCCChHHHHHHHHHhhcCCCcc-ccchhHHHHHHHHHHHHHHHHHhhhhcc-HHHHHHHHHHHHHhccCC--
Confidence 6666 999999999999999999999999 9999999999999999999999998766 223899999999999983
Q ss_pred cchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 88 MKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 88 ~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
++++|+++||||||||||||+|||.|++||||||+||||
T Consensus 83 -----~~~~~~~~~LErRLd~vVyR~GfA~T~~qARQlV~HGHI 121 (205)
T COG0522 83 -----VTGLNLLALLERRLDNVVYRLGFAKTRRQARQLVSHGHI 121 (205)
T ss_pred -----hHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHhhcceE
Confidence 779999999999999999999999999999999999998
No 8
>PF00163 Ribosomal_S4: Ribosomal protein S4/S9 N-terminal domain; InterPro: IPR001912 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S4 is one of the proteins from the small ribosomal subunit. S4 is known to bind directly to 16S ribosomal RNA. The crystal structure of a bacterial S4 protein revealed a two domain molecule. The first domain is composed of four helices in the known structure. The second domain is an insertion within domain 1 and displays some structural homology with the ETS DNA binding domain []. This entry represents the domain found at the N terminus of small ribosomal subunits S4 and S9. ; GO: 0019843 rRNA binding, 0005622 intracellular; PDB: 3BBN_D 2WWL_D 3OR9_D 3OFA_D 2QBB_D 3OFP_D 4A2I_D 2QB9_D 3OFO_D 2QBF_D ....
Probab=98.63 E-value=2.8e-10 Score=79.36 Aligned_cols=89 Identities=36% Similarity=0.448 Sum_probs=80.9
Q ss_pred CCCCccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH----HHHHHHHHHcccc
Q psy7992 8 SVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR----NALLRRLVRIGVL 83 (131)
Q Consensus 8 ~~~~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~----~~LL~kL~~~Gll 83 (131)
+...++|+.|++||..+.+..|..++++||+.+..+.|+.+.. |++++.+..|++++++ ..++++|+++|++
T Consensus 2 R~~~~~~k~~Rr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----rk~s~y~~qL~eKqk~r~~yg~lekql~~~~~~ 77 (94)
T PF00163_consen 2 RYRGPKCKLPRRLGEKLWLTEKAKLIRRYGLRPGQHGWRRKSR----RKLSRYGLQLREKQKLRFYYGILEKQLRRYGKI 77 (94)
T ss_dssp CSHSCCCHHHHHCTSHCTCSCCCSHCCSSSSSSSSSTTSHHHH----HCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred CcCCCccccCCCCCCCccCCCcccccccccccccccccccccc----ccchhhhcccccCCchhhhhhhHHHHHHHHHHH
Confidence 4567889999999999999999999999999999999888765 9999999999999996 6899999999999
Q ss_pred CcCccchhhhhhhhhhhHhh
Q psy7992 84 DESKMKLDYVWGLKIEDFLE 103 (131)
Q Consensus 84 ~e~~~~L~~vl~ltv~~fle 103 (131)
. ..++.+.+.++++|||
T Consensus 78 a---~k~~g~tg~~l~~lLE 94 (94)
T PF00163_consen 78 A---AKLKGVTGENLLQLLE 94 (94)
T ss_dssp H---HHSSSHHHHHHHHHHH
T ss_pred H---HhcCCCHHHHHHHHhC
Confidence 6 5688899999999997
No 9
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=97.65 E-value=3.5e-05 Score=61.25 Aligned_cols=34 Identities=41% Similarity=0.691 Sum_probs=31.9
Q ss_pred hhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 98 IEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 98 v~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
.-.+||.|||.++++.|++.|..+|+|+|.||||
T Consensus 83 ll~~LE~RLD~~L~r~g~~~SR~~ArqlI~~G~V 116 (201)
T CHL00113 83 LLQLLEMRLDNILFRLGMAPTIPAARQLVNHGHI 116 (201)
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCcE
Confidence 4478999999999999999999999999999997
No 10
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=97.44 E-value=0.00011 Score=58.12 Aligned_cols=33 Identities=39% Similarity=0.621 Sum_probs=31.1
Q ss_pred hhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 99 EDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 99 ~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
-.++|.|||.++++.|++.|..+|+++|.||||
T Consensus 85 l~~le~RLD~~L~~~g~~~SR~~ArqlI~~G~V 117 (200)
T TIGR01017 85 LRLLESRLDNVVYRLGFAPTRFAARQLVSHGHI 117 (200)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCE
Confidence 367889999999999999999999999999997
No 11
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=97.42 E-value=0.00012 Score=58.05 Aligned_cols=33 Identities=39% Similarity=0.660 Sum_probs=31.2
Q ss_pred hhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 99 EDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 99 ~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
-.++|.|||+++++.||+.|..+|+++|.||||
T Consensus 88 l~~lE~RLD~iL~~~g~~~SR~~arqlI~~G~V 120 (203)
T PRK05327 88 LQLLESRLDNVVYRLGFAPTRRQARQLVSHGHI 120 (203)
T ss_pred HHHHHHHHHHHHHHcCccCCHHHHHHHHHCCcE
Confidence 468899999999999999999999999999997
No 12
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=97.35 E-value=0.00012 Score=44.51 Aligned_cols=28 Identities=43% Similarity=0.541 Sum_probs=26.7
Q ss_pred hhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 104 RRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 104 rRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
+||+.++.+.|++.|..+|+++|.||+|
T Consensus 1 ~RLd~~L~~~~~~~sr~~a~~~I~~g~V 28 (48)
T PF01479_consen 1 MRLDKFLSRLGLASSRSEARRLIKQGRV 28 (48)
T ss_dssp EBHHHHHHHTTSSSSHHHHHHHHHTTTE
T ss_pred CCHHHHHHHcCCcCCHHHHHHhcCCCEE
Confidence 4899999999999999999999999986
No 13
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=88.36 E-value=0.38 Score=29.11 Aligned_cols=27 Identities=44% Similarity=0.642 Sum_probs=23.9
Q ss_pred hhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 105 RLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 105 RL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
||+.++.+.++..|..+|+++|.+|+|
T Consensus 2 rl~~~l~~~~~~~sr~~~~~~i~~g~V 28 (70)
T cd00165 2 RLDKILARLGLAPSRSEARQLIKHGHV 28 (70)
T ss_pred cHHHHHHHhccccCHHHHHHHHHcCCE
Confidence 677888888888999999999999986
No 14
>smart00363 S4 S4 RNA-binding domain.
Probab=83.59 E-value=0.98 Score=26.46 Aligned_cols=27 Identities=44% Similarity=0.565 Sum_probs=23.2
Q ss_pred hhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 105 RLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 105 RL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
||+.++...++..|..+|+.+|.+|+|
T Consensus 2 rl~~~l~~~~~~~s~~~~~~~i~~g~i 28 (60)
T smart00363 2 RLDKFLARLGLAPSRSQARKLIEQGRV 28 (60)
T ss_pred cHHHHHHHcCcccCHHHHHHHHHcCCE
Confidence 677788777788899999999999975
No 15
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=74.93 E-value=2.8 Score=26.31 Aligned_cols=28 Identities=18% Similarity=0.280 Sum_probs=24.1
Q ss_pred hhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 104 RRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 104 rRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
.||+..+...+++.|-..++.+|..|+|
T Consensus 9 ~rLd~~L~~~~~~~SR~~~k~li~~G~V 36 (59)
T TIGR02988 9 ITLGQLLKELGIIDSGGQAKWFLQENEV 36 (59)
T ss_pred HHHHHHHHHcCCccCHHHHHHHHHcCCE
Confidence 5788888888878899999999999986
No 16
>PF15467 SGIII: Secretogranin-3
Probab=61.62 E-value=9.2 Score=33.71 Aligned_cols=35 Identities=17% Similarity=0.432 Sum_probs=28.5
Q ss_pred HHHHHHHHHhcCChhhHHHHHHHHHHHccccCcCc
Q psy7992 53 KIRKAARELLTLDEKEHRNALLRRLVRIGVLDESK 87 (131)
Q Consensus 53 ~iRk~ar~L~~l~~~d~~~~LL~kL~~~Gll~e~~ 87 (131)
-++++|.++..-+...-|+.++.||-++|||.+++
T Consensus 136 IVqKIAtrIYEEnDRGVFDkIVSKLLnLGLITeSQ 170 (453)
T PF15467_consen 136 IVQKIATRIYEENDRGVFDKIVSKLLNLGLITESQ 170 (453)
T ss_pred HHHHHHHHHHhcccchHHHHHHHHHHhccccchhh
Confidence 35778888887666666899999999999998654
No 17
>PF08656 DASH_Dad3: DASH complex subunit Dad3; InterPro: IPR013965 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ].
Probab=55.89 E-value=22 Score=24.57 Aligned_cols=35 Identities=14% Similarity=0.159 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCC-hhhHHHHHHHHH
Q psy7992 43 EVWRVKYALAKIRKAARELLTLD-EKEHRNALLRRL 77 (131)
Q Consensus 43 E~~ky~~l~~~iRk~ar~L~~l~-~~d~~~~LL~kL 77 (131)
=++.|.++...+.+++..|..|. ..+|...+|+-|
T Consensus 8 VL~eY~~La~~L~~L~~~l~~L~~~~~~~~~lL~~L 43 (78)
T PF08656_consen 8 VLDEYQRLADNLKTLSDTLKDLNSSNSPSEELLDGL 43 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHccCCChHHHHHHH
Confidence 47889999999999999999983 344445555555
No 18
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=50.12 E-value=7.8 Score=28.00 Aligned_cols=29 Identities=17% Similarity=0.235 Sum_probs=27.0
Q ss_pred hhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 103 ERRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 103 erRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
+-|||-.+.-..|.++...|..+++.|||
T Consensus 8 ~mRLDKwL~~aR~~KrRslAk~~~~~GrV 36 (100)
T COG1188 8 RMRLDKWLWAARFIKRRSLAKEMIEGGRV 36 (100)
T ss_pred ceehHHHHHHHHHhhhHHHHHHHHHCCeE
Confidence 56999999999999999999999999986
No 19
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=39.82 E-value=1e+02 Score=26.78 Aligned_cols=27 Identities=33% Similarity=0.404 Sum_probs=23.5
Q ss_pred hhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 105 RLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 105 RL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
.+..++...|++.|-.+||.+|.+|-|
T Consensus 344 ~~~~~l~~~~~~~S~~earr~i~~g~v 370 (408)
T PRK05912 344 DLLALLVEAGLVPSKSEARRLIKQGGV 370 (408)
T ss_pred cHHHHHHHhCCCCCHHHHHHHHHcCCE
Confidence 566778899999999999999999854
No 20
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=39.78 E-value=1.8e+02 Score=25.68 Aligned_cols=54 Identities=30% Similarity=0.300 Sum_probs=36.4
Q ss_pred HHHHHHHHHccccCcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 71 NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 71 ~~LL~kL~~~Gll~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
.+-.+++|.-| .++ +-...++-. -+...+-..+...|++.|-.+||.+|.+|-|
T Consensus 310 ~~~~~~~F~~g-~~~-~l~~~dlk~-----~~~~~~~~~lv~~~L~psr~earr~i~~g~v 363 (401)
T COG0162 310 EEEFEKLFSEG-LPE-NLPPADLKQ-----KLEDGLVDLLVDAGLAPSRSEARRLIQQGGV 363 (401)
T ss_pred HHHHHHHHhcC-Ccc-cCCHHHHhh-----hhHHHHHHHHHHhCCcccHHHHHhhcccCCE
Confidence 56688999988 431 111112111 2222677778899999999999999998853
No 21
>PF12659 Stn1_C: Telomere capping C-terminal wHTH; InterPro: IPR024263 Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length. Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex []. These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast. Two separate protein complexes are required for chromosome end protection in fission yeast while a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution []. S.pombe has Stn1- and Ten1-like proteins that are essential for chromosome end protection. Stn1 orthologues exist in all species that have Pot1, whereas Ten1-like proteins can be found in all fungi. Fission yeast Stn1 and Ten1 localise at telomeres in a manner that correlates with the length of the ssDNA overhang, suggesting that they specifically associate with the telomeric ssDNA. This entry represents the C-terminal domain of telomere capping proteins and consists of tandem winged helix-turn-helix motifs [].; PDB: 3K10_A 3KEY_A.
Probab=39.55 E-value=28 Score=26.02 Aligned_cols=42 Identities=17% Similarity=0.268 Sum_probs=27.8
Q ss_pred HHHHHHHHHHccccCcC-ccc-hhhhhhhhhhhHhhhhhhhhhh
Q psy7992 70 RNALLRRLVRIGVLDES-KMK-LDYVWGLKIEDFLERRLQTQVF 111 (131)
Q Consensus 70 ~~~LL~kL~~~Gll~e~-~~~-L~~vl~ltv~~flerRL~~vv~ 111 (131)
|..+|.+|..+|+|.=. ... +|..--=++..+|.+|+++.+-
T Consensus 12 f~~~L~~L~~~glI~~~~~~~~idL~~Lk~l~~Y~~~ri~~lIk 55 (126)
T PF12659_consen 12 FYDYLQQLVKMGLIKLKSNDNIIDLKPLKNLYRYCQKRISTLIK 55 (126)
T ss_dssp HHHHHHHHHCTTSSEEEETTTTEE-HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCeEEEecCCCEEecHhHHHHHHHHHHHHHHHHH
Confidence 37889999999999521 112 2222223466899999998763
No 22
>PRK12899 secA preprotein translocase subunit SecA; Reviewed
Probab=37.59 E-value=2.3e+02 Score=28.04 Aligned_cols=34 Identities=18% Similarity=0.320 Sum_probs=30.9
Q ss_pred hcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhH
Q psy7992 36 YGLRNKREVWRVKYALAKIRKAARELLTLDEKEH 69 (131)
Q Consensus 36 YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~ 69 (131)
||-.+.+++++|..++.+|-.+...+..|++.+=
T Consensus 9 ~g~~~~r~lk~~~~~~~~In~~e~~~~~lsd~eL 42 (970)
T PRK12899 9 FGSSQERILKRFQKLVEKVNAYDEKFSSLSDDEL 42 (970)
T ss_pred hCCccHhHHHHHHHHHHHHHHHHHHHHcCCHHHH
Confidence 7888999999999999999999999999987653
No 23
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=35.84 E-value=19 Score=29.40 Aligned_cols=27 Identities=15% Similarity=0.159 Sum_probs=23.1
Q ss_pred hhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 104 RRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 104 rRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
.|||.++ ..++.-|...|.++|.+|+|
T Consensus 184 ~RLD~ll-s~~~~~SRs~a~~lI~~G~V 210 (257)
T TIGR03069 184 LRIDAIA-SAGFGLSRSKIVDQIKAGRL 210 (257)
T ss_pred ccHHHHH-HhhhhhhHHHHHHHHHCCeE
Confidence 4999655 77887799999999999986
No 24
>KOG4603|consensus
Probab=33.94 E-value=57 Score=26.14 Aligned_cols=23 Identities=22% Similarity=0.218 Sum_probs=20.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhc
Q psy7992 41 KREVWRVKYALAKIRKAARELLT 63 (131)
Q Consensus 41 k~E~~ky~~l~~~iRk~ar~L~~ 63 (131)
.++|.+|-+.++++++.++.+..
T Consensus 158 ~~~y~~~~~~wrk~krmf~ei~d 180 (201)
T KOG4603|consen 158 YREYQKYCKEWRKRKRMFREIID 180 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999998874
No 25
>PF06777 DUF1227: Protein of unknown function (DUF1227); InterPro: IPR010643 This domain represents a conserved region within a number of eukaryotic DNA repair helicases.; GO: 0005634 nucleus
Probab=32.99 E-value=1.2e+02 Score=23.13 Aligned_cols=65 Identities=18% Similarity=0.171 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcC-ChhhHH----HHHHHHHHHccccCcCccchhhhhhhhhhhHhhhhhhhhhhhcccC
Q psy7992 42 REVWRVKYALAKIRKAARELLTL-DEKEHR----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLA 116 (131)
Q Consensus 42 ~E~~ky~~l~~~iRk~ar~L~~l-~~~d~~----~~LL~kL~~~Gll~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a 116 (131)
-.++++...++-+|++..-|... .-.... ..+|..++...-|+ -..-.||--||.+.+.-++++
T Consensus 54 GnIR~AeHFv~flkR~veylk~rlrv~~v~~e~P~sFL~~~~~~~~id-----------~k~LrFc~eRL~sLl~TLei~ 122 (146)
T PF06777_consen 54 GNIRRAEHFVAFLKRFVEYLKTRLRVQHVISESPLSFLQHLKDETFID-----------RKPLRFCSERLSSLLRTLEIT 122 (146)
T ss_pred chHHhHHHHHHHHHHHHHHHHHHhhhcceeecCHHHHHHHHHHHhCCC-----------cHHHHHHHHHHHHHHHHHCCC
Confidence 45677777777777777777642 111111 56677777666664 234489999999999999987
Q ss_pred C
Q psy7992 117 K 117 (131)
Q Consensus 117 ~ 117 (131)
.
T Consensus 123 d 123 (146)
T PF06777_consen 123 D 123 (146)
T ss_pred c
Confidence 6
No 26
>PRK12906 secA preprotein translocase subunit SecA; Reviewed
Probab=32.00 E-value=2.5e+02 Score=27.04 Aligned_cols=42 Identities=19% Similarity=0.323 Sum_probs=33.5
Q ss_pred hcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH---HHHHHHHH
Q psy7992 36 YGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR---NALLRRLV 78 (131)
Q Consensus 36 YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~---~~LL~kL~ 78 (131)
+| .|.+++++|.+++.+|-.+...+..|++.+=. ..+-.+|-
T Consensus 9 ~~-~~~~~l~~~~~~~~~i~~~~~~~~~lsd~~l~~~t~~~~~rl~ 53 (796)
T PRK12906 9 FD-NDKRELKRLEKIADKVNALEDEYEKLSDEQLQAKTPEFRDRIK 53 (796)
T ss_pred cC-cchHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 46 78889999999999999999999999877632 44445544
No 27
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=31.50 E-value=35 Score=29.79 Aligned_cols=28 Identities=36% Similarity=0.464 Sum_probs=24.5
Q ss_pred hhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 104 RRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 104 rRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
..+..++...|++.|-.+||.+|.+|-|
T Consensus 343 ~~~~~~l~~~~~~~S~~earrli~~ggv 370 (410)
T PRK13354 343 KNLVDLLVDLGLEPSKREARRLIQNGAI 370 (410)
T ss_pred CCHHHHHHHhCCCCCHHHHHHHHHcCCE
Confidence 4577788999999999999999999854
No 28
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=30.83 E-value=1.2e+02 Score=20.56 Aligned_cols=47 Identities=21% Similarity=0.181 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHHHccccCcCccchhhhhhhhhhh
Q psy7992 50 ALAKIRKAARELLTLDEKEHRNALLRRLVRIGVLDESKMKLDYVWGLKIED 100 (131)
Q Consensus 50 l~~~iRk~ar~L~~l~~~d~~~~LL~kL~~~Gll~e~~~~L~~vl~ltv~~ 100 (131)
.+|-|.++|..|-.||+.-...-.|. -+..|+ +...+...++++.+.
T Consensus 2 ~~~~~~~~~~~l~~l~~~~r~af~L~-R~~eGl---S~kEIAe~LGIS~~T 48 (73)
T TIGR03879 2 VLGGIKKLAERLTWVDSLAEAAAALA-REEAGK---TASEIAEELGRTEQT 48 (73)
T ss_pred hhhHHhhHHHHHhcCCHHHHHHHHHH-HHHcCC---CHHHHHHHHCcCHHH
Confidence 47889999999999998764432233 222344 234466667666644
No 29
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=29.05 E-value=1.9e+02 Score=20.41 Aligned_cols=59 Identities=25% Similarity=0.385 Sum_probs=36.9
Q ss_pred hhhhhHHHHHHHHhc---------------------CCChHHHHHHHHHHHHHHHHHHHHhcCChh---------h--HH
Q psy7992 23 KARLDQELKIIGEYG---------------------LRNKREVWRVKYALAKIRKAARELLTLDEK---------E--HR 70 (131)
Q Consensus 23 ~~r~~~E~~i~~~Yg---------------------Lknk~E~~ky~~l~~~iRk~ar~L~~l~~~---------d--~~ 70 (131)
.|.+.+|+.+|-.+| +++++|..++-..+.+- .|.-|..|... | .+
T Consensus 7 ~~~~~~EL~~IVd~Gg~V~DV~veHp~YG~i~~~L~i~sr~Dv~~Fi~~l~~~--~~~~Ls~LT~GvH~HtI~a~~~e~l 84 (98)
T PF02829_consen 7 PDEIEDELEIIVDNGGRVLDVIVEHPVYGEITGNLNISSRRDVDKFIEKLEKS--KAKPLSSLTGGVHYHTIEAPDEEDL 84 (98)
T ss_dssp GGGHHHHHHHHHHTT-EEEEEEEEETTTEEEEEEEEE-SHHHHHHHHHHHHH----S--STTGGGGEEEEEEEESSHHHH
T ss_pred HHHHHHHHHHHHHCCCEEEEEEEeCCCCcEEEEEEecCCHHHHHHHHHHHhcc--CCcchHHhcCCEeeEEEEECCHHHH
Confidence 466777877777776 67999988876555544 45566665531 2 23
Q ss_pred HHHHHHHHHcccc
Q psy7992 71 NALLRRLVRIGVL 83 (131)
Q Consensus 71 ~~LL~kL~~~Gll 83 (131)
+.+.+.|-+.|+|
T Consensus 85 ~~I~~~L~~~G~L 97 (98)
T PF02829_consen 85 DKIEEALKKKGFL 97 (98)
T ss_dssp HHHHHHHHHTT-B
T ss_pred HHHHHHHHHCCCc
Confidence 7888888888876
No 30
>PRK12904 preprotein translocase subunit SecA; Reviewed
Probab=28.81 E-value=2.4e+02 Score=27.32 Aligned_cols=43 Identities=30% Similarity=0.492 Sum_probs=34.8
Q ss_pred hcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH---HHHHHHHH
Q psy7992 36 YGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR---NALLRRLV 78 (131)
Q Consensus 36 YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~---~~LL~kL~ 78 (131)
+|-.|.+++++|..++.+|-.+...+..|++.+=. ..+-.+|.
T Consensus 9 ~~~~~~~~l~~~~~~~~~i~~~~~~~~~lsd~eL~~~t~~~~~rl~ 54 (830)
T PRK12904 9 FGSRNDRELKRLRKIVDKINALEPEMEKLSDEELKAKTAEFKERLA 54 (830)
T ss_pred hCCccHhHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHH
Confidence 68889999999999999999999999999876532 44444444
No 31
>PRK13103 secA preprotein translocase subunit SecA; Reviewed
Probab=28.78 E-value=2.8e+02 Score=27.26 Aligned_cols=33 Identities=21% Similarity=0.464 Sum_probs=30.6
Q ss_pred hcCCChHHHHHHHHHHHHHHHHHHHHhcCChhh
Q psy7992 36 YGLRNKREVWRVKYALAKIRKAARELLTLDEKE 68 (131)
Q Consensus 36 YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d 68 (131)
||-.|.+++++|..++.+|-.+...+..|++.+
T Consensus 10 ~g~~~~r~l~~~~~~v~~i~~~e~~~~~lsd~e 42 (913)
T PRK13103 10 FGSKNEREVKRMLKTVQIVNAFEEQMVALSDEQ 42 (913)
T ss_pred hCCccHhHHHHHHHHHHHHHHHHHHHHcCCHHH
Confidence 788999999999999999999999999998765
No 32
>PF06417 DUF1077: Protein of unknown function (DUF1077); InterPro: IPR009445 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=27.04 E-value=41 Score=25.02 Aligned_cols=14 Identities=21% Similarity=0.223 Sum_probs=12.1
Q ss_pred HHHHHHHHHccccC
Q psy7992 71 NALLRRLVRIGVLD 84 (131)
Q Consensus 71 ~~LL~kL~~~Gll~ 84 (131)
.--+.||+.||||+
T Consensus 97 ~~gl~K~~~MGLLP 110 (124)
T PF06417_consen 97 ALGLYKCNSMGLLP 110 (124)
T ss_pred HHHHHHHhHccCCC
Confidence 45589999999998
No 33
>PRK06771 hypothetical protein; Provisional
Probab=26.08 E-value=64 Score=23.03 Aligned_cols=29 Identities=24% Similarity=0.339 Sum_probs=17.9
Q ss_pred HhhhhhhhhhhhcccCCC----HHHHHhhhccC
Q psy7992 101 FLERRLQTQVFKLGLAKS----IHHARVLIRQR 129 (131)
Q Consensus 101 flerRL~~vv~r~~~a~s----i~~Arq~I~hg 129 (131)
-+|++||.+.-+.|.... ..+.++++..|
T Consensus 34 ~ie~~L~~I~~~~Gi~~~~~~~~~e~~~Li~~G 66 (93)
T PRK06771 34 RMEDRLQLITKEMGIVDREPPVNKELRQLMEEG 66 (93)
T ss_pred HHHHHHHHHHHHcCCCCCcccccHHHHHHHHcC
Confidence 456666666666666665 34556666655
No 34
>PRK13104 secA preprotein translocase subunit SecA; Reviewed
Probab=25.99 E-value=3.3e+02 Score=26.69 Aligned_cols=52 Identities=21% Similarity=0.342 Sum_probs=39.1
Q ss_pred hcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH---HHHHHHHHHccccCcCccchhhhh
Q psy7992 36 YGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR---NALLRRLVRIGVLDESKMKLDYVW 94 (131)
Q Consensus 36 YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~---~~LL~kL~~~Gll~e~~~~L~~vl 94 (131)
+|-.|.+++.+|..++.+|-.+...+..|++.+=. ..|=.+|. .+.+||+++
T Consensus 10 ~~~~~~r~lk~~~~~~~~i~~~~~~~~~lsd~eL~~~t~~~k~~l~-------~~~~ld~~l 64 (896)
T PRK13104 10 FGSRNERTLRRMEKSVMAINAFEPKMQALSNEELAGKTQEFKERFN-------NGESLDELL 64 (896)
T ss_pred cCCccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH-------cCCchHHHH
Confidence 78899999999999999999999999999876532 34444443 234566654
No 35
>PF12617 LdpA_C: Iron-Sulfur binding protein C terminal; InterPro: IPR021039 This entry represents the C-terminal region of the iron-sulphur protein LdpA (Light dependent period), which is found in phototropic organisms. LdpA was originally identified in cyanobacteria where it is involved in light-dependent modulation of the circadian clock. The presence of iron-sulphur clusters on LdpA suggests that it may modulate the circadian clock as an indirect function of light intensity by sensing changes in cellular physiology [].
Probab=25.77 E-value=69 Score=25.48 Aligned_cols=57 Identities=16% Similarity=0.288 Sum_probs=39.3
Q ss_pred HHHHHHHHHccccCcCccchhhhhhhhhhhHhhhhhhhhhhhcc------------cCCCHHHHHhhhc
Q psy7992 71 NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLG------------LAKSIHHARVLIR 127 (131)
Q Consensus 71 ~~LL~kL~~~Gll~e~~~~L~~vl~ltv~~flerRL~~vv~r~~------------~a~si~~Arq~I~ 127 (131)
..-+.+|..+|++.....+-..+-++..-++-|+-++.++-..- +.+.+..|+.+|.
T Consensus 113 ~~Tv~~Lk~~gl~~~~~~~~~~iaGVAyGsyARkll~p~L~~~~~~~~~Led~Pe~l~~Av~~A~sLV~ 181 (183)
T PF12617_consen 113 AHTVEKLKQMGLLQPPPSSSAFIAGVAYGSYARKLLQPILEEAESRGGSLEDWPELLWQAVSLAHSLVS 181 (183)
T ss_pred hhHHHHHHHccCcCCCccccCCCceeeehHHHHHHHHHHHHHHHHcCCchhhChHHHHHHHHHHHHHhc
Confidence 56789999999986323334455577777888888877776544 4556667777765
No 36
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=25.24 E-value=45 Score=18.62 Aligned_cols=13 Identities=31% Similarity=0.439 Sum_probs=11.0
Q ss_pred HHHHHHHccccCc
Q psy7992 73 LLRRLVRIGVLDE 85 (131)
Q Consensus 73 LL~kL~~~Gll~e 85 (131)
-|..||+.|+|++
T Consensus 7 ~L~~l~~~G~Ise 19 (31)
T PF09851_consen 7 KLKELYDKGEISE 19 (31)
T ss_pred HHHHHHHcCCCCH
Confidence 4789999999984
No 37
>PF07899 Frigida: Frigida-like protein; InterPro: IPR012474 This family is composed of plant proteins that are similar to FRIGIDA protein expressed by Arabidopsis thaliana (Mouse-ear cress) (Q9FDW0 from SWISSPROT). This protein is probably nuclear and is required for the regulation of flowering time in the late-flowering phenotype. It is known to increase RNA levels of flowering locus C. Allelic variation at the FRIGIDA locus is a major determinant of natural variation in flowering time [].
Probab=24.62 E-value=3.5e+02 Score=22.59 Aligned_cols=58 Identities=19% Similarity=0.266 Sum_probs=47.5
Q ss_pred HHHHHHHHHccccCcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHh-hhccCC
Q psy7992 71 NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARV-LIRQRH 130 (131)
Q Consensus 71 ~~LL~kL~~~Gll~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq-~I~hgH 130 (131)
-.+|.-|..+||.++ -+-+++.+|=+..-.++.-+.++..+||+..+..-.+ ||..|+
T Consensus 131 ~gFL~lla~fgi~s~--Fd~del~~Lv~~va~~~~a~~L~~sLgl~~k~~d~V~~LI~~g~ 189 (290)
T PF07899_consen 131 LGFLQLLAAFGIVSE--FDEDELLKLVVSVARRKQAPELCRSLGLSDKMPDIVEKLIKKGK 189 (290)
T ss_pred HHHHHHHHHcCCccc--cCHHHHHHHHHHhcchHhhHHHHHHcCchhhhHHHHHHHHHCCC
Confidence 688999999999974 5678888888888888889999999999998877643 565554
No 38
>PF04614 Pex19: Pex19 protein family; InterPro: IPR006708 Peroxisome(s) form an intracellular compartment, bounded by a typical lipid bilayer membrane. Peroxisome functions are often specialised by organism and cell type; two widely distributed and well-conserved functions are H2O2-based respiration and fatty acid beta-oxidation. Other functions include ether lipid (plasmalogen) synthesis and cholesterol synthesis in animals, the glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation and assimilation in some yeasts. PEX genes encode the machinery ("peroxins") required to assemble the peroxisome. Membrane assembly and maintenance requires three of these (peroxins 3, 16, and 19) and may occur without the import of the matrix (lumen) enzymes. Matrix protein import follows a branched pathway of soluble recycling receptors, with one branch for each class of peroxisome targeting sequence (two are well characterised), and a common trunk for all. At least one of these receptors, Pex5p, enters and exits peroxisomes as it functions. Proliferation of the organelle is regulated by Pex11p. Peroxisome biogenesis is remarkably conserved among eukaryotes. A group of fatal, inherited neuropathologies are recognised as peroxisome biogenesis diseases. ; GO: 0005777 peroxisome; PDB: 2WL8_B 2W85_B.
Probab=24.60 E-value=2e+02 Score=23.40 Aligned_cols=45 Identities=9% Similarity=0.117 Sum_probs=30.4
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHhcCChhh--H--H---HHHHHHHHHccccC
Q psy7992 40 NKREVWRVKYALAKIRKAARELLTLDEKE--H--R---NALLRRLVRIGVLD 84 (131)
Q Consensus 40 nk~E~~ky~~l~~~iRk~ar~L~~l~~~d--~--~---~~LL~kL~~~Gll~ 84 (131)
..+||.||.+...-|+++...+-.-+..| + + -.|+.+|-..|=-+
T Consensus 164 ~~ed~~rY~~Q~~~v~~I~~~fE~~~~~d~~~~~~~~i~~lmqemQ~~G~PP 215 (248)
T PF04614_consen 164 SAEDYERYEKQYELVKEICAIFEKPPYDDEDPERREKIMELMQEMQELGQPP 215 (248)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHH--TT--HHHHHHHHHHHHHHHHHT----
T ss_pred CHHHHHHHHHHHHHHHHHHHHHcCCCCCcccHHHHHHHHHHHHHHHHcCCCc
Confidence 46899999999999999999988766555 3 2 56777777778765
No 39
>PF13309 HTH_22: HTH domain
Probab=23.18 E-value=1.6e+02 Score=18.84 Aligned_cols=23 Identities=26% Similarity=0.524 Sum_probs=17.9
Q ss_pred HHHHHHHHHHccccCcCccchhhh
Q psy7992 70 RNALLRRLVRIGVLDESKMKLDYV 93 (131)
Q Consensus 70 ~~~LL~kL~~~Gll~e~~~~L~~v 93 (131)
...++..|++.|+.. -+.+.+.|
T Consensus 26 k~~iV~~L~~~G~F~-lKgav~~v 48 (64)
T PF13309_consen 26 KKEIVRQLYEKGIFL-LKGAVEYV 48 (64)
T ss_pred HHHHHHHHHHCCCcc-cCcHHHHH
Confidence 378999999999997 56555554
No 40
>PF10862 FcoT: FcoT-like thioesterase domain; InterPro: IPR022598 Proteins in this family have a HotDog fold. This family was formerly known as DUF2662. The structure of Rv0098 from M. tuberculosis [] suggested a thioesterase function. Assays showed that this protein was a thioesterase with a preference for long chain fatty acyl groups []. The maximal Kcat was observed for palmitoyl-CoA, although longer and shorter molecules were also cleaved. In solution this protein forms a homo-hexameric complex.; PDB: 2PFC_A 3B18_A.
Probab=22.99 E-value=58 Score=25.36 Aligned_cols=33 Identities=24% Similarity=0.461 Sum_probs=22.4
Q ss_pred HHHHHHHHccccCcCccchhhhhhhhhhhHhhhhhhhhhh
Q psy7992 72 ALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVF 111 (131)
Q Consensus 72 ~LL~kL~~~Gll~e~~~~L~~vl~ltv~~flerRL~~vv~ 111 (131)
.++.+...-|+++. ....|.++|++|.|+.|+-
T Consensus 66 ~~~A~~v~~~l~~~-------f~~Wt~ddf~~rQLsdilI 98 (157)
T PF10862_consen 66 YLIAKCVKNELIPA-------FAGWTLDDFWERQLSDILI 98 (157)
T ss_dssp HHHHHHHHTT-SCC-------CTT--HHHHHHCHHHHEEE
T ss_pred HHHHHHHhhccchh-------hcccCHHHHHHhhcCceeE
Confidence 45677777777752 4478899999999998863
No 41
>PRK13107 preprotein translocase subunit SecA; Reviewed
Probab=22.56 E-value=2.7e+02 Score=27.30 Aligned_cols=43 Identities=23% Similarity=0.362 Sum_probs=35.1
Q ss_pred hcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH---HHHHHHHH
Q psy7992 36 YGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR---NALLRRLV 78 (131)
Q Consensus 36 YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~---~~LL~kL~ 78 (131)
||-++.+++++|..++.+|-.+...+..|++.+=. ..|-.+|-
T Consensus 10 ~g~~~~r~l~~~~~~v~~i~~~~~~~~~lsd~eL~~~t~~~k~~l~ 55 (908)
T PRK13107 10 FGSRNDRTLKGLGKVVIKINALEADYEKLTDEELKAKTAEFRERLA 55 (908)
T ss_pred hCCccHhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 78899999999999999999999999999876532 44444444
No 42
>PRK09200 preprotein translocase subunit SecA; Reviewed
Probab=22.32 E-value=3.7e+02 Score=25.86 Aligned_cols=43 Identities=23% Similarity=0.336 Sum_probs=34.0
Q ss_pred hcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH---HHHHHHHH
Q psy7992 36 YGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR---NALLRRLV 78 (131)
Q Consensus 36 YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~---~~LL~kL~ 78 (131)
+|-.+.+++++|.+++.+|-.+...+..|++.+=. ..+=.+|.
T Consensus 6 ~~~~~~~~l~~~~~~~~~i~~~~~~~~~lsd~~L~~~~~~~~~~l~ 51 (790)
T PRK09200 6 LGDIDKRRLKKYRKIVKQINKLEGKMSSLSDEELRQKTIEFKERLA 51 (790)
T ss_pred cCCccHhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 56788899999999999999999999999876532 34444444
No 43
>PRK14136 recX recombination regulator RecX; Provisional
Probab=22.16 E-value=1.3e+02 Score=25.74 Aligned_cols=63 Identities=16% Similarity=0.221 Sum_probs=34.9
Q ss_pred HHHHHHhcCChh-hHHHHHHHHHHHccccCcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCH
Q psy7992 56 KAARELLTLDEK-EHRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSI 119 (131)
Q Consensus 56 k~ar~L~~l~~~-d~~~~LL~kL~~~Gll~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si 119 (131)
.+..+|....-. +..+.+|++|..+|+|+. ..--+.........+=.+++..-+.+.|+..++
T Consensus 181 ELr~KL~kkG~~ee~IE~VIerLke~gYLDD-eRFAesyVr~R~~kkGp~rIrqELrQKGId~eL 244 (309)
T PRK14136 181 ELARKLAPYADESDSVEPLLDALEREGWLSD-ARFAESLVHRRASRVGSARIVSELKRHAVGDAL 244 (309)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHcCCcCH-HHHHHHHHHHHhhchhHHHHHHHHHHcCCCHHH
Confidence 455556544322 234899999999999983 211111112223334455666666677765544
No 44
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=21.04 E-value=49 Score=27.65 Aligned_cols=35 Identities=20% Similarity=0.338 Sum_probs=28.6
Q ss_pred hhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992 93 VWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131 (131)
Q Consensus 93 vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI 131 (131)
.+.++||+| |||.|+ ..+|-.|...|.|+|+.|-|
T Consensus 173 e~~~~vsSl---RLD~vi-s~~~~~SR~~a~~lIe~g~V 207 (257)
T COG2302 173 ELDVTVSSL---RLDVVI-SEGFGLSRAKAQQLIEKGKV 207 (257)
T ss_pred EEeeeeehh---hHHHHH-HHHHhhhHHHHHHHHHcCce
Confidence 345666665 999988 78899999999999999865
Done!