Query 034360
Match_columns 97
No_of_seqs 116 out of 644
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 12:37:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034360.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034360hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0829 UreH Urease accessory 99.9 2.5E-27 5.3E-32 182.4 10.1 78 5-88 38-115 (269)
2 PF01774 UreD: UreD urease acc 99.9 6E-27 1.3E-31 172.8 8.0 71 14-88 1-71 (209)
3 PF04314 DUF461: Protein of un 86.0 2.3 5E-05 28.3 4.9 34 11-44 76-109 (110)
4 PF01458 UPF0051: Uncharacteri 75.3 16 0.00036 26.8 6.7 16 31-46 8-23 (229)
5 PF01774 UreD: UreD urease acc 70.8 25 0.00054 25.8 6.7 62 13-82 27-94 (209)
6 cd06664 IscU_like Iron-sulfur 67.7 19 0.00041 23.9 5.1 36 1-39 11-46 (123)
7 COG2847 Copper(I)-binding prot 67.6 20 0.00044 25.8 5.5 36 10-45 102-137 (151)
8 COG0829 UreH Urease accessory 65.5 24 0.00051 27.6 5.9 47 28-82 92-138 (269)
9 TIGR03419 NifU_clost FeS clust 59.5 29 0.00062 23.5 4.8 36 1-39 10-45 (121)
10 PF11604 CusF_Ec: Copper bindi 54.0 26 0.00055 21.6 3.6 25 22-46 41-65 (70)
11 TIGR01980 sufB FeS assembly pr 53.0 1.3E+02 0.0028 24.8 8.5 32 13-46 190-221 (448)
12 TIGR01994 SUF_scaf_2 SUF syste 52.6 40 0.00088 23.2 4.8 35 1-39 14-49 (137)
13 TIGR01999 iscU FeS cluster ass 51.4 36 0.00077 23.0 4.3 38 1-38 10-47 (124)
14 PF01458 UPF0051: Uncharacteri 48.8 78 0.0017 23.2 6.0 16 31-46 38-53 (229)
15 TIGR01981 sufD FeS assembly pr 48.7 1.4E+02 0.0029 23.8 8.7 18 29-46 124-141 (366)
16 PRK14738 gmk guanylate kinase; 47.5 22 0.00047 25.7 2.9 22 1-22 2-23 (206)
17 PRK11325 scaffold protein; Pro 47.2 45 0.00098 22.7 4.3 38 1-38 12-49 (127)
18 PF10610 Tafi-CsgC: Thin aggre 46.0 20 0.00043 24.6 2.3 24 24-47 75-98 (106)
19 PF01917 Arch_flagellin: Archa 41.3 98 0.0021 22.0 5.5 11 26-36 149-159 (190)
20 PF07703 A2M_N_2: Alpha-2-macr 40.9 55 0.0012 21.4 3.8 24 22-45 104-127 (136)
21 PF15504 DUF4647: Domain of un 40.8 16 0.00034 30.6 1.3 22 75-96 138-165 (457)
22 CHL00085 ycf24 putative ABC tr 40.2 2.2E+02 0.0048 23.8 8.1 51 27-83 222-272 (485)
23 KOG1631 Translocon-associated 37.7 20 0.00043 28.0 1.4 24 67-90 219-242 (261)
24 PF14326 DUF4384: Domain of un 37.5 60 0.0013 20.2 3.4 23 25-47 4-26 (83)
25 PRK11814 cysteine desulfurase 37.1 2.5E+02 0.0054 23.5 8.5 50 27-82 223-272 (486)
26 PRK10102 csgC curli assembly p 36.6 53 0.0011 22.5 3.2 24 24-47 79-102 (110)
27 PF15099 PIRT: Phosphoinositid 34.9 18 0.00039 25.6 0.7 18 77-94 98-115 (129)
28 TIGR01980 sufB FeS assembly pr 34.6 1.8E+02 0.004 23.9 6.7 44 30-82 236-279 (448)
29 PRK10948 cysteine desulfurase 34.5 2.6E+02 0.0057 23.0 8.2 17 29-45 171-187 (424)
30 PF01592 NifU_N: NifU-like N t 33.5 42 0.00091 22.6 2.4 37 1-39 11-47 (126)
31 PF02752 Arrestin_C: Arrestin 31.5 53 0.0012 20.9 2.6 40 12-51 4-43 (136)
32 PF13464 DUF4115: Domain of un 31.3 1.3E+02 0.0027 18.3 5.0 41 11-53 7-53 (77)
33 KOG1692 Putative cargo transpo 29.6 1.5E+02 0.0033 22.4 4.9 35 25-59 38-76 (201)
34 TIGR03444 gshA_related glutama 28.5 58 0.0013 26.8 2.8 33 20-55 53-85 (390)
35 COG0719 SufB Cysteine desulfur 26.5 3.5E+02 0.0076 22.0 7.4 19 28-46 162-180 (412)
36 cd04451 S1_IF1 S1_IF1: Transla 26.4 1.4E+02 0.003 17.6 3.6 18 24-41 41-58 (64)
37 cd07694 Ig2_CD4 Second immunog 25.9 62 0.0013 21.3 2.1 36 18-53 5-44 (88)
38 COG4540 gpV Phage P2 baseplate 25.4 2.3E+02 0.0049 21.2 5.2 23 6-30 48-70 (184)
39 cd04486 YhcR_OBF_like YhcR_OBF 24.9 1.8E+02 0.0038 18.1 4.0 28 10-38 32-59 (78)
40 PF03777 DUF320: Small secrete 24.7 63 0.0014 19.9 1.8 20 18-37 16-35 (60)
41 PF10632 He_PIG_assoc: He_PIG 24.5 68 0.0015 17.1 1.7 21 2-22 5-25 (29)
42 PF00635 Motile_Sperm: MSP (Ma 24.0 1E+02 0.0022 19.3 2.8 24 15-38 45-69 (109)
43 cd03584 NTR_complement_C4 NTR/ 23.7 58 0.0013 23.0 1.8 20 72-91 113-132 (153)
44 cd03582 NTR_complement_C5 NTR/ 23.4 71 0.0015 22.5 2.2 21 72-92 112-132 (150)
45 PRK15313 autotransport protein 22.6 1.6E+02 0.0035 27.2 4.6 27 32-58 244-270 (955)
46 PF11012 DUF2850: Protein of u 22.6 2.2E+02 0.0049 18.3 5.8 49 10-59 13-61 (79)
47 COG1862 YajC Preprotein transl 21.9 1E+02 0.0023 20.5 2.6 26 19-45 51-81 (97)
48 cd03774 MATH_SPOP Speckle-type 21.4 76 0.0016 21.1 1.9 20 18-37 116-135 (139)
49 cd03775 MATH_Ubp21p Ubiquitin- 20.5 1E+02 0.0022 20.5 2.4 18 20-37 117-134 (134)
50 cd00503 Frataxin Frataxin is a 20.3 1.2E+02 0.0026 20.1 2.7 27 32-58 39-67 (105)
51 KOG1690 emp24/gp25L/p24 family 20.0 91 0.002 23.8 2.2 43 10-52 99-141 (215)
No 1
>COG0829 UreH Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=2.5e-27 Score=182.40 Aligned_cols=78 Identities=27% Similarity=0.414 Sum_probs=73.1
Q ss_pred CCCCCCCcEEEEEEccCCcccCCceEEEEEEECCCcEEEEeCcccceeeecCCCCcceEEEEeeeceeeCCCceEEEech
Q 034360 5 VGSSETDAVWVYTLTYGGGIVSGDSISCEITVADACTAVLTTQASTKVYKSLGSKSSEQILEMAVPAIVEERGVASFFDQ 84 (97)
Q Consensus 5 ~~p~~~~~~~vyl~~~sGGl~~GD~l~i~i~v~~ga~l~lTTQaAtKvy~~~~~~~s~Q~~~v~v~~~ve~gA~Le~lP~ 84 (97)
++|+ ++.|++||+|+|||+++||+++++|+++++|+++||||||||||+|.++. ++|+++| +|++||+|||+||
T Consensus 38 ~y~~-~~~~~~~li~~~GGv~gGD~l~~di~lg~~a~~~iTTQsatKvYrs~~g~-A~Q~~~i----~vg~nA~LewlPq 111 (269)
T COG0829 38 FYPD-EGLCEAMLIHPSGGVVGGDRLEIDIELGDNAKALITTQSATKVYRSPGGQ-ATQTTNI----TVGENARLEWLPQ 111 (269)
T ss_pred CcCC-CCCeEEEEEeCCCCccccceEEEEEEECCCceEEEEccccceeEeCCCCc-eEEEEEE----EECCCCEEEecCC
Confidence 3566 88999999999999999999999999999999999999999999999998 8899988 6999999999999
Q ss_pred hhhh
Q 034360 85 QKEK 88 (97)
Q Consensus 85 ~~~~ 88 (97)
|+|-
T Consensus 112 ~tI~ 115 (269)
T COG0829 112 ETIP 115 (269)
T ss_pred ccee
Confidence 9974
No 2
>PF01774 UreD: UreD urease accessory protein; InterPro: IPR002669 UreD is a urease accessory protein. Urease IPR005848 from INTERPRO hydrolyses urea into ammonia and carbamic acid []. UreD is involved in activation of the urease enzyme via the UreD-UreF-UreG-urease complex [] and is required for urease nickel metallocentre assembly []. See also UreF IPR002639 from INTERPRO, UreG IPR004400 from INTERPRO.; GO: 0016151 nickel ion binding, 0006807 nitrogen compound metabolic process; PDB: 3SF5_D.
Probab=99.94 E-value=6e-27 Score=172.76 Aligned_cols=71 Identities=32% Similarity=0.538 Sum_probs=45.4
Q ss_pred EEEEEccCCcccCCceEEEEEEECCCcEEEEeCcccceeeecCCCCcceEEEEeeeceeeCCCceEEEechhhhh
Q 034360 14 WVYTLTYGGGIVSGDSISCEITVADACTAVLTTQASTKVYKSLGSKSSEQILEMAVPAIVEERGVASFFDQQKEK 88 (97)
Q Consensus 14 ~vyl~~~sGGl~~GD~l~i~i~v~~ga~l~lTTQaAtKvy~~~~~~~s~Q~~~v~v~~~ve~gA~Le~lP~~~~~ 88 (97)
|+||+|+|||+++||+++++|+|++||+++||||||||||+|+++..++|++++ +|++||+|||+|||++-
T Consensus 1 h~yl~~~~gGl~~GD~l~~~i~v~~ga~~~ltTqaatkvy~~~~~~~a~q~~~~----~v~~ga~Le~lP~p~I~ 71 (209)
T PF01774_consen 1 HVYLMNPSGGLLGGDRLRIDITVGPGARLLLTTQAATKVYRMRGGRPARQRIRI----TVEEGAYLEYLPDPTIP 71 (209)
T ss_dssp -EEEEE--S-B-TT-EEEEEEEE-TT-EEEEE----EEE---TTS--EEEEEEE----EE-TT-EEEE----EEE
T ss_pred CEEEEeCCCcCcCCCEEEEEEEECCCCEEEEechhhhhhcCCCCCCcEEEEEEE----EECCCCEEEEcCCCCEe
Confidence 699999999999999999999999999999999999999999988778899988 69999999999999974
No 3
>PF04314 DUF461: Protein of unknown function (DUF461); InterPro: IPR007410 This entry represents a domain found in of proteins of unknown function, including DR1885 from Deinococcus radiodurans and CC3502 from Caulobacter crescentus (Caulobacter vibrioides), which share a potential metal binding motif H(M)X10MX21HXM. DR1885 was found to bind copper(I) through a histidine and three Mets in a cupredoxin-like fold []. The surface location of the copper-binding site as well as the type of coordination are well poised for metal transfer chemistry, suggesting that DR1885 might transfer copper, taking the role of Cox17 in bacteria (Cox17 being an accessory protein required for correct assembly of eukaryotic cyochrome c oxidase). ; PDB: 2K6W_A 2K6Z_A 2K6Y_A 2K70_A 1X9L_A 2JQA_A.
Probab=86.00 E-value=2.3 Score=28.27 Aligned_cols=34 Identities=12% Similarity=0.235 Sum_probs=20.2
Q ss_pred CcEEEEEEccCCcccCCceEEEEEEECCCcEEEE
Q 034360 11 DAVWVYTLTYGGGIVSGDSISCEITVADACTAVL 44 (97)
Q Consensus 11 ~~~~vyl~~~sGGl~~GD~l~i~i~v~~ga~l~l 44 (97)
+-.+++|+..---+..||++.+.++.+.|..+.+
T Consensus 76 gg~HlmL~g~~~~l~~G~~v~ltL~f~~gg~v~v 109 (110)
T PF04314_consen 76 GGYHLMLMGLKRPLKPGDTVPLTLTFEDGGKVTV 109 (110)
T ss_dssp CCCEEEEECESS-B-TTEEEEEEEEETTTEEEEE
T ss_pred CCEEEEEeCCcccCCCCCEEEEEEEECCCCEEEe
Confidence 3456666666666666666666666666666554
No 4
>PF01458 UPF0051: Uncharacterized protein family (UPF0051); InterPro: IPR000825 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents SufB and SufD proteins that form part of the SufBCD complex in the SUF system. No specific functions have been assigned to these proteins.; GO: 0016226 iron-sulfur cluster assembly; PDB: 1VH4_B 2ZU0_A 4DN7_A.
Probab=75.34 E-value=16 Score=26.80 Aligned_cols=16 Identities=13% Similarity=0.156 Sum_probs=6.7
Q ss_pred EEEEEECCCcEEEEeC
Q 034360 31 SCEITVADACTAVLTT 46 (97)
Q Consensus 31 ~i~i~v~~ga~l~lTT 46 (97)
++.|.+++|+.+.|..
T Consensus 8 ~~~I~v~~~s~~~i~~ 23 (229)
T PF01458_consen 8 RNLIIVEEGSEVTIIE 23 (229)
T ss_dssp EEEEEE-TT-EEEEEE
T ss_pred eEEEEECCCCEEEEEE
Confidence 3445555555555443
No 5
>PF01774 UreD: UreD urease accessory protein; InterPro: IPR002669 UreD is a urease accessory protein. Urease IPR005848 from INTERPRO hydrolyses urea into ammonia and carbamic acid []. UreD is involved in activation of the urease enzyme via the UreD-UreF-UreG-urease complex [] and is required for urease nickel metallocentre assembly []. See also UreF IPR002639 from INTERPRO, UreG IPR004400 from INTERPRO.; GO: 0016151 nickel ion binding, 0006807 nitrogen compound metabolic process; PDB: 3SF5_D.
Probab=70.77 E-value=25 Score=25.76 Aligned_cols=62 Identities=13% Similarity=0.090 Sum_probs=32.7
Q ss_pred EEEEEEccCCccc----CCc--eEEEEEEECCCcEEEEeCcccceeeecCCCCcceEEEEeeeceeeCCCceEEEe
Q 034360 13 VWVYTLTYGGGIV----SGD--SISCEITVADACTAVLTTQASTKVYKSLGSKSSEQILEMAVPAIVEERGVASFF 82 (97)
Q Consensus 13 ~~vyl~~~sGGl~----~GD--~l~i~i~v~~ga~l~lTTQaAtKvy~~~~~~~s~Q~~~v~v~~~ve~gA~Le~l 82 (97)
+.+.|.+.|.--+ +|. +.+++|+|++||.+..-.+ -+..| .+..-+|.++| .|+++|.|-|.
T Consensus 27 a~~~ltTqaatkvy~~~~~~~a~q~~~~~v~~ga~Le~lP~-p~I~f---~~A~~~q~~~v----~l~~~A~l~~~ 94 (209)
T PF01774_consen 27 ARLLLTTQAATKVYRMRGGRPARQRIRITVEEGAYLEYLPD-PTIPF---AGARFRQRTRV----DLAPGASLIYW 94 (209)
T ss_dssp -EEEEE----EEE---TTS--EEEEEEEEE-TT-EEEE-----EEE----TT-EEEEEEEE----EE-TT-EEEEE
T ss_pred CEEEEechhhhhhcCCCCCCcEEEEEEEEECCCCEEEEcCC-CCEee---CCCEEEEEEEE----EECCCCEEEEE
Confidence 4566666665544 344 8999999999999988755 34555 22224577777 58999999774
No 6
>cd06664 IscU_like Iron-sulfur cluster scaffold-like proteins. IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.
Probab=67.74 E-value=19 Score=23.90 Aligned_cols=36 Identities=28% Similarity=0.265 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCcEEEEEEccCCcccCCceEEEEEEECCC
Q 034360 1 MNPQVGSSETDAVWVYTLTYGGGIVSGDSISCEITVADA 39 (97)
Q Consensus 1 ~~~~~~p~~~~~~~vyl~~~sGGl~~GD~l~i~i~v~~g 39 (97)
+||+.....++. ......+...-||.+++.+.++++
T Consensus 11 ~~p~~~g~l~~~---~~~~~~~n~~CGD~v~l~l~i~~~ 46 (123)
T cd06664 11 RNPRNVGRLEDA---DGTGEVGNPLCGDEITLYLKVEDG 46 (123)
T ss_pred hCCCCCCCCCCC---CeEEEcCCCCCCceEEEEEEEcCC
Confidence 477777665543 124445666699999999999875
No 7
>COG2847 Copper(I)-binding protein [Inorganic ion transport and metabolism]
Probab=67.58 E-value=20 Score=25.81 Aligned_cols=36 Identities=11% Similarity=0.192 Sum_probs=33.6
Q ss_pred CCcEEEEEEccCCcccCCceEEEEEEECCCcEEEEe
Q 034360 10 TDAVWVYTLTYGGGIVSGDSISCEITVADACTAVLT 45 (97)
Q Consensus 10 ~~~~~vyl~~~sGGl~~GD~l~i~i~v~~ga~l~lT 45 (97)
|+.-+++|+..-=.|..||.+.++++.+.+..+.|.
T Consensus 102 pGgyHvMlm~lK~pl~eGd~v~vtL~f~~~~~~~v~ 137 (151)
T COG2847 102 PGGYHVMLMGLKKPLKEGDKVPVTLKFEKAGKVTVE 137 (151)
T ss_pred CCCEEEEEeccCCCccCCCEEEEEEEEecCCeEEEE
Confidence 567899999999999999999999999999998887
No 8
>COG0829 UreH Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]
Probab=65.47 E-value=24 Score=27.62 Aligned_cols=47 Identities=13% Similarity=0.153 Sum_probs=36.3
Q ss_pred ceEEEEEEECCCcEEEEeCcccceeeecCCCCcceEEEEeeeceeeCCCceEEEe
Q 034360 28 DSISCEITVADACTAVLTTQASTKVYKSLGSKSSEQILEMAVPAIVEERGVASFF 82 (97)
Q Consensus 28 D~l~i~i~v~~ga~l~lTTQaAtKvy~~~~~~~s~Q~~~v~v~~~ve~gA~Le~l 82 (97)
=+.+++|+|++||++.--.|- +.+|+ +..-.|+++| .|+++|.|-|.
T Consensus 92 A~Q~~~i~vg~nA~LewlPq~-tI~F~---~a~f~q~~~~----~L~~sA~l~~~ 138 (269)
T COG0829 92 ATQTTNITVGENARLEWLPQE-TIPFE---GARFKQHTRF----ELASSATLLYW 138 (269)
T ss_pred eEEEEEEEECCCCEEEecCCc-ceecC---CceeEEEEEE----EeCCCceehhh
Confidence 578999999999999988774 56662 2224578888 58999998775
No 9
>TIGR03419 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not.
Probab=59.48 E-value=29 Score=23.45 Aligned_cols=36 Identities=25% Similarity=0.237 Sum_probs=25.9
Q ss_pred CCCCCCCCCCCcEEEEEEccCCcccCCceEEEEEEECCC
Q 034360 1 MNPQVGSSETDAVWVYTLTYGGGIVSGDSISCEITVADA 39 (97)
Q Consensus 1 ~~~~~~p~~~~~~~vyl~~~sGGl~~GD~l~i~i~v~~g 39 (97)
+||+.....++.- .....+...-||.+++.+.++.+
T Consensus 10 ~np~~~g~l~~~~---~~~~~~np~CGD~i~l~l~i~~~ 45 (121)
T TIGR03419 10 MNPRNVGEIENAD---GVGEVGNPKCGDIMKIFLKVEDD 45 (121)
T ss_pred hCCCCCCCCCCCC---eEEEeCCCCCccEEEEEEEEcCC
Confidence 4888877544321 14466777899999999999876
No 10
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=53.96 E-value=26 Score=21.57 Aligned_cols=25 Identities=24% Similarity=0.435 Sum_probs=19.4
Q ss_pred CcccCCceEEEEEEECCCcEEEEeC
Q 034360 22 GGIVSGDSISCEITVADACTAVLTT 46 (97)
Q Consensus 22 GGl~~GD~l~i~i~v~~ga~l~lTT 46 (97)
.|+-.||++++.+...++....|+.
T Consensus 41 ~~l~~Gd~V~F~~~~~~~~~~~I~~ 65 (70)
T PF11604_consen 41 AGLKPGDKVRFTFERTDDGSYVITA 65 (70)
T ss_dssp SS-STT-EEEEEEEEETTCEEEEEE
T ss_pred hcCCCCCEEEEEEEECCCCcEEEEE
Confidence 6788999999999999888777663
No 11
>TIGR01980 sufB FeS assembly protein SufB. This protein, SufB, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component.
Probab=53.01 E-value=1.3e+02 Score=24.84 Aligned_cols=32 Identities=9% Similarity=0.046 Sum_probs=21.3
Q ss_pred EEEEEEccCCcccCCceEEEEEEECCCcEEEEeC
Q 034360 13 VWVYTLTYGGGIVSGDSISCEITVADACTAVLTT 46 (97)
Q Consensus 13 ~~vyl~~~sGGl~~GD~l~i~i~v~~ga~l~lTT 46 (97)
.+++....+.+. .-..+.-|.+++||.+.+-.
T Consensus 190 i~~~~~~~~~~~--~~~~r~lIi~ee~s~~~iie 221 (448)
T TIGR01980 190 LQTYFRINSENT--GQFEHTLIIADEGASVHYIE 221 (448)
T ss_pred EEEEEEEcCCcc--ceeeeEEEEECCCCEEEEEE
Confidence 444444444442 34578889999999999864
No 12
>TIGR01994 SUF_scaf_2 SUF system FeS assembly protein, NifU family. Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred.
Probab=52.62 E-value=40 Score=23.19 Aligned_cols=35 Identities=26% Similarity=0.321 Sum_probs=24.0
Q ss_pred CCCCCCCCCCCc-EEEEEEccCCcccCCceEEEEEEECCC
Q 034360 1 MNPQVGSSETDA-VWVYTLTYGGGIVSGDSISCEITVADA 39 (97)
Q Consensus 1 ~~~~~~p~~~~~-~~vyl~~~sGGl~~GD~l~i~i~v~~g 39 (97)
+||+..+.-++. ... ..+-..-||.+++.+.++.+
T Consensus 14 ~~p~n~g~l~~~~~~~----~~~np~CGD~i~l~l~v~~~ 49 (137)
T TIGR01994 14 KNPRHRGKLEDATVQE----RGHNPTCGDEITLTVKLEGD 49 (137)
T ss_pred hCCCCCCCCCCCCeeE----EeCCCCCCcEEEEEEEEcCC
Confidence 478887754432 222 44556799999999999865
No 13
>TIGR01999 iscU FeS cluster assembly scaffold IscU. This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms.
Probab=51.41 E-value=36 Score=23.03 Aligned_cols=38 Identities=24% Similarity=0.165 Sum_probs=23.7
Q ss_pred CCCCCCCCCCCcEEEEEEccCCcccCCceEEEEEEECC
Q 034360 1 MNPQVGSSETDAVWVYTLTYGGGIVSGDSISCEITVAD 38 (97)
Q Consensus 1 ~~~~~~p~~~~~~~vyl~~~sGGl~~GD~l~i~i~v~~ 38 (97)
+||+..+..++.-........|-..-||.+++.+.+++
T Consensus 10 ~~p~n~G~l~~~~~~~~~~~~~np~CGD~i~l~l~v~~ 47 (124)
T TIGR01999 10 ENPRNVGSLDKDDKNVGTGLVGAPACGDVMKLQIKVND 47 (124)
T ss_pred hCCCCCCCCCCCccccceEEeCCCCCccEEEEEEEECC
Confidence 58888775443211111222355669999999999975
No 14
>PF01458 UPF0051: Uncharacterized protein family (UPF0051); InterPro: IPR000825 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents SufB and SufD proteins that form part of the SufBCD complex in the SUF system. No specific functions have been assigned to these proteins.; GO: 0016226 iron-sulfur cluster assembly; PDB: 1VH4_B 2ZU0_A 4DN7_A.
Probab=48.75 E-value=78 Score=23.19 Aligned_cols=16 Identities=19% Similarity=0.185 Sum_probs=10.9
Q ss_pred EEEEEECCCcEEEEeC
Q 034360 31 SCEITVADACTAVLTT 46 (97)
Q Consensus 31 ~i~i~v~~ga~l~lTT 46 (97)
.++|.+++||++.+..
T Consensus 38 ~~~i~v~~~a~l~~~~ 53 (229)
T PF01458_consen 38 VIEIYVGENARLKYVS 53 (229)
T ss_dssp EEEEEE-TT-EEEEEE
T ss_pred EEEEEECCCcEEEEEE
Confidence 4577899999998875
No 15
>TIGR01981 sufD FeS assembly protein SufD, group 1. This protein, SufD, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. SufB and SufD are homologous. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component.
Probab=48.70 E-value=1.4e+02 Score=23.79 Aligned_cols=18 Identities=11% Similarity=0.021 Sum_probs=14.3
Q ss_pred eEEEEEEECCCcEEEEeC
Q 034360 29 SISCEITVADACTAVLTT 46 (97)
Q Consensus 29 ~l~i~i~v~~ga~l~lTT 46 (97)
..++-|.+++||++.|--
T Consensus 124 ~~~~~i~v~~~s~~~iie 141 (366)
T TIGR01981 124 HPRLLIIVEKGSKITVIE 141 (366)
T ss_pred eeEEEEEECCCCEEEEEE
Confidence 457888899999988764
No 16
>PRK14738 gmk guanylate kinase; Provisional
Probab=47.51 E-value=22 Score=25.67 Aligned_cols=22 Identities=23% Similarity=0.229 Sum_probs=18.4
Q ss_pred CCCCCCCCCCCcEEEEEEccCC
Q 034360 1 MNPQVGSSETDAVWVYTLTYGG 22 (97)
Q Consensus 1 ~~~~~~p~~~~~~~vyl~~~sG 22 (97)
|||+.+-+++....++|+-++|
T Consensus 2 ~~~~~~~~~~~~~~ivi~GpsG 23 (206)
T PRK14738 2 MNPWLFNKPAKPLLVVISGPSG 23 (206)
T ss_pred CCccccCCCCCCeEEEEECcCC
Confidence 8999998888777888877776
No 17
>PRK11325 scaffold protein; Provisional
Probab=47.24 E-value=45 Score=22.70 Aligned_cols=38 Identities=24% Similarity=0.141 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCcEEEEEEccCCcccCCceEEEEEEECC
Q 034360 1 MNPQVGSSETDAVWVYTLTYGGGIVSGDSISCEITVAD 38 (97)
Q Consensus 1 ~~~~~~p~~~~~~~vyl~~~sGGl~~GD~l~i~i~v~~ 38 (97)
+||+.....++.-........|-..-||.+++.+.+++
T Consensus 12 ~~P~n~G~l~~~~~~~~~~~~~np~CGD~i~l~l~v~~ 49 (127)
T PRK11325 12 ENPRNVGSFDKNDPNVGTGMVGAPACGDVMKLQIKVND 49 (127)
T ss_pred hCcCCCCCCCCCccccceEEecCCCCccEEEEEEEECC
Confidence 47888775443211111222345569999999999974
No 18
>PF10610 Tafi-CsgC: Thin aggregative fimbriae synthesis protein; InterPro: IPR014491 Thin aggressive fibres known as curli fibres or fimbriae (curli; Tafi) are cell-surface protein polymers found in Salmonella typhimurium and Escherichia coli that mediate interactions important for host and environmental persistence, development of biofilms, motility, colonisation and invasion of cells, and conjugation []. Four general assembly pathways for different fimbriae have been proposed, one of which is extracellular nucleation-precipitation (ENP), which differs from the others in that fibre-growth occurs extracellularly. Thin aggregative fimbriae are the only fimbriae dependent on the ENP pathway. Tafi were first identified in Salmonella spp and the controlling operon termed agf; however subsequent isolation of the homologous operon in E coli led to its being called csg. Tafi are known as curli because, in the absence of extracellular polysaccharides, their morphology appears curled; however, when expressed with such polysaccharides their morphology appears as a tangled amorphous matrix. The gene agfC is found to be transcribed at low levels, localised to the periplasm in a mature form, and in combination with AgfE is important for AgfA extracellular assembly, which facilitates the synthesis of Tafi. The genes involved in Tafi production are organised into two adjacent divergently transcribed operons, agfBAC and agfDEFG, both of which are required for biosynthesis and assembly [].; PDB: 2XSK_A 2Y2T_A 2Y2Y_A.
Probab=45.99 E-value=20 Score=24.60 Aligned_cols=24 Identities=33% Similarity=0.462 Sum_probs=17.0
Q ss_pred ccCCceEEEEEEECCCcEEEEeCc
Q 034360 24 IVSGDSISCEITVADACTAVLTTQ 47 (97)
Q Consensus 24 l~~GD~l~i~i~v~~ga~l~lTTQ 47 (97)
+-.||.+.|.|+|-+|-.++|+-|
T Consensus 75 i~p~D~v~I~VtvSDG~sl~LsqQ 98 (106)
T PF10610_consen 75 ISPGDKVKIIVTVSDGKSLHLSQQ 98 (106)
T ss_dssp --TT-EEEEEEEEE-SSS-EEEEE
T ss_pred eCCCCeEEEEEEEcCCCeEEeEec
Confidence 457999999999999999999854
No 19
>PF01917 Arch_flagellin: Archaebacterial flagellin; InterPro: IPR002774 Archaeal motility occurs by the rotation of flagella that are different to bacterial flagella, but show similarity to bacterial type IV pili. These similarities include the multiflagellin nature of the flagellar filament, N-terminal sequence similarities, as well as the presence of homologous proteins in the two systems [, ]. Also unlike bacterial flagellins but similar to type IV pilins, archaeal flagellins are initially synthesised with a short leader peptide that is cleaved by a membrane-located peptidase [, ]. The enzyme responsible for the removal of the this leader peptide is FlaK [].; GO: 0005198 structural molecule activity, 0006928 cellular component movement
Probab=41.31 E-value=98 Score=21.98 Aligned_cols=11 Identities=18% Similarity=0.595 Sum_probs=5.6
Q ss_pred CCceEEEEEEE
Q 034360 26 SGDSISCEITV 36 (97)
Q Consensus 26 ~GD~l~i~i~v 36 (97)
.||++.|.|.+
T Consensus 149 ~ge~~~i~I~~ 159 (190)
T PF01917_consen 149 PGETVEITINL 159 (190)
T ss_pred CCcEEEEEEEc
Confidence 45555555544
No 20
>PF07703 A2M_N_2: Alpha-2-macroglobulin family N-terminal region; InterPro: IPR011625 This is a domain of the alpha-2-macroglobulin family. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; PDB: 2QKI_D 3L3O_D 3NMS_A 2ICF_A 2A73_A 2ICE_D 2HR0_A 2A74_A 2XWJ_G 3OHX_A ....
Probab=40.91 E-value=55 Score=21.43 Aligned_cols=24 Identities=13% Similarity=0.209 Sum_probs=15.5
Q ss_pred CcccCCceEEEEEEECCCcEEEEe
Q 034360 22 GGIVSGDSISCEITVADACTAVLT 45 (97)
Q Consensus 22 GGl~~GD~l~i~i~v~~ga~l~lT 45 (97)
.=+-.|+.++++|+++++|.+.|.
T Consensus 104 ~~~~Pg~~~~~~i~~~~~s~v~l~ 127 (136)
T PF07703_consen 104 DEYKPGEEVTLRIKAPPNSLVGLS 127 (136)
T ss_dssp SSBTTTSEEEEEEEESTTEEEEEE
T ss_pred ceeCCCCEEEEEEEeCCCCEEEEE
Confidence 344567777777777767666653
No 21
>PF15504 DUF4647: Domain of unknown function (DUF4647)
Probab=40.79 E-value=16 Score=30.62 Aligned_cols=22 Identities=45% Similarity=0.555 Sum_probs=16.9
Q ss_pred CCceEEEechhhhh------hHHHhhhh
Q 034360 75 ERGVASFFDQQKEK------KKKRKKAA 96 (97)
Q Consensus 75 ~gA~Le~lP~~~~~------~~~~~~~~ 96 (97)
.|-+.-|+|+|.+| ||||||-+
T Consensus 138 ~NmvviWiPee~ek~~sq~gkkkRkks~ 165 (457)
T PF15504_consen 138 RNMVVIWIPEEPEKHVSQDGKKKRKKSA 165 (457)
T ss_pred cceEEEEcCCccccccChhhhhhhhhcc
Confidence 45678999999997 57777754
No 22
>CHL00085 ycf24 putative ABC transporter
Probab=40.21 E-value=2.2e+02 Score=23.80 Aligned_cols=51 Identities=10% Similarity=0.087 Sum_probs=29.5
Q ss_pred CceEEEEEEECCCcEEEEeCcccceeeecCCCCcceEEEEeeeceeeCCCceEEEec
Q 034360 27 GDSISCEITVADACTAVLTTQASTKVYKSLGSKSSEQILEMAVPAIVEERGVASFFD 83 (97)
Q Consensus 27 GD~l~i~i~v~~ga~l~lTTQaAtKvy~~~~~~~s~Q~~~v~v~~~ve~gA~Le~lP 83 (97)
+-..+.-|.+++||.+.|...=.+.-+... .. ....+ .+.|++||.|.|.-
T Consensus 222 ~~~~r~lIi~eega~~~iiE~~~s~~~~~~-~~-~~~v~----Ei~v~~~A~l~~~~ 272 (485)
T CHL00085 222 GQFERTLIIAEENSYVSYLEGCTAPQYDTN-QL-HAAVV----ELIALENAEIKYST 272 (485)
T ss_pred ceeeeEEEEECCCCEEEEEEEeccCCCCcc-ce-EEEEE----EEEECCCCEEEEEE
Confidence 667888999999999998743221111100 10 11122 33678888888753
No 23
>KOG1631 consensus Translocon-associated complex TRAP, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.67 E-value=20 Score=28.01 Aligned_cols=24 Identities=13% Similarity=0.104 Sum_probs=16.1
Q ss_pred eeeceeeCCCceEEEechhhhhhH
Q 034360 67 MAVPAIVEERGVASFFDQQKEKKK 90 (97)
Q Consensus 67 v~v~~~ve~gA~Le~lP~~~~~~~ 90 (97)
|+++..=.+....||+|+++.+++
T Consensus 219 VE~GTas~~~vd~eWip~~tl~q~ 242 (261)
T KOG1631|consen 219 VEVGTASKDAVDDEWIPGTTLKQK 242 (261)
T ss_pred EeecccCcccccccccccHhHHhh
Confidence 444444445567899999998753
No 24
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=37.53 E-value=60 Score=20.17 Aligned_cols=23 Identities=13% Similarity=0.062 Sum_probs=20.3
Q ss_pred cCCceEEEEEEECCCcEEEEeCc
Q 034360 25 VSGDSISCEITVADACTAVLTTQ 47 (97)
Q Consensus 25 ~~GD~l~i~i~v~~ga~l~lTTQ 47 (97)
-.||++.+.|+....+.+.|-..
T Consensus 4 ~~Ge~v~~~~~~~~~~Yl~l~~~ 26 (83)
T PF14326_consen 4 RVGERVRFRVTSNRDGYLYLFYI 26 (83)
T ss_pred cCCCEEEEEEEeCCCeEEEEEEE
Confidence 47999999999999999988765
No 25
>PRK11814 cysteine desulfurase activator complex subunit SufB; Provisional
Probab=37.13 E-value=2.5e+02 Score=23.52 Aligned_cols=50 Identities=6% Similarity=0.034 Sum_probs=28.6
Q ss_pred CceEEEEEEECCCcEEEEeCcccceeeecCCCCcceEEEEeeeceeeCCCceEEEe
Q 034360 27 GDSISCEITVADACTAVLTTQASTKVYKSLGSKSSEQILEMAVPAIVEERGVASFF 82 (97)
Q Consensus 27 GD~l~i~i~v~~ga~l~lTTQaAtKvy~~~~~~~s~Q~~~v~v~~~ve~gA~Le~l 82 (97)
+-..+.-|.+++||.+.|-..=.+... .. ...+ ...+.+.+++||.|.|.
T Consensus 223 ~~~~r~lIi~ee~S~~~iiE~~~s~~~---~~--~~~~-~~v~Ei~v~~~A~l~~~ 272 (486)
T PRK11814 223 GQFERTLIIADEGSYVSYLEGCTAPMR---DE--NQLH-AAVVELVALDDAEIKYS 272 (486)
T ss_pred ceeeEEEEEECCCCEEEEEEEecCCCC---Cc--ccee-eEEEEEEECCCCEEEEE
Confidence 567889999999999988643211100 01 0011 11123368888888874
No 26
>PRK10102 csgC curli assembly protein CsgC; Provisional
Probab=36.64 E-value=53 Score=22.52 Aligned_cols=24 Identities=29% Similarity=0.385 Sum_probs=20.9
Q ss_pred ccCCceEEEEEEECCCcEEEEeCc
Q 034360 24 IVSGDSISCEITVADACTAVLTTQ 47 (97)
Q Consensus 24 l~~GD~l~i~i~v~~ga~l~lTTQ 47 (97)
+-..|.+.|-|+|-+|-.++++-|
T Consensus 79 Is~~DsVkiiVTVSDg~slhlsqQ 102 (110)
T PRK10102 79 ISPDDRVKIVVTVSDGQSLHLSQQ 102 (110)
T ss_pred eCCCCcEEEEEEEcCCCcEEeecc
Confidence 446899999999999999999876
No 27
>PF15099 PIRT: Phosphoinositide-interacting protein family
Probab=34.91 E-value=18 Score=25.63 Aligned_cols=18 Identities=28% Similarity=0.381 Sum_probs=14.5
Q ss_pred ceEEEechhhhhhHHHhh
Q 034360 77 GVASFFDQQKEKKKKRKK 94 (97)
Q Consensus 77 A~Le~lP~~~~~~~~~~~ 94 (97)
+.|-|.|...-|+|||++
T Consensus 98 ~alcW~~~~rkK~~kr~e 115 (129)
T PF15099_consen 98 SALCWKPIIRKKKKKRRE 115 (129)
T ss_pred hhheehhhhHhHHHHhhh
Confidence 458999998888877765
No 28
>TIGR01980 sufB FeS assembly protein SufB. This protein, SufB, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component.
Probab=34.62 E-value=1.8e+02 Score=23.94 Aligned_cols=44 Identities=18% Similarity=0.175 Sum_probs=26.7
Q ss_pred EEEEEEECCCcEEEEeCcccceeeecCCCCcceEEEEeeeceeeCCCceEEEe
Q 034360 30 ISCEITVADACTAVLTTQASTKVYKSLGSKSSEQILEMAVPAIVEERGVASFF 82 (97)
Q Consensus 30 l~i~i~v~~ga~l~lTTQaAtKvy~~~~~~~s~Q~~~v~v~~~ve~gA~Le~l 82 (97)
-..+|.+++||++..+ +|+.-..+...-.+.+ +.++++|.++|.
T Consensus 236 ~v~Ei~v~~~A~v~~~-----~iq~~~~~~~~~~~~~----~~~~~~a~~~~~ 279 (448)
T TIGR01980 236 AVVELIVKEDARVRYS-----TVQNWSKNVYNLVTKR----ALVEENGTMEWV 279 (448)
T ss_pred EEEEEEEcCCCEEEEE-----EEeecCCCeEEEEEEE----EEEcCCCEEEEE
Confidence 4578899999999987 4443333311112222 257788888875
No 29
>PRK10948 cysteine desulfurase activator complex subunit SufD; Provisional
Probab=34.54 E-value=2.6e+02 Score=22.97 Aligned_cols=17 Identities=12% Similarity=0.241 Sum_probs=12.7
Q ss_pred eEEEEEEECCCcEEEEe
Q 034360 29 SISCEITVADACTAVLT 45 (97)
Q Consensus 29 ~l~i~i~v~~ga~l~lT 45 (97)
..+.-|.+++||.+.|-
T Consensus 171 ~~r~lI~~e~~a~~tii 187 (424)
T PRK10948 171 HYRHHLDLAEGAEATVI 187 (424)
T ss_pred cceEEEEECCCCEEEEE
Confidence 45677888888887765
No 30
>PF01592 NifU_N: NifU-like N terminal domain; InterPro: IPR002871 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the N-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal and a C-terminal domain (IPR001075 from INTERPRO) []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 3LVL_A 4EB5_C 4EB7_C 1WFZ_A 2Z7E_C 2AZH_A 1XJS_A 1Q48_A 1R9P_A 2KQK_A ....
Probab=33.54 E-value=42 Score=22.60 Aligned_cols=37 Identities=24% Similarity=0.206 Sum_probs=23.7
Q ss_pred CCCCCCCCCCCcEEEEEEccCCcccCCceEEEEEEECCC
Q 034360 1 MNPQVGSSETDAVWVYTLTYGGGIVSGDSISCEITVADA 39 (97)
Q Consensus 1 ~~~~~~p~~~~~~~vyl~~~sGGl~~GD~l~i~i~v~~g 39 (97)
+||+.....++.-. +...++-..-||.+++.+.++.+
T Consensus 11 ~nP~~~g~l~~~~~--~~~~~~n~~CGD~i~i~l~i~~~ 47 (126)
T PF01592_consen 11 RNPRNYGKLEDADA--GTGEAGNPSCGDEIRIYLKIDDD 47 (126)
T ss_dssp HSTSSBSSSTTTSS--EEEEEEETTTTEEEEEEEEESSS
T ss_pred hCCCCCCCCCCCCc--ceeeecCCCCCCEEEEEEEEecC
Confidence 37888765444321 12223334789999999999984
No 31
>PF02752 Arrestin_C: Arrestin (or S-antigen), C-terminal domain; InterPro: IPR011022 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The C-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=31.53 E-value=53 Score=20.87 Aligned_cols=40 Identities=8% Similarity=0.131 Sum_probs=26.9
Q ss_pred cEEEEEEccCCcccCCceEEEEEEECCCcEEEEeCcccce
Q 034360 12 AVWVYTLTYGGGIVSGDSISCEITVADACTAVLTTQASTK 51 (97)
Q Consensus 12 ~~~vyl~~~sGGl~~GD~l~i~i~v~~ga~l~lTTQaAtK 51 (97)
...+-+.-+.-|+..||.+.+.+++...+...|..=.++-
T Consensus 4 ~i~~~~~i~~~~~~~Ge~i~v~v~i~n~s~~~i~~I~v~L 43 (136)
T PF02752_consen 4 KISLSISIPRTAYVPGETIPVNVEIDNQSKKKIKKIKVSL 43 (136)
T ss_dssp EEEEEEEES-SEEETT--EEEEEEEEE-SSSEEEEEEEEE
T ss_pred EEEEEEEECCCEECCCCEEEEEEEEEECCCCEEEEEEEEE
Confidence 4455666677899999999999999977777766554444
No 32
>PF13464 DUF4115: Domain of unknown function (DUF4115)
Probab=31.32 E-value=1.3e+02 Score=18.33 Aligned_cols=41 Identities=15% Similarity=0.302 Sum_probs=26.2
Q ss_pred CcEEEEEEccCC-----ccc-CCceEEEEEEECCCcEEEEeCcccceee
Q 034360 11 DAVWVYTLTYGG-----GIV-SGDSISCEITVADACTAVLTTQASTKVY 53 (97)
Q Consensus 11 ~~~~vyl~~~sG-----Gl~-~GD~l~i~i~v~~ga~l~lTTQaAtKvy 53 (97)
+.||+-+.+..| |++ .||++++ +.++.-.+.|...++..|+
T Consensus 7 ~~sWv~V~d~dG~~~~~~~l~~G~~~~~--~~~~~~~i~iGna~~v~v~ 53 (77)
T PF13464_consen 7 GDSWVEVTDADGKVLFSGTLKAGETKTF--EGKEPFRIRIGNAGAVEVT 53 (77)
T ss_pred CCeEEEEEeCCCcEeeeeeeCCCcEEEE--eCCCCEEEEEeCCCcEEEE
Confidence 457777776555 444 7777776 5566666666666666655
No 33
>KOG1692 consensus Putative cargo transport protein EMP24 (p24 protein family) [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.59 E-value=1.5e+02 Score=22.44 Aligned_cols=35 Identities=20% Similarity=0.246 Sum_probs=29.5
Q ss_pred cCCceEEEEEEECCC----cEEEEeCcccceeeecCCCC
Q 034360 25 VSGDSISCEITVADA----CTAVLTTQASTKVYKSLGSK 59 (97)
Q Consensus 25 ~~GD~l~i~i~v~~g----a~l~lTTQaAtKvy~~~~~~ 59 (97)
-.||.+.+.+.+.+| -.+.|+.+.-..||+.....
T Consensus 38 ~~gd~~~vsF~v~~gg~~~vd~~I~gP~~~~i~~~~~~s 76 (201)
T KOG1692|consen 38 EEGDKLSVSFEVIDGGFLGVDVEITGPDGKIIHKGKRES 76 (201)
T ss_pred ccCCEEEEEEEEecCCccceeEEEECCCCchhhhccccc
Confidence 479999999999876 45789999999999987653
No 34
>TIGR03444 gshA_related glutamate--cysteine ligase family protein. Members of this bacterial protein family bear homology to glutamate--cysteine ligase, an enzyme in the two-step pathway of glutathione (GSH) biosynthesis, but are distinctly different. Among the bacterial genomes that carry the uncharacterized methyltransferase (TIGR03438) and conserved hypothetical protein TIGR03440, this protein is found in a subset, always in the vicinity of these other genes. Conserved hypothetical protein TIGR03442 is found in these same genomes. The role of this cassette is probably biosynthetic, but the product is unknown.
Probab=28.49 E-value=58 Score=26.83 Aligned_cols=33 Identities=15% Similarity=0.122 Sum_probs=25.8
Q ss_pred cCCcccCCceEEEEEEECCCcEEEEeCcccceeeec
Q 034360 20 YGGGIVSGDSISCEITVADACTAVLTTQASTKVYKS 55 (97)
Q Consensus 20 ~sGGl~~GD~l~i~i~v~~ga~l~lTTQaAtKvy~~ 55 (97)
.+|+.+.|+ ..|+++||+++.|+|.-..-+...
T Consensus 53 ~~~~~lp~g---~~iTlEPGgQvELSt~P~~sl~el 85 (390)
T TIGR03444 53 SPAPPLPGG---SRITVEPGGQLELSGPPADGLTAA 85 (390)
T ss_pred ccCCCCCCC---CeEEeCCCCEEEecCCCCCCHHHH
Confidence 345667777 689999999999999888666554
No 35
>COG0719 SufB Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]
Probab=26.49 E-value=3.5e+02 Score=21.95 Aligned_cols=19 Identities=11% Similarity=0.048 Sum_probs=12.4
Q ss_pred ceEEEEEEECCCcEEEEeC
Q 034360 28 DSISCEITVADACTAVLTT 46 (97)
Q Consensus 28 D~l~i~i~v~~ga~l~lTT 46 (97)
-..++-|.+++||.+++..
T Consensus 162 q~~~~lIiveega~v~~ie 180 (412)
T COG0719 162 QFERTLIIVEEGAEITVIE 180 (412)
T ss_pred eeeeEEEEECCCCEEEEEc
Confidence 4556677777777666553
No 36
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=26.42 E-value=1.4e+02 Score=17.57 Aligned_cols=18 Identities=28% Similarity=0.510 Sum_probs=13.2
Q ss_pred ccCCceEEEEEEECCCcE
Q 034360 24 IVSGDSISCEITVADACT 41 (97)
Q Consensus 24 l~~GD~l~i~i~v~~ga~ 41 (97)
++-||++.+++....+..
T Consensus 41 ~~vGD~V~~~~~~~~~~~ 58 (64)
T cd04451 41 ILPGDRVKVELSPYDLTK 58 (64)
T ss_pred cCCCCEEEEEEeecCCCE
Confidence 578999998887654444
No 37
>cd07694 Ig2_CD4 Second immunoglobulin (Ig) domain of CD4. Ig2_CD4; second immunoglobulin (Ig) domain of CD4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy.
Probab=25.95 E-value=62 Score=21.31 Aligned_cols=36 Identities=8% Similarity=0.088 Sum_probs=25.7
Q ss_pred EccCCcccCCceEEEEEEECCCcE----EEEeCcccceee
Q 034360 18 LTYGGGIVSGDSISCEITVADACT----AVLTTQASTKVY 53 (97)
Q Consensus 18 ~~~sGGl~~GD~l~i~i~v~~ga~----l~lTTQaAtKvy 53 (97)
+++.+=++.||+|++.++..++.. +.-..+.-+.++
T Consensus 5 ~s~~~~lL~G~sLtLtl~~~s~s~p~~~i~w~~P~n~~~~ 44 (88)
T cd07694 5 ATSSDHVLSGTNLTLTLHGSSNSLPAFKVEWRGPGNKSKQ 44 (88)
T ss_pred cCCCCeeecCCcEEEEEecCCCCCCCccEEEeCCCCccce
Confidence 566778899999999999988643 233456555444
No 38
>COG4540 gpV Phage P2 baseplate assembly protein gpV [General function prediction only]
Probab=25.43 E-value=2.3e+02 Score=21.21 Aligned_cols=23 Identities=26% Similarity=0.241 Sum_probs=17.1
Q ss_pred CCCCCCcEEEEEEccCCcccCCceE
Q 034360 6 GSSETDAVWVYTLTYGGGIVSGDSI 30 (97)
Q Consensus 6 ~p~~~~~~~vyl~~~sGGl~~GD~l 30 (97)
.|+..+ .+.+++++||...|+-+
T Consensus 48 ~PsiGE--QV~vl~~~g~~~~~~~l 70 (184)
T COG4540 48 LPSIGE--QVVVLSPSGGEALGGVL 70 (184)
T ss_pred CCCCCc--eEEEEcCCCCcccceEE
Confidence 466666 78899999998766654
No 39
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=24.95 E-value=1.8e+02 Score=18.11 Aligned_cols=28 Identities=29% Similarity=0.576 Sum_probs=17.6
Q ss_pred CCcEEEEEEccCCcccCCceEEEEEEECC
Q 034360 10 TDAVWVYTLTYGGGIVSGDSISCEITVAD 38 (97)
Q Consensus 10 ~~~~~vyl~~~sGGl~~GD~l~i~i~v~~ 38 (97)
++-..||.-+ ...+-.||++++.=.+.+
T Consensus 32 s~gifV~~~~-~~~~~~Gd~V~vtG~v~e 59 (78)
T cd04486 32 SEGIFVYTGS-GADVAVGDLVRVTGTVTE 59 (78)
T ss_pred cceEEEecCC-CCCCCCCCEEEEEEEEEe
Confidence 3444444433 667778888888777765
No 40
>PF03777 DUF320: Small secreted domain (DUF320) ; InterPro: IPR005528 This is a small domain found in a family of streptomyces proteins, which are annotated as 'putative secreted protein'. The domain occurs singly or as a pair and many have two cysteines that may form a disulphide bridge.
Probab=24.72 E-value=63 Score=19.95 Aligned_cols=20 Identities=20% Similarity=0.443 Sum_probs=16.4
Q ss_pred EccCCcccCCceEEEEEEEC
Q 034360 18 LTYGGGIVSGDSISCEITVA 37 (97)
Q Consensus 18 ~~~sGGl~~GD~l~i~i~v~ 37 (97)
-.-|+|+++|+.+.+-|++-
T Consensus 16 a~gSpGv~SGN~vqvPv~vP 35 (60)
T PF03777_consen 16 AAGSPGVLSGNQVQVPVDVP 35 (60)
T ss_pred ecCCCccccCCEEEEEeeCc
Confidence 34589999999999888764
No 41
>PF10632 He_PIG_assoc: He_PIG associated, NEW1 domain of bacterial glycohydrolase; InterPro: IPR019599 This domain has been named NEW1 but its actual function is not known. It is found on proteins which are bacterial galactosidases []. The domain is associated with IPR008009 from INTERPRO, a putative Ig-containing domain.
Probab=24.52 E-value=68 Score=17.13 Aligned_cols=21 Identities=19% Similarity=0.458 Sum_probs=16.5
Q ss_pred CCCCCCCCCCcEEEEEEccCC
Q 034360 2 NPQVGSSETDAVWVYTLTYGG 22 (97)
Q Consensus 2 ~~~~~p~~~~~~~vyl~~~sG 22 (97)
+|+++...|+.+.+|.+-.+|
T Consensus 5 ~~~v~G~rPg~pfl~~IpatG 25 (29)
T PF10632_consen 5 SPRVFGARPGSPFLFTIPATG 25 (29)
T ss_pred cCcEEcccCCCcEEEEeeccC
Confidence 577888888888888887665
No 42
>PF00635 Motile_Sperm: MSP (Major sperm protein) domain; InterPro: IPR000535 Major sperm proteins (MSP) are central components in molecular interactions underlying sperm motility in Caenorhabditis elegans, whose sperm employ an amoebae-like crawling motion using a MSP-containing lamellipod, rather than the flagellar-based swimming motion associated with other sperm. These proteins oligomerise to form an extensive filament system that extends from sperm villipoda, along the leading edge of the pseudopod. About 30 MSP isoforms may exist in C. elegans. MSPs form a fibrous network, whereby MSP dimers form helical subfilaments that coil around one another to produce filaments, which in turn form supercoils to produce bundles. The crystal structure of MSP from C. elegans reveals an immunoglobulin (Ig)-like seven-stranded beta sandwich fold []. ; GO: 0005198 structural molecule activity; PDB: 1MSP_A 3MSP_B 2BVU_B 2MSP_C 1Z9O_F 1Z9L_A 3IKK_A 1WIC_A 2CRI_A 2RR3_A ....
Probab=23.97 E-value=1e+02 Score=19.28 Aligned_cols=24 Identities=29% Similarity=0.476 Sum_probs=16.0
Q ss_pred EEEEccCCccc-CCceEEEEEEECC
Q 034360 15 VYTLTYGGGIV-SGDSISCEITVAD 38 (97)
Q Consensus 15 vyl~~~sGGl~-~GD~l~i~i~v~~ 38 (97)
.|.+.+.-|++ .|+...+.|.+.+
T Consensus 45 ~y~v~P~~G~i~p~~~~~i~I~~~~ 69 (109)
T PF00635_consen 45 RYRVKPSYGIIEPGESVEITITFQP 69 (109)
T ss_dssp TEEEESSEEEE-TTEEEEEEEEE-S
T ss_pred eEEecCCCEEECCCCEEEEEEEEEe
Confidence 45666777777 6777777777665
No 43
>cd03584 NTR_complement_C4 NTR/C345C domain, complement C4 subfamily; The NTR domain found in complement C4 is also known as the C345C domain because it occurs at the C-terminus of complement C3, C4 and C5. Complement C4 is a key player in the activation of the component classical pathway. C4 is cleaved by activated C1 to yield C4a anaphylatoxin, and the larger fragment C4b, an essential component of the C3- and C5-convertase enzymes. C4b binds covalently to the surface of pathogens through a reactive thioester. The role of the NTR/C345C domain in C4 (C4b) is unclear.
Probab=23.72 E-value=58 Score=23.02 Aligned_cols=20 Identities=10% Similarity=0.159 Sum_probs=16.8
Q ss_pred eeCCCceEEEechhhhhhHH
Q 034360 72 IVEERGVASFFDQQKEKKKK 91 (97)
Q Consensus 72 ~ve~gA~Le~lP~~~~~~~~ 91 (97)
.|++++++||.|.+.+-+..
T Consensus 113 ~L~~~tWvE~wP~~~~C~~~ 132 (153)
T cd03584 113 LLDSKTWVEKIPSEKRCKAT 132 (153)
T ss_pred EeCCCceEEECCChHHhcCh
Confidence 59999999999998776643
No 44
>cd03582 NTR_complement_C5 NTR/C345C domain, complement C5 subfamily; The NTR domain found in complement C5 is also known as C345C because it occurs at the C-terminus of complement C3, C4 and C5. Complement C5 is activated by C5 convertase, which itself is a complex between C3b and C3 convertase. The small cleavage fragment, C5a, is the most important small peptide mediator of inflammation, and the larger active fragment, C5b, initiates late events of complement activation. The NTR/C345C domain is important in the function of C5 as it interacts with enzymes that convert C5 to the active form, C5b. The domain has also been found to bind to complement components C6 and C7, and may specifically interact with their factor I modules.
Probab=23.37 E-value=71 Score=22.53 Aligned_cols=21 Identities=0% Similarity=0.050 Sum_probs=17.5
Q ss_pred eeCCCceEEEechhhhhhHHH
Q 034360 72 IVEERGVASFFDQQKEKKKKR 92 (97)
Q Consensus 72 ~ve~gA~Le~lP~~~~~~~~~ 92 (97)
.|++++++||.|.+.+-+.-|
T Consensus 112 ~L~~~TWvE~WP~~~~C~~~~ 132 (150)
T cd03582 112 PLDSEAWIEWWPTDTGCPECQ 132 (150)
T ss_pred EcCCceeEEECCChHHhHHHH
Confidence 599999999999988876533
No 45
>PRK15313 autotransport protein MisL; Provisional
Probab=22.58 E-value=1.6e+02 Score=27.18 Aligned_cols=27 Identities=26% Similarity=0.295 Sum_probs=21.1
Q ss_pred EEEEECCCcEEEEeCcccceeeecCCC
Q 034360 32 CEITVADACTAVLTTQASTKVYKSLGS 58 (97)
Q Consensus 32 i~i~v~~ga~l~lTTQaAtKvy~~~~~ 58 (97)
-.|+|+.++.+..++-++.-||.....
T Consensus 244 ~~~~lg~~~~i~~~~~~~~~iya~~~~ 270 (955)
T PRK15313 244 SLIRLGDDATIETSGASSTGIYAASSS 270 (955)
T ss_pred ceEEecCcceEEEecccceeEecCCce
Confidence 378888888888888888888876543
No 46
>PF11012 DUF2850: Protein of unknown function (DUF2850); InterPro: IPR021271 This family of proteins with unknown function appear to be restricted to Vibrionaceae.
Probab=22.57 E-value=2.2e+02 Score=18.30 Aligned_cols=49 Identities=20% Similarity=0.184 Sum_probs=43.8
Q ss_pred CCcEEEEEEccCCcccCCceEEEEEEECCCcEEEEeCcccceeeecCCCC
Q 034360 10 TDAVWVYTLTYGGGIVSGDSISCEITVADACTAVLTTQASTKVYKSLGSK 59 (97)
Q Consensus 10 ~~~~~vyl~~~sGGl~~GD~l~i~i~v~~ga~l~lTTQaAtKvy~~~~~~ 59 (97)
|-.+..+.++..|=...|--+.-+++.. |..+.+++-+.+.+|...+..
T Consensus 13 ~Ya~e~~~l~~~GV~~ngrlV~T~F~fD-G~~l~~~~G~~~~~y~~~~~~ 61 (79)
T PF11012_consen 13 PYAAEEFTLNESGVFRNGRLVATSFEFD-GKTLEYRTGSGTYRYQISGEN 61 (79)
T ss_pred CccccEEEECCCcEEECCCEEeeEEEEC-CCEEEEEECCeEEEEEEcCCC
Confidence 4456788899999999999999999997 999999999999999998764
No 47
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=21.91 E-value=1e+02 Score=20.52 Aligned_cols=26 Identities=35% Similarity=0.511 Sum_probs=15.4
Q ss_pred ccCCcccC-----CceEEEEEEECCCcEEEEe
Q 034360 19 TYGGGIVS-----GDSISCEITVADACTAVLT 45 (97)
Q Consensus 19 ~~sGGl~~-----GD~l~i~i~v~~ga~l~lT 45 (97)
.+.||+.+ +|+. +.|.+++++.+.+.
T Consensus 51 vT~gGi~G~V~~v~d~~-v~I~l~~~~~i~~~ 81 (97)
T COG1862 51 VTIGGIVGTVTKVGDDT-VEIELGDGTKIKFE 81 (97)
T ss_pred EEcCCeEEEEEEEecCc-EEEEECCCeEEEEE
Confidence 35666654 4433 66666677776654
No 48
>cd03774 MATH_SPOP Speckle-type POZ protein (SPOP) family, MATH domain; composed of proteins with similarity to human SPOP. SPOP was isolated as a novel antigen recognized by serum from a scleroderma patient, whose overexpression in COS cells results in a discrete speckled pattern in the nuclei. It contains an N-terminal MATH domain and a C-terminal BTB (also called POZ) domain. Together with Cul3, SPOP constitutes an ubiquitin E3 ligase which is able to ubiquitinate the PcG protein BMI1, the variant histone macroH2A1 and the death domain-associated protein Daxx. Therefore, SPOP may be involved in the regulation of these proteins and may play a role in transcriptional regulation, apoptosis and X-chromosome inactivation. Cul3 binds to the BTB domain of SPOP whereas Daxx and the macroH2A1 nonhistone region have been shown to bind to the MATH domain. Both MATH and BTB domains are necessary for the nuclear speckled accumulation of SPOP. There are many proteins, mostly uncharacterized, conta
Probab=21.43 E-value=76 Score=21.13 Aligned_cols=20 Identities=20% Similarity=0.350 Sum_probs=15.6
Q ss_pred EccCCcccCCceEEEEEEEC
Q 034360 18 LTYGGGIVSGDSISCEITVA 37 (97)
Q Consensus 18 ~~~sGGl~~GD~l~i~i~v~ 37 (97)
.+...|++.+|.+.|.++|.
T Consensus 116 ~~~~~g~l~dD~l~I~c~I~ 135 (139)
T cd03774 116 LDEANGLLPDDKLTLFCEVS 135 (139)
T ss_pred hhhhcccccCCEEEEEEEEE
Confidence 45567899999999888763
No 49
>cd03775 MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p) family, MATH domain; composed of fungal proteins with similarity to Ubp21p of fission yeast. Ubp21p is a deubiquitinating enzyme that may be involved in the regulation of the protein kinase Prp4p, which controls the formation of active spliceosomes. Members of this family are similar to human HAUSP (Herpesvirus-associated ubiquitin-specific protease) in that they contain an N-terminal MATH domain and a C-terminal catalytic protease (C19 family) domain. HAUSP is also an ubiquitin-specific protease that specifically catalyzes the deubiquitylation of p53 and MDM2. The MATH domain of HAUSP contains the binding site for p53 and MDM2. Similarly, the MATH domain of members in this family may be involved in substrate binding.
Probab=20.46 E-value=1e+02 Score=20.48 Aligned_cols=18 Identities=6% Similarity=0.100 Sum_probs=14.8
Q ss_pred cCCcccCCceEEEEEEEC
Q 034360 20 YGGGIVSGDSISCEITVA 37 (97)
Q Consensus 20 ~sGGl~~GD~l~i~i~v~ 37 (97)
...|.+..|.+.|++.+.
T Consensus 117 ~~~g~l~nD~l~I~~~~~ 134 (134)
T cd03775 117 KPSPFLENGELNITVYVR 134 (134)
T ss_pred CCCceeECCEEEEEEEEC
Confidence 357999999999998763
No 50
>cd00503 Frataxin Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in the mitochondrial matrix suggesting that frataxin is involved in mitochondrial iron homeostasis and possibly in iron transport; the domain has an alpha-beta fold consisting of two helices flanking an antiparallel beta sheet.
Probab=20.32 E-value=1.2e+02 Score=20.14 Aligned_cols=27 Identities=19% Similarity=0.175 Sum_probs=19.5
Q ss_pred EEEEECCCcEEEEeCcccce--eeecCCC
Q 034360 32 CEITVADACTAVLTTQASTK--VYKSLGS 58 (97)
Q Consensus 32 i~i~v~~ga~l~lTTQaAtK--vy~~~~~ 58 (97)
++|+++.+++.+|..|.+.+ ++.++.+
T Consensus 39 Lti~f~~~~~~VINkQ~p~~QIWlaSp~G 67 (105)
T cd00503 39 LTLTFGNGSTIVINRQEPLRQIWLASKVG 67 (105)
T ss_pred EEEEECCCCEEEEeCCchhhhhheecCCC
Confidence 35566799999999888765 5666543
No 51
>KOG1690 consensus emp24/gp25L/p24 family of membrane trafficking proteins [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.00 E-value=91 Score=23.84 Aligned_cols=43 Identities=9% Similarity=0.074 Sum_probs=30.6
Q ss_pred CCcEEEEEEccCCcccCCceEEEEEEECCCcEEEEeCccccee
Q 034360 10 TDAVWVYTLTYGGGIVSGDSISCEITVADACTAVLTTQASTKV 52 (97)
Q Consensus 10 ~~~~~vyl~~~sGGl~~GD~l~i~i~v~~ga~l~lTTQaAtKv 52 (97)
|+.-.+++.+.+++.+.|-.+.+.|++..|-+.-+-.|.+.+.
T Consensus 99 ~GeH~IC~~s~s~awf~~aklRvhld~qvG~~a~l~a~~ke~~ 141 (215)
T KOG1690|consen 99 PGEHRICIQSNSTAWFNGAKLRVHLDIQVGDHANLDAQIKETD 141 (215)
T ss_pred CCceEEEEecccchhhccceEEEEEEEeeCchhhhhhhhhhhh
Confidence 4555677777777888888877777777777776666665543
Done!