Query psy8661
Match_columns 71
No_of_seqs 110 out of 268
Neff 4.5
Searched_HMMs 46136
Date Sat Aug 17 00:32:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8661.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8661hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK04313 30S ribosomal protein 100.0 5.3E-39 1.1E-43 233.8 6.0 70 1-70 15-84 (237)
2 PLN00036 40S ribosomal protein 100.0 7.9E-39 1.7E-43 235.5 6.1 70 1-70 19-88 (261)
3 PTZ00118 40S ribosomal protein 100.0 1.2E-38 2.6E-43 234.6 6.1 70 1-70 19-88 (262)
4 PTZ00223 40S ribosomal protein 100.0 2E-38 4.4E-43 234.5 6.1 70 1-70 16-85 (273)
5 COG1471 RPS4A Ribosomal protei 100.0 9.7E-37 2.1E-41 222.5 3.1 70 1-70 18-87 (241)
6 KOG0378|consensus 100.0 2.5E-32 5.4E-37 200.9 -0.1 70 1-70 19-88 (263)
7 PF08071 RS4NT: RS4NT (NUC023) 98.9 2.6E-10 5.7E-15 63.5 1.3 22 1-22 17-38 (38)
8 PF01479 S4: S4 domain; Inter 98.9 6.2E-09 1.3E-13 57.6 4.6 46 25-71 2-47 (48)
9 COG0522 RpsD Ribosomal protein 97.5 9.6E-05 2.1E-09 53.1 3.3 34 33-66 102-135 (205)
10 cd00165 S4 S4/Hsp/ tRNA synthe 97.4 0.00049 1.1E-08 37.7 4.9 42 26-68 3-44 (70)
11 TIGR01018 rpsD_arch ribosomal 97.3 0.0002 4.4E-09 50.1 3.0 34 33-66 112-145 (162)
12 PTZ00155 40S ribosomal protein 97.3 0.00023 5E-09 50.5 2.8 33 34-66 116-148 (181)
13 TIGR02988 YaaA_near_RecF S4 do 97.2 0.001 2.2E-08 38.3 4.8 42 24-66 9-50 (59)
14 smart00363 S4 S4 RNA-binding d 97.2 0.0015 3.2E-08 34.8 4.8 42 26-68 3-44 (60)
15 PRK04051 rps4p 30S ribosomal p 97.1 0.00062 1.4E-08 48.1 3.7 33 34-66 112-144 (177)
16 PLN00189 40S ribosomal protein 97.0 0.00043 9.4E-09 49.8 2.3 34 33-66 117-150 (194)
17 TIGR01017 rpsD_bact ribosomal 96.0 0.011 2.3E-07 41.9 4.0 34 34-67 99-132 (200)
18 CHL00113 rps4 ribosomal protei 95.9 0.012 2.6E-07 42.2 3.8 33 34-66 98-130 (201)
19 PRK05327 rpsD 30S ribosomal pr 95.8 0.015 3.3E-07 41.2 4.0 34 34-67 102-135 (203)
20 PRK11507 ribosome-associated p 95.5 0.019 4.1E-07 35.5 3.2 39 22-61 10-48 (70)
21 TIGR00478 tly hemolysin TlyA f 95.1 0.031 6.7E-07 40.3 3.7 37 29-66 5-41 (228)
22 PF13275 S4_2: S4 domain; PDB: 94.3 0.0094 2E-07 36.2 -0.5 40 22-62 6-45 (65)
23 PRK05912 tyrosyl-tRNA syntheta 94.2 0.092 2E-06 40.7 4.7 43 23-66 342-384 (408)
24 COG2501 S4-like RNA binding pr 94.2 0.052 1.1E-06 33.9 2.7 37 23-60 11-47 (73)
25 PRK13354 tyrosyl-tRNA syntheta 93.6 0.13 2.9E-06 39.9 4.5 42 23-65 342-383 (410)
26 TIGR00005 rluA_subfam pseudour 93.3 0.26 5.6E-06 35.6 5.4 45 22-67 4-48 (299)
27 COG1187 RsuA 16S rRNA uridine- 93.0 0.11 2.4E-06 38.4 3.2 29 34-63 12-40 (248)
28 TIGR03069 PS_II_S4 photosystem 91.4 0.42 9E-06 35.1 4.5 43 23-67 183-225 (257)
29 PRK10839 16S rRNA pseudouridyl 90.8 0.55 1.2E-05 33.0 4.5 39 26-66 3-41 (232)
30 PRK11180 rluD 23S rRNA pseudou 90.4 0.64 1.4E-05 34.4 4.8 43 23-66 17-59 (325)
31 COG0564 RluA Pseudouridylate s 89.4 0.7 1.5E-05 34.3 4.3 43 23-68 12-54 (289)
32 KOG4655|consensus 88.7 0.36 7.9E-06 34.7 2.3 34 33-66 115-148 (181)
33 COG1189 Predicted rRNA methyla 88.4 0.57 1.2E-05 35.0 3.2 31 35-65 13-43 (245)
34 PRK10475 23S rRNA pseudouridin 87.8 1.2 2.6E-05 33.2 4.6 42 22-66 5-46 (290)
35 PRK10348 ribosome-associated h 87.1 2 4.3E-05 29.3 5.0 42 23-66 8-49 (133)
36 PRK10700 23S rRNA pseudouridyl 87.0 0.78 1.7E-05 34.0 3.2 36 28-66 7-42 (289)
37 PRK11025 23S rRNA pseudouridyl 85.2 2.4 5.3E-05 31.3 5.1 42 23-66 19-60 (317)
38 PF03417 AAT: Acyl-coenzyme A: 83.9 1.3 2.9E-05 30.4 3.0 29 21-50 69-97 (225)
39 COG0162 TyrS Tyrosyl-tRNA synt 81.4 1.5 3.3E-05 34.4 2.9 33 34-66 345-377 (401)
40 PLN00051 RNA-binding S4 domain 75.1 4.5 9.8E-05 30.0 3.6 43 23-67 191-233 (267)
41 COG1188 Ribosome-associated he 74.2 3.7 8.1E-05 27.0 2.6 27 35-61 19-45 (100)
42 PF08828 DSX_dimer: Doublesex 73.2 4 8.7E-05 24.9 2.4 35 20-57 20-55 (62)
43 COG2302 Uncharacterized conser 72.9 5.4 0.00012 30.1 3.6 47 22-70 179-225 (257)
44 TIGR00234 tyrS tyrosyl-tRNA sy 72.2 4.8 0.0001 31.0 3.2 43 23-66 329-371 (377)
45 cd01935 Ntn_CGH_like Choloylgl 58.7 12 0.00026 25.5 2.9 32 21-52 94-125 (229)
46 TIGR03198 pucE xanthine dehydr 58.4 3.5 7.5E-05 28.4 0.1 41 22-66 19-64 (151)
47 cd01903 Ntn_AC_NAAA AC_NAAA Th 54.5 13 0.00028 26.5 2.5 30 22-51 97-126 (231)
48 cd00542 Ntn_PVA Penicillin V a 51.1 41 0.00089 24.8 4.8 31 22-52 97-127 (303)
49 KOG3301|consensus 50.0 17 0.00037 26.3 2.5 31 33-63 105-135 (183)
50 KOG2404|consensus 49.0 17 0.00038 29.3 2.7 51 2-52 117-168 (477)
51 KOG2623|consensus 48.4 26 0.00057 28.5 3.6 38 23-61 398-435 (467)
52 TIGR03193 4hydroxCoAred 4-hydr 46.9 12 0.00026 25.8 1.4 44 22-69 17-65 (148)
53 COG2080 CoxS Aerobic-type carb 40.2 18 0.0004 25.3 1.5 42 21-66 18-64 (156)
54 cd00131 PAX Paired Box domain 38.4 77 0.0017 20.7 4.2 54 6-59 60-115 (128)
55 COG0103 RpsI Ribosomal protein 37.8 12 0.00026 25.7 0.2 16 49-65 25-40 (130)
56 PF03793 PASTA: PASTA domain; 35.5 49 0.0011 18.2 2.5 31 38-68 9-39 (63)
57 PF08528 Whi5: Whi5 like; Int 34.1 17 0.00037 18.3 0.4 9 30-38 2-10 (25)
58 PF12476 DUF3696: Protein of u 33.0 18 0.00039 20.2 0.4 13 55-70 30-42 (52)
59 PHA02754 hypothetical protein; 32.1 58 0.0013 20.0 2.6 32 22-56 5-36 (67)
60 PF00473 CRF: Corticotropin-re 31.0 15 0.00033 20.3 -0.1 23 29-51 12-34 (39)
61 COG4753 Response regulator con 30.7 54 0.0012 26.6 2.9 29 35-66 32-60 (475)
62 PF06953 ArsD: Arsenical resis 28.7 62 0.0013 21.6 2.5 26 41-66 59-90 (123)
63 TIGR02309 HpaB-1 4-hydroxyphen 28.5 72 0.0016 25.4 3.2 27 37-63 1-29 (477)
64 PRK11433 aldehyde oxidoreducta 24.5 51 0.0011 24.2 1.6 42 21-66 66-112 (217)
65 PF00076 RRM_1: RNA recognitio 24.3 1.2E+02 0.0026 15.9 3.1 22 38-59 47-69 (70)
66 TIGR03311 Se_dep_Molyb_1 selen 24.0 41 0.0009 28.6 1.2 42 22-67 14-60 (848)
67 PF12471 GTP_CH_N: GTP cyclohy 24.0 58 0.0013 23.8 1.8 24 39-62 133-156 (194)
68 PF08194 DIM: DIM protein; In 22.8 58 0.0013 17.8 1.3 11 49-59 23-33 (36)
69 PF11829 DUF3349: Protein of u 22.5 80 0.0017 20.4 2.1 23 22-48 24-46 (96)
70 cd04457 S1_S28E S1_S28E: S28E, 21.9 28 0.00061 21.0 -0.1 16 31-46 44-59 (60)
71 PF13881 Rad60-SLD_2: Ubiquiti 21.6 14 0.00031 24.0 -1.6 23 45-67 52-74 (111)
72 COG4814 Uncharacterized protei 21.6 57 0.0012 25.1 1.4 19 48-66 85-103 (288)
73 PF14259 RRM_6: RNA recognitio 21.4 1.2E+02 0.0026 16.4 2.5 22 38-59 47-69 (70)
74 cd03515 Link_domain_TSG_6_like 21.2 68 0.0015 20.7 1.5 16 35-50 11-26 (93)
75 cd01814 NTGP5 Ubiquitin-like N 20.7 14 0.00031 24.7 -1.7 26 42-67 51-76 (113)
76 PF07384 DUF1497: Protein of u 20.5 71 0.0015 19.0 1.4 15 34-48 1-15 (59)
77 PHA03311 helicase-primase subu 20.4 39 0.00084 29.4 0.4 43 18-65 271-314 (828)
No 1
>PRK04313 30S ribosomal protein S4e; Validated
Probab=100.00 E-value=5.3e-39 Score=233.76 Aligned_cols=70 Identities=39% Similarity=0.668 Sum_probs=69.3
Q ss_pred CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661 1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV 70 (71)
Q Consensus 1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md 70 (71)
||+|++++||++||||||+++|||||+|||||+||||+|++||++||+||+|+|||+||||++|||||||
T Consensus 15 ~i~kk~~~~a~kpspGPH~~~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmD 84 (237)
T PRK04313 15 PIPRKEYKWTVKPSPGPHSIEESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMD 84 (237)
T ss_pred ccccccceeccCCCCCCCCcccccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCcee
Confidence 7899999999999999999999999999999999999999999999999999999999999999999999
No 2
>PLN00036 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=7.9e-39 Score=235.48 Aligned_cols=70 Identities=76% Similarity=1.200 Sum_probs=69.4
Q ss_pred CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661 1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV 70 (71)
Q Consensus 1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md 70 (71)
||+|++++|||+||||||+++|||||+|||||+||||+|++||++||+|++|+|||+||||++|||||||
T Consensus 19 ~l~kk~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mD 88 (261)
T PLN00036 19 MLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMD 88 (261)
T ss_pred ccccccCeeccCCCCCCCccccccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeE
Confidence 7999999999999999999999999999999999999999999999999999999999999999999999
No 3
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=1.2e-38 Score=234.59 Aligned_cols=70 Identities=71% Similarity=1.155 Sum_probs=69.4
Q ss_pred CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661 1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV 70 (71)
Q Consensus 1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md 70 (71)
||+|++++|||+||||||+++|||||+|||||+|+||+|++||++||+|++|+|||+||||++|||||||
T Consensus 19 ~i~kk~~~~a~rpspGPHk~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mD 88 (262)
T PTZ00118 19 MLDKLGGQYAPKTSPGPHKLRECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMD 88 (262)
T ss_pred ccccccceeccCCCCCCCccccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeE
Confidence 7899999999999999999999999999999999999999999999999999999999999999999999
No 4
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=2e-38 Score=234.48 Aligned_cols=70 Identities=67% Similarity=1.061 Sum_probs=69.4
Q ss_pred CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661 1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV 70 (71)
Q Consensus 1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md 70 (71)
||+|++++|||+||||||+++|||||+|||||+|+||+|++||++||+|++|+|||+||||++|||||||
T Consensus 16 ~i~kk~~~~a~rpspGPH~~~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMD 85 (273)
T PTZ00223 16 MLSKLTGVFAPRPRAGPHKLRECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMD 85 (273)
T ss_pred ccccccceeccCCCCCCCccccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeE
Confidence 7899999999999999999999999999999999999999999999999999999999999999999999
No 5
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.7e-37 Score=222.45 Aligned_cols=70 Identities=47% Similarity=0.758 Sum_probs=69.0
Q ss_pred CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661 1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV 70 (71)
Q Consensus 1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md 70 (71)
+++|++++|+++|+||||++++|+||++++||+|+||+|+|||++||++|.|+|||+||+|++|||||||
T Consensus 18 ~i~rK~~kw~~~P~pGPH~~~~slPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmD 87 (241)
T COG1471 18 PIPRKTGKWAVRPSPGPHKAEESLPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMD 87 (241)
T ss_pred EeccccceEeccCCCCCCcccccccEEeeehhHHHhccchHHHHHHHhcCcEEECCEEeccccCCcceEE
Confidence 5789999999999999999999999999999999999999999999999999999999999999999998
No 6
>KOG0378|consensus
Probab=99.97 E-value=2.5e-32 Score=200.87 Aligned_cols=70 Identities=81% Similarity=1.280 Sum_probs=69.6
Q ss_pred CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661 1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV 70 (71)
Q Consensus 1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md 70 (71)
||||++|.|||+||+|||+++||+||++||||+|+||+|.+|+++||+|+.|+|||+||||.+||+||||
T Consensus 19 mldk~~G~fa~~ps~gphk~reclpl~~~~~~~Lkya~~~~e~~~I~~qr~i~v~gkvrt~~~yp~g~mD 88 (263)
T KOG0378|consen 19 MLDKLGGVFAPMPSSGPHKLRECLPLIVFLRNRLKYALNGKEVKKILMQREIKVDGKVRTDSTYPAGFMD 88 (263)
T ss_pred eecccCcEEecCCCCCCcccccceeEEEEeehhhhhhhcccHHHHHHHHhhhhccceeecccccccceeE
Confidence 8999999999999999999999999999999999999999999999999999999999999999999998
No 7
>PF08071 RS4NT: RS4NT (NUC023) domain; InterPro: IPR013843 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the N-terminal region of these proteins.; PDB: 2XZM_W 2XZN_W 3U5G_E 3U5C_E.
Probab=98.95 E-value=2.6e-10 Score=63.51 Aligned_cols=22 Identities=77% Similarity=1.271 Sum_probs=13.0
Q ss_pred CccccccccccCCCCCCCCCcc
Q psy8661 1 MLDKLGGVFAPRPSTGPHKLRE 22 (71)
Q Consensus 1 ~l~K~~~~~a~~pspGPH~~~~ 22 (71)
||+|++++||++||||||+++|
T Consensus 17 ~i~kk~~~~a~rpspGPH~~~e 38 (38)
T PF08071_consen 17 MIDKKTGKFAPRPSPGPHKLRE 38 (38)
T ss_dssp T--SSSSSB-----SSSS-CCC
T ss_pred ccccccCccccCCCCCCccCCC
Confidence 6899999999999999999986
No 8
>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=98.85 E-value=6.2e-09 Score=57.60 Aligned_cols=46 Identities=33% Similarity=0.354 Sum_probs=41.3
Q ss_pred hHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCcccccC
Q psy8661 25 PLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMVR 71 (71)
Q Consensus 25 PL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md~ 71 (71)
+|..|| ..++++.|..||++++.+|.|+|||++++|+.|++...|.
T Consensus 2 RLd~~L-~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~ 47 (48)
T PF01479_consen 2 RLDKFL-SRLGLASSRSEARRLIKQGRVKVNGKVVKDPSYIVKPGDV 47 (48)
T ss_dssp BHHHHH-HHTTSSSSHHHHHHHHHTTTEEETTEEESSTTSBESTTEE
T ss_pred CHHHHH-HHcCCcCCHHHHHHhcCCCEEEECCEEEcCCCCCCCCcCC
Confidence 567777 4589999999999999999999999999999999988763
No 9
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=97.50 E-value=9.6e-05 Score=53.15 Aligned_cols=34 Identities=26% Similarity=0.359 Sum_probs=31.3
Q ss_pred hhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
++|+|.|.++|++.+.+|.|.|||++++.+.|=|
T Consensus 102 R~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V 135 (205)
T COG0522 102 RLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLV 135 (205)
T ss_pred HhcccccHHHHHHHhhcceEEECCEEeccCcEEe
Confidence 4799999999999999999999999999997744
No 10
>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=97.44 E-value=0.00049 Score=37.72 Aligned_cols=42 Identities=24% Similarity=0.257 Sum_probs=33.5
Q ss_pred HHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccc
Q psy8661 26 LVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGF 68 (71)
Q Consensus 26 L~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~ 68 (71)
|.-+|+.. +.+.+..++++++.+|.|+|||+..++..+++-.
T Consensus 3 l~~~l~~~-~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~ 44 (70)
T cd00165 3 LDKILARL-GLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKP 44 (70)
T ss_pred HHHHHHHh-ccccCHHHHHHHHHcCCEEECCEEccCCccCcCC
Confidence 44566543 3567899999999999999999999888887643
No 11
>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=97.32 E-value=0.0002 Score=50.08 Aligned_cols=34 Identities=24% Similarity=0.330 Sum_probs=31.7
Q ss_pred hhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
++|+|.|..+|++.+.||.|.|||++++++.|-|
T Consensus 112 r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V 145 (162)
T TIGR01018 112 KKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIV 145 (162)
T ss_pred hccCcCCHHHHHHHhhCCCeeECCEEeccCceEe
Confidence 4799999999999999999999999999998765
No 12
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=97.26 E-value=0.00023 Score=50.53 Aligned_cols=33 Identities=18% Similarity=0.213 Sum_probs=30.7
Q ss_pred hcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
+|+|.|..+|++++.+|.|.|||++++++.|=|
T Consensus 116 ~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V 148 (181)
T PTZ00155 116 LGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLV 148 (181)
T ss_pred ccCcCCHHHhhhheeCCCEEECCEEeccCceEe
Confidence 499999999999999999999999999997744
No 13
>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=97.22 E-value=0.001 Score=38.27 Aligned_cols=42 Identities=12% Similarity=0.128 Sum_probs=34.7
Q ss_pred hhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 24 LPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 24 lPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
.-|--||... .++.+...+++++.+|.|.|||++++...|.+
T Consensus 9 ~rLd~~L~~~-~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l 50 (59)
T TIGR02988 9 ITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGELENRRGKKL 50 (59)
T ss_pred HHHHHHHHHc-CCccCHHHHHHHHHcCCEEECCEEccCCCCCC
Confidence 5566777777 77779999999999999999999997666543
No 14
>smart00363 S4 S4 RNA-binding domain.
Probab=97.16 E-value=0.0015 Score=34.83 Aligned_cols=42 Identities=29% Similarity=0.294 Sum_probs=32.7
Q ss_pred HHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccc
Q psy8661 26 LVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGF 68 (71)
Q Consensus 26 L~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~ 68 (71)
+..+|... +.+.+..++++++.+|.|.|||++.++..+.+--
T Consensus 3 l~~~l~~~-~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~ 44 (60)
T smart00363 3 LDKFLARL-GLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKP 44 (60)
T ss_pred HHHHHHHc-CcccCHHHHHHHHHcCCEEECCEEecCCCeEeCC
Confidence 44556543 3457899999999999999999999888777643
No 15
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=97.11 E-value=0.00062 Score=48.11 Aligned_cols=33 Identities=21% Similarity=0.294 Sum_probs=31.3
Q ss_pred hcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
+|+|.|..+|++.+.+|.|.|||++++++.|-|
T Consensus 112 ~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V 144 (177)
T PRK04051 112 KGLARTPKQARQFIVHGHIAVNGRRVTSPSYLV 144 (177)
T ss_pred ccCcCCHHHHHHHHHcCCEEECCEEeCCCCeEC
Confidence 699999999999999999999999999998866
No 16
>PLN00189 40S ribosomal protein S9; Provisional
Probab=97.02 E-value=0.00043 Score=49.76 Aligned_cols=34 Identities=15% Similarity=0.184 Sum_probs=31.4
Q ss_pred hhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
++|+|.|..+|++++.+|.|.|||++++++.|-|
T Consensus 117 r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V 150 (194)
T PLN00189 117 KSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMV 150 (194)
T ss_pred ecCCcCCHHHHHHheeCCCEeECCEEEecCcEEE
Confidence 4789999999999999999999999999998754
No 17
>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=96.01 E-value=0.011 Score=41.94 Aligned_cols=34 Identities=24% Similarity=0.263 Sum_probs=30.6
Q ss_pred hcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661 34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG 67 (71)
Q Consensus 34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG 67 (71)
++++.|..+|++.+.+|.|.|||+++++..|.+-
T Consensus 99 ~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~ 132 (200)
T TIGR01017 99 LGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVR 132 (200)
T ss_pred cCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCC
Confidence 4678899999999999999999999999888774
No 18
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=95.89 E-value=0.012 Score=42.15 Aligned_cols=33 Identities=21% Similarity=0.253 Sum_probs=30.2
Q ss_pred hcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
+++|.+..+|++++.+|.|.|||+++++..|.+
T Consensus 98 ~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~V 130 (201)
T CHL00113 98 LGMAPTIPAARQLVNHGHILVNGRIVDIPSYRC 130 (201)
T ss_pred cCCCCCHHHHHHHHHCCcEEECCEEecCccccC
Confidence 578889999999999999999999999888776
No 19
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=95.78 E-value=0.015 Score=41.24 Aligned_cols=34 Identities=24% Similarity=0.317 Sum_probs=30.6
Q ss_pred hcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661 34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG 67 (71)
Q Consensus 34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG 67 (71)
++++.+..+|++++.+|.|.|||++++...|++-
T Consensus 102 ~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~ 135 (203)
T PRK05327 102 LGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVK 135 (203)
T ss_pred cCccCCHHHHHHHHHCCcEEECCEEECCCCcCCC
Confidence 3778899999999999999999999998888774
No 20
>PRK11507 ribosome-associated protein; Provisional
Probab=95.49 E-value=0.019 Score=35.53 Aligned_cols=39 Identities=21% Similarity=0.276 Sum_probs=31.4
Q ss_pred cchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecC
Q psy8661 22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTD 61 (71)
Q Consensus 22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD 61 (71)
+-|-|.=||. ..+++.|+=|||..+.++.|+|||.+.+-
T Consensus 10 e~I~L~QlLK-~~~~v~SGG~AK~~I~eg~V~VNGeve~r 48 (70)
T PRK11507 10 PHVELCDLLK-LEGWSESGAQAKIAIAEGQVKVDGAVETR 48 (70)
T ss_pred CeEEHHHHHh-hhCcccChHHHHHHHHcCceEECCEEecc
Confidence 3455666665 35788999999999999999999998653
No 21
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=95.09 E-value=0.031 Score=40.31 Aligned_cols=37 Identities=11% Similarity=0.200 Sum_probs=31.3
Q ss_pred HHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 29 FLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 29 ~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
+|.+ .+++.|.++|+.++++|.|.|||+++++..+.+
T Consensus 5 ~L~~-~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V 41 (228)
T TIGR00478 5 LLVR-RGLFESREKAKRLILKGFVLVNGKKVDKPSALV 41 (228)
T ss_pred HHHH-cCCccHHHHHHHHHHCCcEEECCEEeCCCCCCC
Confidence 3443 467889999999999999999999999887766
No 22
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=94.30 E-value=0.0094 Score=36.20 Aligned_cols=40 Identities=23% Similarity=0.292 Sum_probs=27.2
Q ss_pred cchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCC
Q psy8661 22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDT 62 (71)
Q Consensus 22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~ 62 (71)
+.|.|.=||.- .+++.|+-|||..+.++.|+|||.+.+..
T Consensus 6 e~I~L~qlLK~-~glv~sGGeAK~~I~~g~V~VNGe~e~rr 45 (65)
T PF13275_consen 6 EYITLGQLLKL-AGLVSSGGEAKALIQEGEVKVNGEVETRR 45 (65)
T ss_dssp S---HHHHHHH-HTS-SSSSTTSHHHHHHHHEETTB----S
T ss_pred CcEEHHHHHhH-cCCcccHHHHHHHHHcCceEECCEEcccc
Confidence 45666666664 57889999999999999999999998765
No 23
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=94.23 E-value=0.092 Score=40.67 Aligned_cols=43 Identities=21% Similarity=0.362 Sum_probs=37.2
Q ss_pred chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
.++++-+|.+ .+.|.+..||++.+.||-|+|||..++|..+-+
T Consensus 342 ~~~~~~~l~~-~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~ 384 (408)
T PRK05912 342 GIDLLALLVE-AGLVPSKSEARRLIKQGGVKINGEKVSDENYVL 384 (408)
T ss_pred CCcHHHHHHH-hCCCCCHHHHHHHHHcCCEEECCEEecCccccc
Confidence 4677777764 699999999999999999999999999987543
No 24
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=94.23 E-value=0.052 Score=33.89 Aligned_cols=37 Identities=19% Similarity=0.242 Sum_probs=30.3
Q ss_pred chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEec
Q psy8661 23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60 (71)
Q Consensus 23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrt 60 (71)
-|-|.=||. .++.++|+-+||..+.++.|+|||++-|
T Consensus 11 ~I~L~qlLK-~~g~i~sGG~AK~~i~eg~V~vNGe~Et 47 (73)
T COG2501 11 FITLGQLLK-LAGLIESGGQAKAFIAEGEVKVNGEVET 47 (73)
T ss_pred eEEHHHHHH-HhCcccCcHHHHHHHHCCeEEECCeeee
Confidence 445555655 4689999999999999999999999854
No 25
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=93.56 E-value=0.13 Score=39.94 Aligned_cols=42 Identities=24% Similarity=0.328 Sum_probs=36.5
Q ss_pred chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCC
Q psy8661 23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYP 65 (71)
Q Consensus 23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~p 65 (71)
.++++-+|-. .|.|.+..||++.+.||-|.|||..++|..+-
T Consensus 342 ~~~~~~~l~~-~~~~~S~~earrli~~ggv~in~~~v~~~~~~ 383 (410)
T PRK13354 342 TKNLVDLLVD-LGLEPSKREARRLIQNGAIKINGEKVTDVDAI 383 (410)
T ss_pred CCCHHHHHHH-hCCCCCHHHHHHHHHcCCEEECCEEccCcccc
Confidence 4677777764 79999999999999999999999999998653
No 26
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=93.35 E-value=0.26 Score=35.63 Aligned_cols=45 Identities=24% Similarity=0.351 Sum_probs=34.7
Q ss_pred cchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661 22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG 67 (71)
Q Consensus 22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG 67 (71)
.+.-|.-||...+. ..+.+++++.+.+|.|.|||+++++..+.+-
T Consensus 4 ~g~rLd~~L~~~~~-~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~ 48 (299)
T TIGR00005 4 AGQRLDDFLASLLP-DLSRSRIQKLIENGQVKVNGKVTANPKLKVK 48 (299)
T ss_pred cchhHHHHHHHhcc-cCCHHHHHHHHHCCcEEECCEeccCcccCCC
Confidence 34667778877664 3568899999999999999987777666663
No 27
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=93.03 E-value=0.11 Score=38.40 Aligned_cols=29 Identities=24% Similarity=0.298 Sum_probs=24.7
Q ss_pred hcccccHHHHHHHHHcCceEeCCeEecCCc
Q psy8661 34 LKYALTNQEVLKILMQRLIKVDGKVRTDTN 63 (71)
Q Consensus 34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~ 63 (71)
+++| +.+||+++|.+|.|.|||++.++..
T Consensus 12 ~G~~-SRr~ae~lI~~G~V~VnG~v~~~~~ 40 (248)
T COG1187 12 AGVG-SRREAEKLIEEGRVTVNGKVATLGG 40 (248)
T ss_pred cCCC-CHHHHHHHHHcCCEEECCEEeccCC
Confidence 3555 5789999999999999999998864
No 28
>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=91.42 E-value=0.42 Score=35.07 Aligned_cols=43 Identities=12% Similarity=0.160 Sum_probs=34.7
Q ss_pred chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661 23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG 67 (71)
Q Consensus 23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG 67 (71)
|+=|-.++...+ ..+.+.|++.+.+|.|+|||+++++..+.+-
T Consensus 183 s~RLD~lls~~~--~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~ 225 (257)
T TIGR03069 183 SLRIDAIASAGF--GLSRSKIVDQIKAGRLRLNWKTVTQPSRELK 225 (257)
T ss_pred cccHHHHHHhhh--hhhHHHHHHHHHCCeEEECCEEcCCCCCcCC
Confidence 445666777654 4588999999999999999999998887664
No 29
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=90.84 E-value=0.55 Score=32.96 Aligned_cols=39 Identities=18% Similarity=0.312 Sum_probs=29.3
Q ss_pred HHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 26 LVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 26 L~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
|.-||...+ ..+.+.+++++.+|.|.|||++.++..+.+
T Consensus 3 ld~~L~~~~--~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l 41 (232)
T PRK10839 3 LDKFISQQL--GVSRAIAGRELRANRVTVDGEIVKNGAFKL 41 (232)
T ss_pred HHHHHHHcC--CCCHHHHHHHHHcCeEEECCEEeccCCcCc
Confidence 345666555 357899999999999999999987554433
No 30
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=90.45 E-value=0.64 Score=34.43 Aligned_cols=43 Identities=14% Similarity=0.178 Sum_probs=33.5
Q ss_pred chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
...|.-+|+..+. ..+.+++++++.+|.|.|||+.++...+.+
T Consensus 17 g~RLd~~L~~~~~-~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v 59 (325)
T PRK11180 17 GQRLDQALAELFP-DYSRSRIKEWILDQRVLVNGKVINKPKEKV 59 (325)
T ss_pred CccHHHHHHhhcc-ccCHHHHHHHHHCCCEEECCEEccCCCcCc
Confidence 4677788887654 357889999999999999999886554443
No 31
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=89.43 E-value=0.7 Score=34.31 Aligned_cols=43 Identities=21% Similarity=0.301 Sum_probs=35.3
Q ss_pred chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccc
Q psy8661 23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGF 68 (71)
Q Consensus 23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~ 68 (71)
..-+--||++ |.- .+..+..+++.+|.|.|||++++ ..|.+.-
T Consensus 12 g~rld~~L~~-l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~ 54 (289)
T COG0564 12 GQRLDKFLAK-LLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKP 54 (289)
T ss_pred CCCHHHHHHH-ccC-cCHHHHHHHHHCCCEEECCEEcc-CCeeeCC
Confidence 4567788888 665 67889999999999999999998 7776643
No 32
>KOG4655|consensus
Probab=88.70 E-value=0.36 Score=34.69 Aligned_cols=34 Identities=29% Similarity=0.419 Sum_probs=31.1
Q ss_pred hhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
.|+.|.+-+||-+.+.||.|.|.-+++||+.|=|
T Consensus 115 ~l~m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lv 148 (181)
T KOG4655|consen 115 RLRMAESVKEAVRFVEQGHVRVGPKVVTDPAFLV 148 (181)
T ss_pred echhhhhHHHHHHHHHcCceeeCCeeccCchHHh
Confidence 4789999999999999999999999999997743
No 33
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=88.41 E-value=0.57 Score=34.98 Aligned_cols=31 Identities=10% Similarity=0.138 Sum_probs=27.8
Q ss_pred cccccHHHHHHHHHcCceEeCCeEecCCcCC
Q psy8661 35 KYALTNQEVLKILMQRLIKVDGKVRTDTNYP 65 (71)
Q Consensus 35 kyA~t~~EakkIl~~~~V~VdGkvrtD~~~p 65 (71)
|++.|..+|+..++.|+|+|||...+-+.+=
T Consensus 13 gl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~ 43 (245)
T COG1189 13 GLFESREKAKELILAGNVLVNGEKVTKPSQL 43 (245)
T ss_pred cchhhHHHHHHHHHcCeEEECCEEecCccee
Confidence 7899999999999999999999998876543
No 34
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=87.77 E-value=1.2 Score=33.20 Aligned_cols=42 Identities=14% Similarity=0.150 Sum_probs=31.3
Q ss_pred cchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
+++-|.-||.+. ++ .+.+||++.+.+|.|+|||++. +..+.+
T Consensus 5 ~~~RL~k~La~~-g~-~SRr~a~~lI~~G~V~VNGk~v-~~~~~V 46 (290)
T PRK10475 5 SSTRLNKYISES-GI-CSRREADRYIEQGNVFINGKRA-TIGDQV 46 (290)
T ss_pred hHHHHHHHHHhC-CC-CCHHHHHHHHHCCcEEECCEEc-cCCCCc
Confidence 356677777653 43 4689999999999999999987 344444
No 35
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=87.08 E-value=2 Score=29.28 Aligned_cols=42 Identities=10% Similarity=0.125 Sum_probs=34.5
Q ss_pred chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
++-|-.||.. .+++.|..-|+..|..|.|.|||.+ .-....|
T Consensus 8 ~~RlDk~L~~-~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V 49 (133)
T PRK10348 8 EVRLDKWLWA-ARFYKTRALAREMIEGGKVHYNGQR-SKPSKIV 49 (133)
T ss_pred cccHHHHHHH-cCccccHHHHHHHHHCCCEEECCEE-CCCCCcc
Confidence 4677777775 5899999999999999999999998 5555544
No 36
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=86.98 E-value=0.78 Score=33.95 Aligned_cols=36 Identities=19% Similarity=0.193 Sum_probs=26.3
Q ss_pred HHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 28 IFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 28 i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
=||.+ +++ .+.++|++++.+|.|+|||++. +..+-|
T Consensus 7 k~La~-~g~-~SRr~a~~lI~~G~V~VNG~~~-~~g~~V 42 (289)
T PRK10700 7 KVLAR-AGH-GSRREIESIIEAGRVSVDGKIA-TLGDRV 42 (289)
T ss_pred HHHHH-CCC-CCHHHHHHHHHcCCEEECCEec-cCCCEe
Confidence 34443 343 5789999999999999999986 444433
No 37
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=85.17 E-value=2.4 Score=31.32 Aligned_cols=42 Identities=24% Similarity=0.377 Sum_probs=32.6
Q ss_pred chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
...|.-||.+.+. ..+.+.+++++.+|.|.|||++++ ..+.+
T Consensus 19 g~RLd~~L~~~~~-~~sr~~i~~li~~G~V~VNg~~v~-~~~~v 60 (317)
T PRK11025 19 GQRIDNFLRTQLK-GVPKSMIYRILRKGEVRVNKKRIK-PEYKL 60 (317)
T ss_pred CchHHHHHHHhcc-cCCHHHHHHHHHcCCEEECCEEcC-ccccc
Confidence 4567788887663 356889999999999999999874 45554
No 38
>PF03417 AAT: Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase This family belongs to family C45 of the peptidase classification.; InterPro: IPR005079 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C45 (clan PB(C)). The active site residue for members of this family and family T1 is C-terminal to the autolytic cleavage site. They represent a family of enzymes which catalyse the final step in penicillin biosynthesis []. ; GO: 0042318 penicillin biosynthetic process; PDB: 3GVZ_A 2X1D_D 2X1E_B 2X1C_A.
Probab=83.86 E-value=1.3 Score=30.42 Aligned_cols=29 Identities=28% Similarity=0.394 Sum_probs=25.0
Q ss_pred ccchhHHHHHHhhhcccccHHHHHHHHHcC
Q psy8661 21 RESLPLVIFLRNRLKYALTNQEVLKILMQR 50 (71)
Q Consensus 21 ~~slPL~i~LRd~LkyA~t~~EakkIl~~~ 50 (71)
...+|..+++|..|. |.|..||..+|.+-
T Consensus 69 ~~G~p~~~l~R~iLe-~~t~~eA~~~l~~~ 97 (225)
T PF03417_consen 69 QPGLPRHFLVRKILE-CRTVEEAIAILRSA 97 (225)
T ss_dssp TTSB-HHHHHHHHHC--SSHHHHHHCHHCC
T ss_pred cCCChHHHHHHHHhc-CCCHHHHHHHHHhc
Confidence 669999999999999 99999999999875
No 39
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=81.41 E-value=1.5 Score=34.43 Aligned_cols=33 Identities=24% Similarity=0.352 Sum_probs=30.8
Q ss_pred hcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
.+++.+.+||++.+.++.|++||..+.|.+++.
T Consensus 345 ~~L~psr~earr~i~~g~v~in~~~v~d~~~~~ 377 (401)
T COG0162 345 AGLAPSRSEARRLIQQGGVKINGEKVEDENYVL 377 (401)
T ss_pred hCCcccHHHHHhhcccCCEEECCEeccccccch
Confidence 578999999999999999999999999998776
No 40
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=75.07 E-value=4.5 Score=30.04 Aligned_cols=43 Identities=12% Similarity=0.171 Sum_probs=32.9
Q ss_pred chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661 23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG 67 (71)
Q Consensus 23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG 67 (71)
|+=|--++-..+ -.+...|+..+.+|.|+|||++.++..|-+-
T Consensus 191 s~RLD~vla~~~--~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~ 233 (267)
T PLN00051 191 SLRLDALASAGF--RMSRSKLVDLISSGDVRVNWREVTKNGTTLK 233 (267)
T ss_pred cccHHHHHHHHh--ccCHHHHHHHHHcCcEEECCEEcCCCCCCCC
Confidence 344555556555 3567789999999999999999998887664
No 41
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=74.17 E-value=3.7 Score=26.96 Aligned_cols=27 Identities=11% Similarity=0.218 Sum_probs=23.0
Q ss_pred cccccHHHHHHHHHcCceEeCCeEecC
Q psy8661 35 KYALTNQEVLKILMQRLIKVDGKVRTD 61 (71)
Q Consensus 35 kyA~t~~EakkIl~~~~V~VdGkvrtD 61 (71)
.+..+...|+..|..|.|.|||...+-
T Consensus 19 R~~KrRslAk~~~~~GrV~vNG~~aKp 45 (100)
T COG1188 19 RFIKRRSLAKEMIEGGRVKVNGQRAKP 45 (100)
T ss_pred HHhhhHHHHHHHHHCCeEEECCEEccc
Confidence 345788899999999999999998753
No 42
>PF08828 DSX_dimer: Doublesex dimerisation domain; InterPro: IPR014932 Doublesex (DSX) is a transcription factor that regulates somatic sexual differences in Drosophila. The structure has revealed a novel dimeric arrangement of ubiquitin-associated folds that has not previously been identified in a transcription factor []. ; PDB: 1ZV1_B 2JZ0_A 2JZ1_B.
Probab=73.24 E-value=4 Score=24.89 Aligned_cols=35 Identities=26% Similarity=0.271 Sum_probs=21.7
Q ss_pred CccchhHHHHHHhhhcccc-cHHHHHHHHHcCceEeCCe
Q psy8661 20 LRESLPLVIFLRNRLKYAL-TNQEVLKILMQRLIKVDGK 57 (71)
Q Consensus 20 ~~~slPL~i~LRd~LkyA~-t~~EakkIl~~~~V~VdGk 57 (71)
.+|.+||..++ ||||. +.+||-+-+.+++-.|+--
T Consensus 20 pWEmmpLmyVI---LK~A~~D~eeA~rrI~E~~~~v~~~ 55 (62)
T PF08828_consen 20 PWEMMPLMYVI---LKYADADVEEASRRIDEAKNVVNEY 55 (62)
T ss_dssp -GGGHHHHHHH---HHHTTT-HHHHHHHHHH--------
T ss_pred CHHHHHHHHHH---HHhcCCCHHHHHHHHHHHHHHHHHH
Confidence 35889998884 78999 8999999998887766643
No 43
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=72.93 E-value=5.4 Score=30.10 Aligned_cols=47 Identities=17% Similarity=0.184 Sum_probs=38.3
Q ss_pred cchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661 22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV 70 (71)
Q Consensus 22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md 70 (71)
.|+=|-.++-+.++... .-|...+..|+|+||.+++++..|-+..=|
T Consensus 179 sSlRLD~vis~~~~~SR--~~a~~lIe~g~VkVN~k~v~~~s~~v~~GD 225 (257)
T COG2302 179 SSLRLDVVISEGFGLSR--AKAQQLIEKGKVKVNWKVVDKASYEVQEGD 225 (257)
T ss_pred ehhhHHHHHHHHHhhhH--HHHHHHHHcCceEEeeEEeccccceeccCC
Confidence 37778888888887655 457899999999999999999888776544
No 44
>TIGR00234 tyrS tyrosyl-tRNA synthetase. This tyrosyl-tRNA synthetase model starts picking up tryptophanyl-tRNA synthetases at scores of 0 and below. The proteins found by this model have a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples.
Probab=72.20 E-value=4.8 Score=30.98 Aligned_cols=43 Identities=16% Similarity=0.075 Sum_probs=34.7
Q ss_pred chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
++++.=++.. .+.+.+.+||++.++++-|+|||...+|..+-.
T Consensus 329 ~~~~~~~~~~-~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~v~ 371 (377)
T TIGR00234 329 DITLADLLVL-SGLFPSKSEARRDIKQGGVYINGEKVTDLEPIR 371 (377)
T ss_pred CcCHHHHHHH-cCCCcChHHHHHHHHhCCEEECCEeccCchhhh
Confidence 3565555553 588899999999999999999999999986544
No 45
>cd01935 Ntn_CGH_like Choloylglycine hydrolase (CGH)_like. This family of choloylglycine hydrolase-like proteins includes conjugated bile acid hydrolase (CBAH), penicillin V acylase (PVA), acid ceramidase (AC), and N-acylethanolamine-hydrolyzing acid amidase (NAAA) which cleave non-peptide carbon-nitrogen bonds in bile salt constituents. These enzymes have an N-terminal nucleophilic cysteine, as do other members of the Ntn hydrolase family to which they belong. This nucleophilic cysteine is exposed by post-translational prossessing of the precursor protein.
Probab=58.65 E-value=12 Score=25.52 Aligned_cols=32 Identities=25% Similarity=0.288 Sum_probs=28.6
Q ss_pred ccchhHHHHHHhhhcccccHHHHHHHHHcCce
Q psy8661 21 RESLPLVIFLRNRLKYALTNQEVLKILMQRLI 52 (71)
Q Consensus 21 ~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V 52 (71)
...+|...++|-.|..+.|-+||+.++.+-.+
T Consensus 94 ~~~~~~~~~~r~vL~~~~tv~ea~~~l~~~~~ 125 (229)
T cd01935 94 KDGLPAFELIRWVLENCDSVEEVKEALKKIPI 125 (229)
T ss_pred CCccCHHHHHHHHHHHcCCHHHHHHHHHhCcc
Confidence 36899999999999999999999999987655
No 46
>TIGR03198 pucE xanthine dehydrogenase E subunit. This gene has been characterized in B. subtilis as the Iron-sulfur cluster binding-subunit of xanthine dehydrogenase (pucE), acting in conjunction with pucC, the FAD-binding subunit and pucD, the molybdopterin binding subunit. The more common XDH complex (GenProp0640) includes the xdhA gene as the Fe-S cluster binding component.
Probab=58.42 E-value=3.5 Score=28.45 Aligned_cols=41 Identities=22% Similarity=0.132 Sum_probs=30.3
Q ss_pred cchhHHHHHHhhhcccccHHHHHHHHHcC-----ceEeCCeEecCCcCCc
Q psy8661 22 ESLPLVIFLRNRLKYALTNQEVLKILMQR-----LIKVDGKVRTDTNYPA 66 (71)
Q Consensus 22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~-----~V~VdGkvrtD~~~pv 66 (71)
...+|+-+||+.|++-.+. .=|.+| .|.|||+.+..--.|+
T Consensus 19 ~~~~Ll~~LR~~~~ltgtK----~gC~~G~CGACtVlvdG~~v~SCl~~~ 64 (151)
T TIGR03198 19 PTTRLSDLLRKELQLTGTK----VSCGIGRCGACSVLIDGKLANACLTMA 64 (151)
T ss_pred CCcHHHHHHHhccCCCCCC----CCCCCCcCCccEEEECCcEEechHHHH
Confidence 4789999999998886654 336666 6999999876554444
No 47
>cd01903 Ntn_AC_NAAA AC_NAAA This conserved domain includes two closely related proteins, acid ceramidase (AC, also known as N-acylsphingosine amidohydrolase), and N-acylethanolamine-hydrolyzing acid amidase (NAAA). AC catalyzes the hydrolysis of ceramide to sphingosine and fatty acid. Ceramide is required for the biosynthesis of most sphingolipids and plays an important role in many signal transduction pathways by inducing apoptosis and/or arresting cell growth. An inherited deficiency of AC activity leads to the lysosomal storage disorder known as Farber disease. AC is considered a "rheostat" important for maintaining the proper intracellular levels of these lipids since hydrolysis of ceramide is the only source of sphingosine in cells. NAAA is a eukaryotic glycoprotein that hydrolyzes bioactive N-acylethanolamines, including anandamide (an endocannabinoid) and N-palmitoylethanolamine (an anti-inflammatory and neuroprotective substance), to fatty acids and ethanolamine at acidic pH
Probab=54.53 E-value=13 Score=26.48 Aligned_cols=30 Identities=17% Similarity=0.370 Sum_probs=26.6
Q ss_pred cchhHHHHHHhhhcccccHHHHHHHHHcCc
Q psy8661 22 ESLPLVIFLRNRLKYALTNQEVLKILMQRL 51 (71)
Q Consensus 22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~ 51 (71)
..+|..+++|..|.-+.|.+||+..|.+-.
T Consensus 97 ~g~p~~~liR~vLe~~~s~~eA~~~L~~~~ 126 (231)
T cd01903 97 DGIPVSWLIRETLENATSYEDAVEKLSTTP 126 (231)
T ss_pred CCCchhhhHHHHHhccCCHHHHHHHhccCc
Confidence 588999999999998899999999997653
No 48
>cd00542 Ntn_PVA Penicillin V acylase (PVA), also known as conjugated bile salt acid hydrolase (CBAH), catalyzes the hydrolysis of penicillin V to yield 6-amino penicillanic acid (6-APA), an important key intermediate of semisynthetic penicillins. PVA has an N-terminal nucleophilic cysteine, as do other members of the Ntn hydrolase family to which PVA belongs. This nucleophilic cysteine is exposed by post-translational prossessing of the PVA precursor. PVA forms a homotetramer.
Probab=51.09 E-value=41 Score=24.85 Aligned_cols=31 Identities=16% Similarity=0.091 Sum_probs=26.4
Q ss_pred cchhHHHHHHhhhcccccHHHHHHHHHcCce
Q psy8661 22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLI 52 (71)
Q Consensus 22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V 52 (71)
..|...-|+|-.|.-..|-+||++.|.+-.|
T Consensus 97 ~~l~~~~~i~~iL~n~~TV~Ev~~~l~~i~i 127 (303)
T cd00542 97 TNIAPFEFITWVLGNFASVEEVKEALKNINV 127 (303)
T ss_pred CccCHHHHHHHHHHcCCCHHHHHHHhcCceE
Confidence 4677778889999999999999999987544
No 49
>KOG3301|consensus
Probab=49.98 E-value=17 Score=26.26 Aligned_cols=31 Identities=19% Similarity=0.230 Sum_probs=27.3
Q ss_pred hhcccccHHHHHHHHHcCceEeCCeEecCCc
Q psy8661 33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTN 63 (71)
Q Consensus 33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~ 63 (71)
.||.|.+-.-|+..+.|+.|.|++.++-=+.
T Consensus 105 klGlAkSIhhARvLi~~rhI~V~~qiV~IPs 135 (183)
T KOG3301|consen 105 KLGLAKSIHHARVLIRQRHIRVGKQIVNIPS 135 (183)
T ss_pred HHhhhhhhHHHHHHhcCccEEecCeEeeccc
Confidence 3799999999999999999999999875543
No 50
>KOG2404|consensus
Probab=49.01 E-value=17 Score=29.32 Aligned_cols=51 Identities=35% Similarity=0.494 Sum_probs=43.0
Q ss_pred ccccccccccCCCCCCCCCccchhHHHHHHhhhc-ccccHHHHHHHHHcCce
Q psy8661 2 LDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLK-YALTNQEVLKILMQRLI 52 (71)
Q Consensus 2 l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~Lk-yA~t~~EakkIl~~~~V 52 (71)
|+.++|-=+|++.-+.|+.--..|+.-.|+++|+ .|.+.-|+-+|+.|-.|
T Consensus 117 la~lgGHSvpRTHr~s~plppgfei~~~L~~~l~k~as~~pe~~ki~~nskv 168 (477)
T KOG2404|consen 117 LAQLGGHSVPRTHRSSGPLPPGFEIVKALSTRLKKKASENPELVKILLNSKV 168 (477)
T ss_pred HHHhcCCCCCcccccCCCCCCchHHHHHHHHHHHHhhhcChHHHhhhhccee
Confidence 4556777889999999999999999999999994 77778888899887754
No 51
>KOG2623|consensus
Probab=48.43 E-value=26 Score=28.49 Aligned_cols=38 Identities=13% Similarity=0.216 Sum_probs=31.7
Q ss_pred chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecC
Q psy8661 23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTD 61 (71)
Q Consensus 23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD 61 (71)
.++++=.+|+ ++.-.+..||++++.||-|.||++..+|
T Consensus 398 ~~s~~~l~~k-a~~~~s~~~a~r~i~qG~vslnh~~v~~ 435 (467)
T KOG2623|consen 398 GVSILDLLRK-ASRFPSGKEARRMIQQGGVSLNHEKVRD 435 (467)
T ss_pred CCcHHHHHHH-hhcCCCcHHHHHHHHccceeecCccccC
Confidence 5677777776 4555677899999999999999999998
No 52
>TIGR03193 4hydroxCoAred 4-hydroxybenzoyl-CoA reductase, gamma subunit. 4-hydroxybenzoyl-CoA reductase converts 4-hydroxybenzoyl-CoA to benzoyl-CoA, a common intermediate in the degradation of aromatic compounds. This protein family represents the gamma chain of this three-subunit enzyme.
Probab=46.93 E-value=12 Score=25.83 Aligned_cols=44 Identities=23% Similarity=0.194 Sum_probs=32.7
Q ss_pred cchhHHHHHHhhhcccccHHHHHHHHHcC-----ceEeCCeEecCCcCCcccc
Q psy8661 22 ESLPLVIFLRNRLKYALTNQEVLKILMQR-----LIKVDGKVRTDTNYPAGFM 69 (71)
Q Consensus 22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~-----~V~VdGkvrtD~~~pvG~m 69 (71)
...+|+=+||+.|++-.+ |.=|.+| .|+|||+++..--+|+.-+
T Consensus 17 ~~~~Ll~~LR~~lgltg~----K~gC~~G~CGACtVlvdg~~v~SCl~~~~~~ 65 (148)
T TIGR03193 17 DNMLLVDYLRDTVGLTGT----KQGCDGGECGACTVLVDGRPRLACSTLAHRV 65 (148)
T ss_pred CCCcHHHHHHHhcCCCCC----CCCCCCCCCCCCEEEECCeEeeccHhhHhhc
Confidence 467899999999876443 4566666 5999999998777766433
No 53
>COG2080 CoxS Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]
Probab=40.20 E-value=18 Score=25.33 Aligned_cols=42 Identities=26% Similarity=0.196 Sum_probs=30.6
Q ss_pred ccchhHHHHHHhhhcccccHHHHHHHHHcC-----ceEeCCeEecCCcCCc
Q psy8661 21 RESLPLVIFLRNRLKYALTNQEVLKILMQR-----LIKVDGKVRTDTNYPA 66 (71)
Q Consensus 21 ~~slPL~i~LRd~LkyA~t~~EakkIl~~~-----~V~VdGkvrtD~~~pv 66 (71)
....||+=+|||.|++.-+. +=|-++ -|.|||+.+..--.|+
T Consensus 18 ~p~~~Ll~~LRd~l~ltgtk----~GC~~g~CGACtVlvDG~~v~SCl~~a 64 (156)
T COG2080 18 DPRTPLLDVLRDELGLTGTK----KGCGHGQCGACTVLVDGEAVNSCLTLA 64 (156)
T ss_pred CCCChHHHHHHHhcCCCCcC----CCCCCccCCceEEEECCeEehHHHHHH
Confidence 34579999999999988764 334444 7999999887654443
No 54
>cd00131 PAX Paired Box domain
Probab=38.36 E-value=77 Score=20.66 Aligned_cols=54 Identities=15% Similarity=0.094 Sum_probs=30.4
Q ss_pred ccccccCCCCCCCCCccchhHHHHHHh--hhcccccHHHHHHHHHcCceEeCCeEe
Q psy8661 6 GGVFAPRPSTGPHKLRESLPLVIFLRN--RLKYALTNQEVLKILMQRLIKVDGKVR 59 (71)
Q Consensus 6 ~~~~a~~pspGPH~~~~slPL~i~LRd--~LkyA~t~~EakkIl~~~~V~VdGkvr 59 (71)
+|..+|+|.+|+++....-+..-++.. .-.=..|.+|....|.+..|.|+|...
T Consensus 60 ~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~ 115 (128)
T cd00131 60 TGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVP 115 (128)
T ss_pred cCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCC
Confidence 566789998887443212222111111 112235788888887777777766543
No 55
>COG0103 RpsI Ribosomal protein S9 [Translation, ribosomal structure and biogenesis]
Probab=37.75 E-value=12 Score=25.65 Aligned_cols=16 Identities=25% Similarity=0.420 Sum_probs=14.5
Q ss_pred cCceEeCCeEecCCcCC
Q psy8661 49 QRLIKVDGKVRTDTNYP 65 (71)
Q Consensus 49 ~~~V~VdGkvrtD~~~p 65 (71)
+|.|.|||++..++ ||
T Consensus 25 ~G~i~vNg~~~e~y-f~ 40 (130)
T COG0103 25 KGKITVNGRPLELY-FP 40 (130)
T ss_pred CcEEEECCcCHHHh-cc
Confidence 68999999999998 87
No 56
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=35.54 E-value=49 Score=18.17 Aligned_cols=31 Identities=23% Similarity=0.209 Sum_probs=22.5
Q ss_pred ccHHHHHHHHHcCceEeCCeEecCCcCCccc
Q psy8661 38 LTNQEVLKILMQRLIKVDGKVRTDTNYPAGF 68 (71)
Q Consensus 38 ~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~ 68 (71)
.+.+||+.+|.+..+.++=.-+.+..++.|.
T Consensus 9 ~~~~~a~~~l~~~g~~~~~~~~~~~~~~~g~ 39 (63)
T PF03793_consen 9 MTYDEAKSILEAAGLTVNVVEEYSDSVPKGT 39 (63)
T ss_dssp SBHHHHHHHHHHTT-EEEEEEEEESSSSTTS
T ss_pred CcHHHHHHHHHHCCCEEEEEEEecCCCCCCE
Confidence 5789999999998886665555666666663
No 57
>PF08528 Whi5: Whi5 like; InterPro: IPR013734 This is a short conserved sequence found in the Nrm1/Whi5 transcription factors. Nrm1 is a negative regulatory component of the MBF complex involved in cell-cycle-dependent transcription []. Whi5 is a transcriptional repressor that negatively regulates G1-specific, SBF- and MBF-dependent transcription [, ].
Probab=34.10 E-value=17 Score=18.29 Aligned_cols=9 Identities=56% Similarity=0.910 Sum_probs=7.4
Q ss_pred HHhhhcccc
Q psy8661 30 LRNRLKYAL 38 (71)
Q Consensus 30 LRd~LkyA~ 38 (71)
||.||.||.
T Consensus 2 Lr~RL~lA~ 10 (25)
T PF08528_consen 2 LRTRLQLAM 10 (25)
T ss_pred HHHHHhHhH
Confidence 688899985
No 58
>PF12476 DUF3696: Protein of unknown function (DUF3696); InterPro: IPR022532 This domain is found in bacteria and archaea, and is approximately 50 amino acids in length.
Probab=32.97 E-value=18 Score=20.18 Aligned_cols=13 Identities=46% Similarity=1.155 Sum_probs=10.1
Q ss_pred CCeEecCCcCCccccc
Q psy8661 55 DGKVRTDTNYPAGFMV 70 (71)
Q Consensus 55 dGkvrtD~~~pvG~md 70 (71)
+|.. ..+|-||||
T Consensus 30 ~G~l---~~WP~GFFD 42 (52)
T PF12476_consen 30 DGRL---SNWPEGFFD 42 (52)
T ss_pred CCCC---ccCCCchhh
Confidence 4555 579999998
No 59
>PHA02754 hypothetical protein; Provisional
Probab=32.10 E-value=58 Score=19.96 Aligned_cols=32 Identities=25% Similarity=0.306 Sum_probs=23.9
Q ss_pred cchhHHHHHHhhhcccccHHHHHHHHHcCceEeCC
Q psy8661 22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDG 56 (71)
Q Consensus 22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdG 56 (71)
+-+|-++.=.|+ ..-+||.|-||.+.-|+||-
T Consensus 5 eEi~k~i~eK~F---ke~MRelkD~LSe~GiYi~R 36 (67)
T PHA02754 5 EEIPKAIMEKDF---KEAMRELKDILSEAGIYIDR 36 (67)
T ss_pred HHHHHHHHHhHH---HHHHHHHHHHHhhCceEEEE
Confidence 456766665543 45579999999999999874
No 60
>PF00473 CRF: Corticotropin-releasing factor family; InterPro: IPR000187 Corticotropin-releasing factor (CRF), urotensin-I, urocortin and sauvagine form a family of related neuropeptides in vertebrates. The family can be grouped into 2 separate paralogous lineages, with urotensin-I, urocortin and sauvagine in one group and CRF forming the other group. Urocortin and sauvagine appear to represent orthologues of fish urotensin-I in mammals and amphibians, respectively. The peptides have a variety of physiological effects on stress and anxiety, vasoregulation, thermoregulation, growth and metabolism, metamorphosis and reproduction in various species, and are all released as preprohormones []. CRF [] is a hormone found mainly in the paraventricular nucleus of the mammalian hypothalamus that regulates the release of corticotropin (ACTH) from the pituitary gland. From here, CRF is transported to the anterior pituitary, stimulating adrenocorticotropic hormone (ACTH) release via CRF type 1 receptors, thereby activating the hypothalamo-pituitary-adrenocortical axis (HPA) and thus glucocorticoid release. CRF is evolutionary related to a number of other active peptides. Urocortin acts in vitro to stimulate the secretion of adrenocorticotropic hormone. Urotensin is found in the teleost caudal neurosecretory system and may play a role in osmoregulation and as a corticotropin-releasing factor. Urotensin-I is released from the urophysis of fish, and produces ACTH and subsequent cortisol release in vivo. The nonhormonal portion of the prohormone is thought to be the urotensin binding protein (urophysin). Sauvagine (P01144 from SWISSPROT), isolated from frog skin, has a potent hypotensive and diuretic effect.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 3EHU_C 3EHT_B 2RMF_A 3N96_G.
Probab=31.04 E-value=15 Score=20.30 Aligned_cols=23 Identities=22% Similarity=0.336 Sum_probs=17.6
Q ss_pred HHHhhhcccccHHHHHHHHHcCc
Q psy8661 29 FLRNRLKYALTNQEVLKILMQRL 51 (71)
Q Consensus 29 ~LRd~LkyA~t~~EakkIl~~~~ 51 (71)
+||++|..|...+.+++.-.++.
T Consensus 12 vLR~~l~~~~a~~~~~q~~~NR~ 34 (39)
T PF00473_consen 12 VLRQRLELERAERQMKQAQANRK 34 (39)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 56999999998888777665543
No 61
>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]
Probab=30.65 E-value=54 Score=26.63 Aligned_cols=29 Identities=28% Similarity=0.331 Sum_probs=24.6
Q ss_pred cccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661 35 KYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 35 kyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv 66 (71)
+=|.|++||-.++.+-.+ --|.||++.|+
T Consensus 32 gtA~NG~eAleli~e~~p---DiviTDI~MP~ 60 (475)
T COG4753 32 GTAANGKEALELIQETQP---DIVITDINMPG 60 (475)
T ss_pred EecccHHHHHHHHHhcCC---CEEEEecCCCC
Confidence 459999999999999874 35889999995
No 62
>PF06953 ArsD: Arsenical resistance operon trans-acting repressor ArsD; InterPro: IPR010712 This family consists of several bacterial arsenical resistance operon trans-acting repressor ArsD proteins. ArsD is a trans-acting repressor of the arsRDABC operon that confers resistance to arsenicals and antimonials in Escherichia coli. It possesses two-pairs of vicinal cysteine residues, Cys(12)-Cys(13) and Cys(112)-Cys(113), that potentially form separate binding sites for the metalloids that trigger dissociation of ArsD from the operon. However, as a homodimer it has four vicinal cysteine pairs [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent, 0046685 response to arsenic-containing substance; PDB: 3MWH_A 3KGK_A 3KTB_B.
Probab=28.66 E-value=62 Score=21.55 Aligned_cols=26 Identities=31% Similarity=0.567 Sum_probs=18.2
Q ss_pred HHHHHHHH-cC-----ceEeCCeEecCCcCCc
Q psy8661 41 QEVLKILM-QR-----LIKVDGKVRTDTNYPA 66 (71)
Q Consensus 41 ~EakkIl~-~~-----~V~VdGkvrtD~~~pv 66 (71)
.+++.+|. +| -++|||++++--+||.
T Consensus 59 ~~V~~~L~~~G~e~LPitlVdGeiv~~G~YPt 90 (123)
T PF06953_consen 59 PEVNQLLQTEGAEALPITLVDGEIVKTGRYPT 90 (123)
T ss_dssp HHHHHHHHHH-GGG-SEEEETTEEEEESS---
T ss_pred HHHHHHHHHcCcccCCEEEECCEEEEecCCCC
Confidence 46777777 45 6899999999999984
No 63
>TIGR02309 HpaB-1 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component. This gene for this monooxygenase is found within apparent operons for the degradation of 4-hydroxyphenylacetic acid in Deinococcus, Thermus and Oceanobacillus. Phylogenetic trees support inclusion of the Bacillus halodurans sequence above trusted although the complete 4-hydroxyphenylacetic acid degradation pathway may not exist in that organism. Generally, this enzyme acts with the assistance of a small flavin reductase domain protein (HpaC) to provide the cycle the flavin reductant for the reaction. This family of sequences is a member of a larger subfamily of monooxygenases (pfam03241).
Probab=28.51 E-value=72 Score=25.35 Aligned_cols=27 Identities=26% Similarity=0.283 Sum_probs=21.8
Q ss_pred cccHHHHHHHHHc-C-ceEeCCeEecCCc
Q psy8661 37 ALTNQEVLKILMQ-R-LIKVDGKVRTDTN 63 (71)
Q Consensus 37 A~t~~EakkIl~~-~-~V~VdGkvrtD~~ 63 (71)
|.|+.|=..-|++ + .|.|+|+.++|.+
T Consensus 1 ~~tg~eYlesL~~~~~~Vy~~Ge~V~dvt 29 (477)
T TIGR02309 1 ARTGQEYIDALKTRPPNLYIKGERVEDPT 29 (477)
T ss_pred CCCHHHHHHHHhcCCCeEEECCEEccCcC
Confidence 5688887778888 3 6999999998863
No 64
>PRK11433 aldehyde oxidoreductase 2Fe-2S subunit; Provisional
Probab=24.49 E-value=51 Score=24.17 Aligned_cols=42 Identities=21% Similarity=0.097 Sum_probs=29.6
Q ss_pred ccchhHHHHHHhhhcccccHHHHHHHHHcC-----ceEeCCeEecCCcCCc
Q psy8661 21 RESLPLVIFLRNRLKYALTNQEVLKILMQR-----LIKVDGKVRTDTNYPA 66 (71)
Q Consensus 21 ~~slPL~i~LRd~LkyA~t~~EakkIl~~~-----~V~VdGkvrtD~~~pv 66 (71)
+...+|+-+||+.|++--+. +=|.+| .|.|||+++..--.++
T Consensus 66 ~~~~tLLd~LR~~l~ltGtK----~GC~~G~CGACTVlVdG~~v~SCl~la 112 (217)
T PRK11433 66 DTRTTLLDALREHLHLTGTK----KGCDHGQCGACTVLVNGRRLNACLTLA 112 (217)
T ss_pred CCCCcHHHHHHHhcCCCCCC----CCCCCCCcCceEEEECCEEeeeeeeeh
Confidence 35688999999988753332 336666 5999999876555544
No 65
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=24.34 E-value=1.2e+02 Score=15.88 Aligned_cols=22 Identities=18% Similarity=0.178 Sum_probs=15.4
Q ss_pred ccHHHHHHHHH-cCceEeCCeEe
Q psy8661 38 LTNQEVLKILM-QRLIKVDGKVR 59 (71)
Q Consensus 38 ~t~~EakkIl~-~~~V~VdGkvr 59 (71)
.+.++|++++. -....++|+..
T Consensus 47 ~~~~~a~~a~~~l~g~~~~~~~i 69 (70)
T PF00076_consen 47 ESEEDAEKALEELNGKKINGRKI 69 (70)
T ss_dssp SSHHHHHHHHHHHTTEEETTEEE
T ss_pred cCHHHHHHHHHHcCCCEECccCc
Confidence 35778888887 45577777764
No 66
>TIGR03311 Se_dep_Molyb_1 selenium-dependent molybdenum hydroxylase 1. Members of this protein family show full length homology to the molybdenum-containing aldehyde oxido-reductase of Desulfovibrio gigas. Members, however, are found only within species that have, and near those genes that encode, a set of predicted accessory proteins for selenium-dependent molybdenum hydroxylases. The best known examples of such enzymes are forms of xanthine dehydrogenase and purine hydroxylase; this family appears to be another such enzyme.
Probab=24.03 E-value=41 Score=28.59 Aligned_cols=42 Identities=21% Similarity=0.256 Sum_probs=31.9
Q ss_pred cchhHHHHHHhhhcccccHHHHHHHHHcC-----ceEeCCeEecCCcCCcc
Q psy8661 22 ESLPLVIFLRNRLKYALTNQEVLKILMQR-----LIKVDGKVRTDTNYPAG 67 (71)
Q Consensus 22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~-----~V~VdGkvrtD~~~pvG 67 (71)
...+|+=+||+.|++-.+ |.=|.+| .|+|||+.+..--.|+.
T Consensus 14 ~~~~l~~~lr~~~~~~~~----k~gc~~g~cgactv~~dg~~~~sc~~~~~ 60 (848)
T TIGR03311 14 EEKKLLEFLREDLRLTGV----KNGCGEGACGACTVIVNGKAVRACRFTTA 60 (848)
T ss_pred CCCcHHHHHHHhcCCCcC----CCCCCCCCCCCcEEEECCeEEehhhhhHH
Confidence 457899999999987543 4566666 79999999887666654
No 67
>PF12471 GTP_CH_N: GTP cyclohydrolase N terminal ; InterPro: IPR022163 This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. This family is the N-terminal of GTP cyclohydrolase, the rate limiting enzyme in the synthesis of tetrahydrobiopterin.
Probab=23.99 E-value=58 Score=23.78 Aligned_cols=24 Identities=17% Similarity=0.245 Sum_probs=20.3
Q ss_pred cHHHHHHHHHcCceEeCCeEecCC
Q psy8661 39 TNQEVLKILMQRLIKVDGKVRTDT 62 (71)
Q Consensus 39 t~~EakkIl~~~~V~VdGkvrtD~ 62 (71)
+.-|....+..|.+.+|||++.+.
T Consensus 133 ~lpEi~eav~~GrL~~DGki~~~~ 156 (194)
T PF12471_consen 133 KLPEIREAVRKGRLVPDGKIVLNS 156 (194)
T ss_pred CcHHHHHHHHhCCCCCCCeEEecC
Confidence 345888889999999999999873
No 68
>PF08194 DIM: DIM protein; InterPro: IPR013172 Drosophila immune-induced molecules (DIMs) are short proteins induced during the immune response of Drosophila []. This entry includes DIMs 1 to 4 and DIM23.
Probab=22.84 E-value=58 Score=17.78 Aligned_cols=11 Identities=18% Similarity=0.289 Sum_probs=9.5
Q ss_pred cCceEeCCeEe
Q psy8661 49 QRLIKVDGKVR 59 (71)
Q Consensus 49 ~~~V~VdGkvr 59 (71)
-|+|.|||+-+
T Consensus 23 pG~ViING~C~ 33 (36)
T PF08194_consen 23 PGNVIINGKCI 33 (36)
T ss_pred CCeEEECceee
Confidence 79999999865
No 69
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=22.53 E-value=80 Score=20.42 Aligned_cols=23 Identities=39% Similarity=0.706 Sum_probs=17.3
Q ss_pred cchhHHHHHHhhhcccccHHHHHHHHH
Q psy8661 22 ESLPLVIFLRNRLKYALTNQEVLKILM 48 (71)
Q Consensus 22 ~slPL~i~LRd~LkyA~t~~EakkIl~ 48 (71)
.-+||+-+||.+ +|.+|++.|..
T Consensus 24 Dy~PLlALL~r~----Ltd~ev~~Va~ 46 (96)
T PF11829_consen 24 DYVPLLALLRRR----LTDDEVAEVAA 46 (96)
T ss_dssp HHHHHHHHHTTT----S-HHHHHHHHH
T ss_pred ccHHHHHHhccc----CCHHHHHHHHH
Confidence 357999999987 68888877754
No 70
>cd04457 S1_S28E S1_S28E: S28E, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. S28E protein is a component of the 30S ribosomal subunit. S28E is highly conserved among archaea and eukaryotes. S28E may control precursor RNA splicing and turnover in mRNA maturation process but its function in the ribosome is largely unknown. The structure contains an OB-fold found in many oligosaccharide and nucleic acid binding proteins. This implies that S28E might be involved in protein synthesis.
Probab=21.92 E-value=28 Score=21.03 Aligned_cols=16 Identities=19% Similarity=0.196 Sum_probs=12.5
Q ss_pred HhhhcccccHHHHHHH
Q psy8661 31 RNRLKYALTNQEVLKI 46 (71)
Q Consensus 31 Rd~LkyA~t~~EakkI 46 (71)
=|.|-+..|.+||+++
T Consensus 44 GDIl~L~EteREArrl 59 (60)
T cd04457 44 GDILMLLETEREARRL 59 (60)
T ss_pred CcEEeehhhhhhhhhc
Confidence 3667777899999875
No 71
>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A.
Probab=21.58 E-value=14 Score=23.99 Aligned_cols=23 Identities=26% Similarity=0.466 Sum_probs=17.3
Q ss_pred HHHHcCceEeCCeEecCCcCCcc
Q psy8661 45 KILMQRLIKVDGKVRTDTNYPAG 67 (71)
Q Consensus 45 kIl~~~~V~VdGkvrtD~~~pvG 67 (71)
++|..|.|+=|++...|.++|+|
T Consensus 52 RLI~~GriL~d~~tL~~~~~~~~ 74 (111)
T PF13881_consen 52 RLIYAGRILEDNKTLSDCRLPSG 74 (111)
T ss_dssp EEEETTEEE-SSSBTGGGT--TT
T ss_pred EEEeCCeecCCcCcHHHhCCCCC
Confidence 47788889999999999999886
No 72
>COG4814 Uncharacterized protein with an alpha/beta hydrolase fold [General function prediction only]
Probab=21.58 E-value=57 Score=25.14 Aligned_cols=19 Identities=32% Similarity=0.581 Sum_probs=17.1
Q ss_pred HcCceEeCCeEecCCcCCc
Q psy8661 48 MQRLIKVDGKVRTDTNYPA 66 (71)
Q Consensus 48 ~~~~V~VdGkvrtD~~~pv 66 (71)
.+|.|++-|+..+|.+||+
T Consensus 85 ~dgslk~tGk~~Kd~~nP~ 103 (288)
T COG4814 85 VDGSLKVTGKISKDAKNPI 103 (288)
T ss_pred CCCcEEEeeeecccCCCCe
Confidence 4679999999999999995
No 73
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=21.39 E-value=1.2e+02 Score=16.38 Aligned_cols=22 Identities=14% Similarity=0.185 Sum_probs=16.5
Q ss_pred ccHHHHHHHHHcCc-eEeCCeEe
Q psy8661 38 LTNQEVLKILMQRL-IKVDGKVR 59 (71)
Q Consensus 38 ~t~~EakkIl~~~~-V~VdGkvr 59 (71)
.+.++|++.+..-. ..++|+..
T Consensus 47 ~~~~~a~~al~~~~~~~~~g~~l 69 (70)
T PF14259_consen 47 SSEEDAKRALELLNGKEIDGRKL 69 (70)
T ss_dssp SSHHHHHHHHHHHTTEEETTEEE
T ss_pred CCHHHHHHHHHHCCCcEECCEEc
Confidence 36778888887766 88888764
No 74
>cd03515 Link_domain_TSG_6_like This is the extracellular link domain of the type found in human TSG-6. The link domain is a hyaluronan (HA)-binding domain. TSG-6 is the protein product of tumor necrosis factor-stimulated gene-6. TSG-6 is up-regulated in inflammatory lesions and in the ovary during ovulation. It has a strong anti-inflammatory and chondroprotective effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. Also included in this group are the stabilins: stabilin-1 (FEEL-1, CLEVER-1) and stabilin-2 (FEEL-2). Stabilin-2 functions as the major liver and lymph node-scavenging receptor for HA and related glycosaminoglycans. Stabilin-2 is a scavenger receptor with a broad range of ligands including advanced glycation end (AGE) products, acetylated low density lipoprotein and procollagen peptides. In contrast, stabilin-1 does not bind HA, but binds acetylated low density lipoprotein and AGEs with lower affinity. As AGEs accum
Probab=21.17 E-value=68 Score=20.65 Aligned_cols=16 Identities=31% Similarity=0.268 Sum_probs=14.0
Q ss_pred cccccHHHHHHHHHcC
Q psy8661 35 KYALTNQEVLKILMQR 50 (71)
Q Consensus 35 kyA~t~~EakkIl~~~ 50 (71)
+|+.|..||++.|.+.
T Consensus 11 rY~l~f~eA~~aC~~~ 26 (93)
T cd03515 11 KYKLTYTEAKAACEAE 26 (93)
T ss_pred ccccCHHHHHHHHHHc
Confidence 5889999999999865
No 75
>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and ATGP4 are plant-specific isoprenylated GTP-binding proteins with a single fold that resembles ubiquitin. The function of these proteins is unknown.
Probab=20.72 E-value=14 Score=24.71 Aligned_cols=26 Identities=19% Similarity=0.290 Sum_probs=22.7
Q ss_pred HHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661 42 EVLKILMQRLIKVDGKVRTDTNYPAG 67 (71)
Q Consensus 42 EakkIl~~~~V~VdGkvrtD~~~pvG 67 (71)
+..++|.+|+|+=|++-..|++-|+|
T Consensus 51 ~~qKLIysGKiLeD~~TL~d~~~p~g 76 (113)
T cd01814 51 NEVKLISAGKILENSKTVGECRSPVG 76 (113)
T ss_pred HHeEEEeCCeecCCCCcHHHhCCccc
Confidence 45678899999999999999998888
No 76
>PF07384 DUF1497: Protein of unknown function (DUF1497); InterPro: IPR009972 This entry is represented by Bacteriophage r1t, Orf17. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins of around 59 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this organism. The function of this family is unknown.
Probab=20.52 E-value=71 Score=19.04 Aligned_cols=15 Identities=20% Similarity=0.204 Sum_probs=12.0
Q ss_pred hcccccHHHHHHHHH
Q psy8661 34 LKYALTNQEVLKILM 48 (71)
Q Consensus 34 LkyA~t~~EakkIl~ 48 (71)
++|-++..||++|-+
T Consensus 1 mgyyd~~nearrisk 15 (59)
T PF07384_consen 1 MGYYDKRNEARRISK 15 (59)
T ss_pred CCcccchhHHHHHHH
Confidence 478888999999854
No 77
>PHA03311 helicase-primase subunit BBLF4; Provisional
Probab=20.44 E-value=39 Score=29.42 Aligned_cols=43 Identities=23% Similarity=0.248 Sum_probs=31.2
Q ss_pred CCCccchhH-HHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCC
Q psy8661 18 HKLRESLPL-VIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYP 65 (71)
Q Consensus 18 H~~~~slPL-~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~p 65 (71)
|..++|.=+ ..++.| .+.+|--.|-+++-|.||.|-|+|+.|+
T Consensus 271 ~~Vr~~~NILs~LI~n-----~~l~~Y~~i~~NWaiFINNKRCtd~eFG 314 (828)
T PHA03311 271 CSVRESENVLTALICN-----PTLREYVDLSNNWAIFINNKRCTDPEFG 314 (828)
T ss_pred ccccccchHHHHHhcC-----HHHHHHcCcccceEEEEeccccCChhHH
Confidence 444555443 334455 3777878889999999999999999875
Done!