Query 028870
Match_columns 202
No_of_seqs 158 out of 236
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 03:51:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028870.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028870hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08294 TIM21: TIM21; InterP 100.0 5.8E-52 1.3E-56 335.1 10.8 142 53-196 1-144 (145)
2 KOG4836 Uncharacterized conser 100.0 5.1E-43 1.1E-47 294.4 7.7 146 50-199 68-213 (215)
3 PF08695 Coa1: Cytochrome oxid 99.7 1.1E-15 2.4E-20 117.9 12.1 106 70-194 7-115 (116)
4 PHA02669 hypothetical protein; 77.2 3.4 7.3E-05 34.9 3.8 37 64-111 7-43 (210)
5 smart00500 SFM Splicing Factor 65.9 2.8 6E-05 27.6 0.7 27 104-132 2-31 (44)
6 COG3944 Capsular polysaccharid 65.8 6.9 0.00015 34.2 3.3 42 65-118 176-217 (226)
7 PF05961 Chordopox_A13L: Chord 63.5 6.2 0.00013 28.4 2.2 22 64-85 5-26 (68)
8 PHA03049 IMV membrane protein; 61.6 7.1 0.00015 28.0 2.2 22 64-85 5-26 (68)
9 PF08799 PRP4: pre-mRNA proces 59.0 2.9 6.3E-05 25.4 -0.1 18 109-126 5-22 (30)
10 PF06905 FAIM1: Fas apoptotic 42.2 1.9E+02 0.0041 24.4 8.1 25 149-176 54-78 (177)
11 PF01006 HCV_NS4a: Hepatitis C 41.0 9 0.0002 26.6 0.0 19 65-83 2-20 (56)
12 PF00630 Filamin: Filamin/ABP2 39.6 1.4E+02 0.003 21.2 6.4 40 139-179 31-77 (101)
13 PF12399 BCA_ABC_TP_C: Branche 39.5 20 0.00044 20.3 1.3 13 99-111 8-20 (23)
14 PRK07118 ferredoxin; Validated 39.1 19 0.00041 32.1 1.7 37 62-112 5-41 (280)
15 PF02342 TerD: TerD domain; I 38.0 65 0.0014 26.0 4.7 40 141-183 132-171 (186)
16 PF10183 ESSS: ESSS subunit of 37.1 53 0.0011 25.0 3.7 55 43-103 43-99 (105)
17 TIGR01944 rnfB electron transp 35.2 29 0.00062 28.3 2.1 27 64-90 5-31 (165)
18 PF06522 B12D: NADH-ubiquinone 35.1 35 0.00077 24.3 2.3 26 63-89 7-32 (73)
19 PF04355 SmpA_OmlA: SmpA / Oml 30.9 1.2E+02 0.0026 20.7 4.5 14 105-118 18-31 (71)
20 PF14927 Neurensin: Neurensin 30.1 61 0.0013 26.4 3.2 52 62-113 48-109 (140)
21 cd06574 TM_PBP1_branched-chain 29.0 57 0.0012 28.2 3.1 23 95-117 145-167 (266)
22 COG4177 LivM ABC-type branched 28.3 46 0.001 30.2 2.4 26 89-117 179-204 (314)
23 PF02982 Scytalone_dh: Scytalo 27.6 1.2E+02 0.0026 25.3 4.6 46 130-183 97-142 (160)
24 cd06974 TerD_like Uncharacteri 27.3 2.4E+02 0.0052 22.2 6.2 46 137-185 106-152 (162)
25 PRK13254 cytochrome c-type bio 26.3 1E+02 0.0022 25.1 3.9 21 65-85 10-30 (148)
26 PF15050 SCIMP: SCIMP protein 25.8 51 0.0011 26.4 2.0 26 65-91 15-40 (133)
27 PRK05113 electron transport co 25.6 58 0.0013 27.3 2.5 24 63-86 6-29 (191)
28 PF09604 Potass_KdpF: F subuni 25.5 73 0.0016 18.5 2.1 10 75-84 10-19 (25)
29 COG2310 TerZ Uncharacterized p 25.5 2.4E+02 0.0051 24.0 6.0 37 146-184 133-171 (182)
30 cd06263 MAM Meprin, A5 protein 25.2 3.2E+02 0.0068 21.0 7.2 52 142-196 71-136 (157)
31 KOG4056 Translocase of outer m 25.2 93 0.002 25.5 3.4 22 64-85 10-31 (143)
32 TIGR03409 urea_trans_UrtB urea 24.8 57 0.0012 28.6 2.3 23 95-117 167-189 (291)
33 TIGR01006 polys_exp_MPA1 polys 24.8 60 0.0013 27.2 2.4 39 68-118 181-219 (226)
34 PF09315 DUF1973: Domain of un 24.6 2.8E+02 0.0061 23.1 6.3 41 134-178 44-84 (179)
35 PLN00063 photosystem II core c 24.2 2.7E+02 0.0058 23.9 6.1 61 49-114 34-94 (194)
36 TIGR00985 3a0801s04tom mitocho 23.8 1.1E+02 0.0023 25.2 3.5 35 65-101 9-43 (148)
37 PF06724 DUF1206: Domain of Un 23.3 66 0.0014 22.4 2.0 25 61-85 45-69 (73)
38 PF10661 EssA: WXG100 protein 23.2 53 0.0011 26.6 1.7 17 70-86 128-144 (145)
39 cd01324 cbb3_Oxidase_CcoQ Cyto 22.8 99 0.0021 20.4 2.6 31 64-100 14-44 (48)
40 PHA03048 IMV membrane protein; 22.6 1.3E+02 0.0028 22.8 3.5 52 62-114 10-61 (93)
41 cd00226 PRCH Photosynthetic re 22.1 1.9E+02 0.0041 25.7 5.0 30 159-191 162-191 (246)
42 PF14167 YfkD: YfkD-like prote 22.0 1.9E+02 0.0041 25.3 4.9 40 153-192 164-203 (232)
43 PRK10692 hypothetical protein; 22.0 1.3E+02 0.0028 22.8 3.4 37 63-99 11-47 (92)
44 TIGR03622 urea_t_UrtB_arc urea 21.6 72 0.0016 27.9 2.3 23 95-117 157-179 (283)
45 TIGR03408 urea_trans_UrtC urea 21.6 64 0.0014 28.7 2.0 22 95-116 191-212 (313)
46 PRK01741 cell division protein 21.5 65 0.0014 29.8 2.1 33 65-100 7-39 (332)
47 PF14029 DUF4244: Protein of u 20.9 56 0.0012 22.6 1.2 23 60-83 17-39 (56)
48 PF06305 DUF1049: Protein of u 20.9 1E+02 0.0022 20.8 2.5 12 93-104 51-62 (68)
49 PF06422 PDR_CDR: CDR ABC tran 20.6 92 0.002 23.5 2.5 25 66-90 53-77 (103)
50 PF12729 4HB_MCP_1: Four helix 20.5 1.6E+02 0.0035 22.1 3.9 46 64-111 12-57 (181)
51 PRK10740 branched-chain amino 20.1 56 0.0012 29.2 1.3 22 95-116 180-201 (308)
No 1
>PF08294 TIM21: TIM21; InterPro: IPR013261 TIM21 interacts with the outer mitochondrial TOM complex and promotes the insertion of proteins into the inner mitochondrial membrane [].; PDB: 2CIU_A.
Probab=100.00 E-value=5.8e-52 Score=335.14 Aligned_cols=142 Identities=39% Similarity=0.653 Sum_probs=78.1
Q ss_pred CceeeeecceehhhhHHHHHHHHHhHhhhhhhhccCCcchHHHHHHHHHHhcchhhHhhhCCCceeccccCc-ccccccc
Q 028870 53 KPVTFTEGASYSLIILAGLGVAGAAAYAVFKELIFEPKEYKIFNKALKRIQDDGQVRVRIGSPITGYGQESR-NRAARQR 131 (202)
Q Consensus 53 K~~~at~~~~~~~vIl~G~gltg~v~Y~l~~ELf~~~s~~~iy~~Al~~ik~d~~V~~~LG~PI~ayG~~s~-~r~~R~r 131 (202)
|++|++++++|++|||+|+||+|+++|+|++|||+++||+.+||+|+++|++||+|+++||+||+|||++++ +||+|||
T Consensus 1 Kv~~~~~~~~~~~vil~G~gl~g~v~Y~l~sELFs~~s~~~ifn~A~~~i~~d~~v~~~LG~~ikayGe~~~~~Rw~R~R 80 (145)
T PF08294_consen 1 KVKRATKQTSYFGVILAGLGLTGLVIYALFSELFSPSSPTRIFNRAVDRIKKDPRVQDLLGEPIKAYGEETGRNRWRRNR 80 (145)
T ss_dssp -------------------------------------HHHHHHHHHHHHHHH-HHHHHHT----EEEE-EEE-SS-EEE-
T ss_pred ChheehcceeeeEeeeehHHHHHHhHHHHhHHHhCCCCchHHHHHHHHHHhcCHHHHHHhCCCeEEecCCCCCCcccccC
Confidence 789999999999999999999999999999999999999999999999999999999999999999999998 8999988
Q ss_pred -ccceEEECCCCceEEEEEEEEEcCCCceEEEEEEEEcCCCCceEEEEEEEEECCCCeeEEEecCC
Q 028870 132 -IPNRVYTDEFGIEHVEVNFYIRGPHGAGKVFTEMFKDKEDKQWKFTYLIVEITSPYKAQLMLESY 196 (202)
Q Consensus 132 -I~~~~~~d~~G~eh~~m~F~V~Gp~g~G~V~le~~k~~~~g~wey~yL~VdV~g~~r~~Iile~~ 196 (202)
+.++.+.|++|++||+|+|||+||+|+|+||+||+|++.+++|||+||+||++|++ +|+|||+
T Consensus 81 ~~~s~~~~d~~G~eh~~m~F~V~G~~~~G~V~~e~~k~~~~~~~e~~yL~vdv~g~~--ri~l~dn 144 (145)
T PF08294_consen 81 PIVSHREYDKDGREHMRMKFYVEGPRGKGVVHLEMVKDDGSGEYEYRYLYVDVPGHK--RIYLEDN 144 (145)
T ss_dssp ---EEEEE-TTS-EEEEEEEEEE-SS-EEEEEEEEE--SS-SS-EEEEEEEE-TTS----EEEE--
T ss_pred CccceEEEcCCCCEEEEEEEEEEeCCCeEEEEEEEEECCCCCCeeEEEEEEecCCCe--EEEEEcC
Confidence 66666779999999999999999999999999999986669999999999999876 8999984
No 2
>KOG4836 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=5.1e-43 Score=294.43 Aligned_cols=146 Identities=30% Similarity=0.580 Sum_probs=138.1
Q ss_pred CCCCceeeeecceehhhhHHHHHHHHHhHhhhhhhhccCCcchHHHHHHHHHHhcchhhHhhhCCCceeccccCcccccc
Q 028870 50 IPEKPVTFTEGASYSLIILAGLGVAGAAAYAVFKELIFEPKEYKIFNKALKRIQDDGQVRVRIGSPITGYGQESRNRAAR 129 (202)
Q Consensus 50 ~~eK~~~at~~~~~~~vIl~G~gltg~v~Y~l~~ELf~~~s~~~iy~~Al~~ik~d~~V~~~LG~PI~ayG~~s~~r~~R 129 (202)
.+.||++++.+++|+.+||+|+||+|+++|+|++|||++++|+.+||+||++|++||+|+.++|++||||||+++ |+||
T Consensus 68 ~~gkVke~s~nt~~~~iVI~GiGv~g~~iY~i~~ElFs~~sp~~ifn~Al~~v~~~~~~~~ifG~~iKgfGE~t~-rgRR 146 (215)
T KOG4836|consen 68 FGGKVKEASSNTFYYIIVIAGIGVTGAFIYAIFGELFSSSSPQTIFNRALELVRANPEVQGIFGESIKGFGEETR-RGRR 146 (215)
T ss_pred CccchhhccccceeeeeeeeeccHHHHhHHHHHHHHhcCCCcHHHHHHHHHHHhcChHHhhHhhhhhhhhhhhhc-Cccc
Confidence 445999999999999999999999999999999999999999999999999999999999999999999999998 6789
Q ss_pred ccccceEEECCCCceEEEEEEEEEcCCCceEEEEEEEEcCCCCceEEEEEEEEECCCCeeEEEecCCCCC
Q 028870 130 QRIPNRVYTDEFGIEHVEVNFYIRGPHGAGKVFTEMFKDKEDKQWKFTYLIVEITSPYKAQLMLESYMPA 199 (202)
Q Consensus 130 ~rI~~~~~~d~~G~eh~~m~F~V~Gp~g~G~V~le~~k~~~~g~wey~yL~VdV~g~~r~~Iile~~~p~ 199 (202)
+||+|..| |+||.+|++|+|||+|.+.+|+|+++++.+ +|+|+|+||+|||++++|.+||+||+-|.
T Consensus 147 ~hVa~~~y-dk~G~~h~~m~Fhv~g~~~~g~v~~~~k~~--~g~~~~~flfVdv~~ypr~tii~~dnr~~ 213 (215)
T KOG4836|consen 147 QHVAHHKY-DKDGMEHLRMQFHVEGSEPQGHVFARLKEV--DGDYEWDFLFVDVARYPRTTIILEDNRVR 213 (215)
T ss_pred ceeeeeee-ecCCceEEEEEEEEEcCCcccchhhhhhcc--CCCCceeEEEEecCCCceeEEEccCCccc
Confidence 99999999 899999999999999999999999999885 78888888999999999999999998654
No 3
>PF08695 Coa1: Cytochrome oxidase complex assembly protein 1; InterPro: IPR014807 Coa1 is an inner mitochondrial membrane protein that associates with Shy1 and is required for cytochrome oxidase complex IV assembly. It contains a conserved hydrophobic segment (amino acids 74-92) with the potential to form a membrane-spanning helix. The N terminus of Coa1 is rich in positively charged amino acids and could form an amphipathic alpha helix, characteristic of a mitochondrial presequence. A cleavage site for the mitochondrial processing peptidase is predicted adjacent to the presequence. Upon in vitro import into mitochondria, Coa1 is processed to a mature form, indicating that it possesses a cleavable presequence []. The eukaryotic cytochrome oxidase complex consists of 12-13 subunits, with three mitochondrial encoded subunits, Cox1-Cox3, forming the core enzyme. Translation of the Cox1 transcript requires the two promoters, Pet309 and Mss51, and the latter has an additional role in translational elongation. Coa1 is necessary for linking the activity of Mss51 to Cox1 insertion into the assembly complex [].
Probab=99.67 E-value=1.1e-15 Score=117.93 Aligned_cols=106 Identities=25% Similarity=0.381 Sum_probs=80.1
Q ss_pred HHHHHHHhHhhhhhhhccCCcchHHHHHHHHHHhcchhhHhhhCC--Cceeccc-cCccccccccccceEEECCCCceEE
Q 028870 70 GLGVAGAAAYAVFKELIFEPKEYKIFNKALKRIQDDGQVRVRIGS--PITGYGQ-ESRNRAARQRIPNRVYTDEFGIEHV 146 (202)
Q Consensus 70 G~gltg~v~Y~l~~ELf~~~s~~~iy~~Al~~ik~d~~V~~~LG~--PI~ayG~-~s~~r~~R~rI~~~~~~d~~G~eh~ 146 (202)
++++++.++|.+..++ +.+.+|+.|++.+++||+|+++||+ ||+.... .+++ ... . ..++
T Consensus 7 ~~~~~~~~~~~~~~~~----~~s~~y~~al~~l~~~~~v~~~LGe~ipi~~~~~~i~G~----------~~~-~--~g~a 69 (116)
T PF08695_consen 7 VIGWGVFLFYAINSEK----KSSEYYKEALEQLRSNPEVVEALGENIPIKDGWPWISGS----------INT-S--KGRA 69 (116)
T ss_pred eHHHHHHHHHHHHHHH----hcCHHHHHHHHHHHhCHHHHHHcCCCCCcccCcccccce----------eec-c--CcEE
Confidence 3344455667777776 6678899999999999999999999 8886442 2331 121 2 4468
Q ss_pred EEEEEEEcCCCceEEEEEEEEcCCCCceEEEEEEEEECCCCeeEEEec
Q 028870 147 EVNFYIRGPHGAGKVFTEMFKDKEDKQWKFTYLIVEITSPYKAQLMLE 194 (202)
Q Consensus 147 ~m~F~V~Gp~g~G~V~le~~k~~~~g~wey~yL~VdV~g~~r~~Iile 194 (202)
.++|+|+||+|+|+||+++.++.....|+|..|.|.++ +.+.|-|-
T Consensus 70 ~~~~pV~G~k~~G~v~~~a~r~~~~~~W~~~~~~v~~~--~g~~I~L~ 115 (116)
T PF08695_consen 70 DLSFPVKGPKGKGTVYVEATRSGGKDPWEILRLEVEID--DGQVIDLL 115 (116)
T ss_pred EEEEEEEcCCCcEEEEEEEEecCCCCceEEEEEEEEeC--CCCEEeCc
Confidence 89999999999999999999975444599999999998 33455553
No 4
>PHA02669 hypothetical protein; Provisional
Probab=77.21 E-value=3.4 Score=34.86 Aligned_cols=37 Identities=30% Similarity=0.399 Sum_probs=27.1
Q ss_pred hhhhHHHHHHHHHhHhhhhhhhccCCcchHHHHHHHHHHhcchhhHhh
Q 028870 64 SLIILAGLGVAGAAAYAVFKELIFEPKEYKIFNKALKRIQDDGQVRVR 111 (202)
Q Consensus 64 ~~vIl~G~gltg~v~Y~l~~ELf~~~s~~~iy~~Al~~ik~d~~V~~~ 111 (202)
.+||++.+.|||+++|+|+ || .-|.+|+.+-.||++-
T Consensus 7 i~iIvavi~LTgAaiYlLi-Ei----------GLAaERanKrsRvK~n 43 (210)
T PHA02669 7 IGIIVAVIYLTGAAIYLLI-EI----------GLAAERANKRSRVKAN 43 (210)
T ss_pred hHHHHHHHHHHHHHHHHHH-HH----------HHHHHHhhhHHHHHHH
Confidence 3578888999999999886 44 4566666666666654
No 5
>smart00500 SFM Splicing Factor Motif, present in Prp18 and Pr04.
Probab=65.88 E-value=2.8 Score=27.61 Aligned_cols=27 Identities=41% Similarity=0.770 Sum_probs=18.6
Q ss_pred cchhhHhh---hCCCceeccccCccccccccc
Q 028870 104 DDGQVRVR---IGSPITGYGQESRNRAARQRI 132 (202)
Q Consensus 104 ~d~~V~~~---LG~PI~ayG~~s~~r~~R~rI 132 (202)
.|.+|+.. ||+||+=|||.... ||+|+
T Consensus 2 ~d~eV~~~LR~lgePi~lFGE~~~~--Rr~RL 31 (44)
T smart00500 2 PDSEVIRRLRELGEPITLFGEDDQE--RRQRL 31 (44)
T ss_pred CHHHHHHHHHHcCCCeeecCCChHH--HHHHH
Confidence 35666544 69999999998754 45553
No 6
>COG3944 Capsular polysaccharide biosynthesis protein [Cell envelope biogenesis, outer membrane]
Probab=65.83 E-value=6.9 Score=34.18 Aligned_cols=42 Identities=26% Similarity=0.468 Sum_probs=35.7
Q ss_pred hhhHHHHHHHHHhHhhhhhhhccCCcchHHHHHHHHHHhcchhhHhhhCCCcee
Q 028870 65 LIILAGLGVAGAAAYAVFKELIFEPKEYKIFNKALKRIQDDGQVRVRIGSPITG 118 (202)
Q Consensus 65 ~vIl~G~gltg~v~Y~l~~ELf~~~s~~~iy~~Al~~ik~d~~V~~~LG~PI~a 118 (202)
.+|-+++||+|++.++++.|++ + ++||.-.++.+.||-|+=|
T Consensus 176 i~iaf~~Gl~~~igiafl~e~l---------D---~tIKs~edie~~l~lPvLG 217 (226)
T COG3944 176 IVIAFLAGLAGAIGIAFLLEYL---------D---KTIKSEEDIEEVLDLPVLG 217 (226)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH---------h---hhcCCHHHHHHhhCCceee
Confidence 4788899999999999999984 1 4788899999999999654
No 7
>PF05961 Chordopox_A13L: Chordopoxvirus A13L protein; InterPro: IPR009236 This family consists of A13L proteins from the Chordopoxviruses. A13L or p8 is one of the three most abundant membrane proteins of the intracellular mature Vaccinia virus [].
Probab=63.52 E-value=6.2 Score=28.36 Aligned_cols=22 Identities=14% Similarity=0.462 Sum_probs=18.2
Q ss_pred hhhhHHHHHHHHHhHhhhhhhh
Q 028870 64 SLIILAGLGVAGAAAYAVFKEL 85 (202)
Q Consensus 64 ~~vIl~G~gltg~v~Y~l~~EL 85 (202)
++++++++++.|+++|+++.--
T Consensus 5 ~iLi~ICVaii~lIlY~iYnr~ 26 (68)
T PF05961_consen 5 FILIIICVAIIGLILYGIYNRK 26 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHhcc
Confidence 4677888889999999998764
No 8
>PHA03049 IMV membrane protein; Provisional
Probab=61.59 E-value=7.1 Score=28.02 Aligned_cols=22 Identities=9% Similarity=0.437 Sum_probs=18.1
Q ss_pred hhhhHHHHHHHHHhHhhhhhhh
Q 028870 64 SLIILAGLGVAGAAAYAVFKEL 85 (202)
Q Consensus 64 ~~vIl~G~gltg~v~Y~l~~EL 85 (202)
+.++++++++.|+++|.+++--
T Consensus 5 ~~l~iICVaIi~lIvYgiYnkk 26 (68)
T PHA03049 5 IILVIICVVIIGLIVYGIYNKK 26 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHhcc
Confidence 4577888999999999998754
No 9
>PF08799 PRP4: pre-mRNA processing factor 4 (PRP4) like; InterPro: IPR014906 This small protein is found on PRP4 ribonuleoproteins. PRP4 is a U4/U6 small nuclear ribonucleoprotein that is involved in pre-mRNA processing. ; PDB: 1MZW_B 2DK4_A.
Probab=59.04 E-value=2.9 Score=25.40 Aligned_cols=18 Identities=33% Similarity=0.660 Sum_probs=10.4
Q ss_pred HhhhCCCceeccccCccc
Q 028870 109 RVRIGSPITGYGQESRNR 126 (202)
Q Consensus 109 ~~~LG~PI~ayG~~s~~r 126 (202)
...||+||+=|||....|
T Consensus 5 LR~lgePi~lFGE~~~~R 22 (30)
T PF08799_consen 5 LRELGEPITLFGETDADR 22 (30)
T ss_dssp HHHCT--SCETT--HHHH
T ss_pred HHhcCCChhhhCCChHHH
Confidence 346899999999987543
No 10
>PF06905 FAIM1: Fas apoptotic inhibitory molecule (FAIM1); InterPro: IPR010695 This family consists of several fas apoptotic inhibitory molecule (FAIM) proteins. FAIM expression is upregulated in B cells by anti-Ig treatment that induces Fas-resistance, and overexpression of FAIM diminishes sensitivity to Fas-mediated apoptosis of B and non-B cell lines. FAIM is highly evolutionarily conserved and is widely expressed in murine tissues, suggesting that FAIM plays an important role in cellular physiology [].; GO: 0043066 negative regulation of apoptosis; PDB: 3MX7_A 2KW1_A 2KD2_A.
Probab=42.20 E-value=1.9e+02 Score=24.38 Aligned_cols=25 Identities=16% Similarity=0.308 Sum_probs=18.3
Q ss_pred EEEEEcCCCceEEEEEEEEcCCCCceEE
Q 028870 149 NFYIRGPHGAGKVFTEMFKDKEDKQWKF 176 (202)
Q Consensus 149 ~F~V~Gp~g~G~V~le~~k~~~~g~wey 176 (202)
.|.|.+.+.+..+.+++.. ...|+|
T Consensus 54 ~F~ig~~~~k~~I~I~~~~---g~~YeY 78 (177)
T PF06905_consen 54 TFTIGGKNTKCEINIEAVS---GFAYEY 78 (177)
T ss_dssp EEEETTTTEEEEEEEEEET---TTEEEE
T ss_pred EEEECCCceEEEEEEEecC---CceEEE
Confidence 5778777778888888864 455665
No 11
>PF01006 HCV_NS4a: Hepatitis C virus non-structural protein NS4a; InterPro: IPR000745 NS4a (non-structural protein) forms an integral part of the NS3 serine protease in Hepatitis C virus, as it is required in a number of cases as a cofactor of cleavage [, ]. It has also been reported that NS4a interacts with NS4b and NS3 to form a multi-subunit replicase complex [].; GO: 0016032 viral reproduction, 0044423 virion part; PDB: 3M5M_C 2FM2_D 3KNX_D 2A4R_B 2F9V_B 2OBQ_B 2O8M_C 3KEE_F 3KF2_C 1NS3_D ....
Probab=40.97 E-value=9 Score=26.56 Aligned_cols=19 Identities=32% Similarity=0.389 Sum_probs=0.0
Q ss_pred hhhHHHHHHHHHhHhhhhh
Q 028870 65 LIILAGLGVAGAAAYAVFK 83 (202)
Q Consensus 65 ~vIl~G~gltg~v~Y~l~~ 83 (202)
.++++|++++++++|++++
T Consensus 2 ~~vlvGg~lAa~aay~~~t 20 (56)
T PF01006_consen 2 PWVLVGGALAALAAYCLTT 20 (56)
T ss_dssp -------------------
T ss_pred cEEEEhHHHHHHHHHHhcc
Confidence 3578899999999998765
No 12
>PF00630 Filamin: Filamin/ABP280 repeat; InterPro: IPR017868 The many different actin cross-linking proteins share a common architecture, consisting of a globular actin-binding domain and an extended rod. Whereas their actin-binding domains consist of two calponin homology domains (see IPR001715 from INTERPRO), their rods fall into three families. The rod domain of the family including the Dictyostelium discoideum (Slime mould) gelation factor (ABP120) and human filamin (ABP280) is constructed from tandem repeats of a 100-residue motif that is glycine and proline rich []. The gelation factor's rod contains 6 copies of the repeat, whereas filamin has a rod constructed from 24 repeats. The resolution of the 3D structure of rod repeats from the gelation factor has shown that they consist of a beta-sandwich, formed by two beta-sheets arranged in an immunoglobulin-like fold [, ]. Because conserved residues that form the core of the repeats are preserved in filamin, the repeat structure should be common to the members of the gelation factor/filamin family. The head to tail homodimerisation is crucial to the function of the ABP120 and ABP280 proteins. This interaction involves a small portion at the distal end of the rod domains. For the gelation factor it has been shown that the carboxy-terminal repeat 6 dimerises through a double edge-to-edge extension of the beta-sheet and that repeat 5 contributes to dimerisation to some extent [, , ].; PDB: 2DI9_A 2EEC_A 2DIC_A 2EEA_A 2DMC_A 2EE9_A 2D7O_A 2D7N_A 2K7P_A 2NQC_A ....
Probab=39.64 E-value=1.4e+02 Score=21.23 Aligned_cols=40 Identities=25% Similarity=0.360 Sum_probs=28.5
Q ss_pred CCCCceEE----EEEEEEEcCCCce---EEEEEEEEcCCCCceEEEEE
Q 028870 139 DEFGIEHV----EVNFYIRGPHGAG---KVFTEMFKDKEDKQWKFTYL 179 (202)
Q Consensus 139 d~~G~eh~----~m~F~V~Gp~g~G---~V~le~~k~~~~g~wey~yL 179 (202)
|..|.... .+++.|.+|.+.. .+.+++.++ .+|.|...|.
T Consensus 31 d~~g~~~~~~~~~~~v~i~~p~~~~~~~~~~~~v~~~-~~G~y~v~y~ 77 (101)
T PF00630_consen 31 DAGGNPVSSGGDEFQVTITSPDGKEEPVPVPVEVIDN-GDGTYTVSYT 77 (101)
T ss_dssp TTTSSBEESTSSEEEEEEESSSSESS--EEEEEEEEE-SSSEEEEEEE
T ss_pred cCCCCccccCCceeEEEEeCCCCCccccccceEEEEC-CCCEEEEEEE
Confidence 45555433 5778899998874 677787665 6799887765
No 13
>PF12399 BCA_ABC_TP_C: Branched-chain amino acid ATP-binding cassette transporter
Probab=39.48 E-value=20 Score=20.34 Aligned_cols=13 Identities=23% Similarity=0.319 Sum_probs=10.8
Q ss_pred HHHHhcchhhHhh
Q 028870 99 LKRIQDDGQVRVR 111 (202)
Q Consensus 99 l~~ik~d~~V~~~ 111 (202)
-+.|.+||+|+++
T Consensus 8 p~~i~~n~~V~~a 20 (23)
T PF12399_consen 8 PEEIRANPEVREA 20 (23)
T ss_pred HHHHhcCHHHHHh
Confidence 4678999999987
No 14
>PRK07118 ferredoxin; Validated
Probab=39.05 E-value=19 Score=32.12 Aligned_cols=37 Identities=16% Similarity=0.264 Sum_probs=27.5
Q ss_pred eehhhhHHHHHHHHHhHhhhhhhhccCCcchHHHHHHHHHHhcchhhHhhh
Q 028870 62 SYSLIILAGLGVAGAAAYAVFKELIFEPKEYKIFNKALKRIQDDGQVRVRI 112 (202)
Q Consensus 62 ~~~~vIl~G~gltg~v~Y~l~~ELf~~~s~~~iy~~Al~~ik~d~~V~~~L 112 (202)
.+.+++|.++|+..+++-.+.+..| .|+.||++.++.
T Consensus 5 ~~~~~~~~~~g~~~g~~l~~a~~~f--------------~v~~d~~~~~i~ 41 (280)
T PRK07118 5 LFAVLSLGALGLVFGILLAFASKKF--------------AVEEDPRVEAVR 41 (280)
T ss_pred HHHHHHHHHHHHHHHHHHHHHeeee--------------eccCCCcHHHHH
Confidence 3456788889998888888888887 456677666654
No 15
>PF02342 TerD: TerD domain; InterPro: IPR003325 This domain is found in tellurite resistance proteins, cAMP binding protein, and chemical-damaging agent resistance proteins and general stress proteins. Tellurium compounds are used in several industrial processes, although they are relatively rare in the environment. Genes associated with tellurite resistance (TeR) are found in many pathogenic bacteria []. The cellular Slime mould, Dictyostelium discoideum, contains a cAMP-binding protein, CABP1, which is composed of two subunits. The C-terminal half of these subunits contain this domain [].; GO: 0006950 response to stress; PDB: 2QNG_A 2QZ7_A 2KXV_A 2KXT_A 3IBZ_A.
Probab=38.00 E-value=65 Score=26.01 Aligned_cols=40 Identities=18% Similarity=0.271 Sum_probs=30.7
Q ss_pred CCceEEEEEEEEEcCCCceEEEEEEEEcCCCCceEEEEEEEEE
Q 028870 141 FGIEHVEVNFYIRGPHGAGKVFTEMFKDKEDKQWKFTYLIVEI 183 (202)
Q Consensus 141 ~G~eh~~m~F~V~Gp~g~G~V~le~~k~~~~g~wey~yL~VdV 183 (202)
.|.+-++..+. ..+..++++..++.+. .+.|+|+-+---.
T Consensus 132 ~~~~~~~~~l~-~~~~~~a~v~~~lyr~--~~~W~~~avg~g~ 171 (186)
T PF02342_consen 132 PGTELARYDLD-DFSGETALVLAELYRR--GGGWKFRAVGQGF 171 (186)
T ss_dssp TTEEEEEEECH-HCTT-SEEEEEEEEEE--TTCEEEEEEEEEE
T ss_pred CcceeEEEecc-CCCCceEEEEEEEEEc--CCeEEEEEEEEec
Confidence 67777775555 6788999999999996 7999998775443
No 16
>PF10183 ESSS: ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) ; InterPro: IPR019329 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry represents the ESSS subunit from mitochondrial NADH:ubiquinone oxidoreductase (complex I). It carries mitochondrial import sequences [].
Probab=37.10 E-value=53 Score=25.03 Aligned_cols=55 Identities=13% Similarity=-0.055 Sum_probs=28.4
Q ss_pred CCCCCcCCCCCcee-eeecceehhhhHHHHHHHHHhHhhhhh-hhccCCcchHHHHHHHHHHh
Q 028870 43 FDAPTYNIPEKPVT-FTEGASYSLIILAGLGVAGAAAYAVFK-ELIFEPKEYKIFNKALKRIQ 103 (202)
Q Consensus 43 ~~~~~l~~~eK~~~-at~~~~~~~vIl~G~gltg~v~Y~l~~-ELf~~~s~~~iy~~Al~~ik 103 (202)
|++.+++.+||... .-+..+|+++.+..+.+ .+++.+. +. ...+..-.+|..+++
T Consensus 43 ~~~~p~~~G~~~d~e~we~~~f~~~~~~~v~~---~~~~~y~PD~---~i~~WA~rEA~~rl~ 99 (105)
T PF10183_consen 43 FGKNPPSPGEKRDWEGWELPFFFGFSGSLVFG---GVFLAYKPDT---SIQTWARREAYRRLE 99 (105)
T ss_pred cCCCCCcCCCcchHhhhHHHHHHHHHHHHHHH---HHHHHcCCCC---CHHHHHHHHHHHHHh
Confidence 45555666666555 45666665543333332 2222222 21 114677788888865
No 17
>TIGR01944 rnfB electron transport complex, RnfABCDGE type, B subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the B subunit.
Probab=35.21 E-value=29 Score=28.26 Aligned_cols=27 Identities=19% Similarity=0.109 Sum_probs=19.8
Q ss_pred hhhhHHHHHHHHHhHhhhhhhhccCCc
Q 028870 64 SLIILAGLGVAGAAAYAVFKELIFEPK 90 (202)
Q Consensus 64 ~~vIl~G~gltg~v~Y~l~~ELf~~~s 90 (202)
.++++.++|+..+++-++.+.+|.=..
T Consensus 5 ~~~~~~~~g~~~~~~l~~~~~~~~ve~ 31 (165)
T TIGR01944 5 AVAALSALGLALGAILGYAARRFPVEA 31 (165)
T ss_pred HHHHHHHHHHHHHHHHHHheeeeeccC
Confidence 456777888888888888888875443
No 18
>PF06522 B12D: NADH-ubiquinone reductase complex 1 MLRQ subunit; InterPro: IPR010530 The MLRQ subunit of mitochondrial NADH-ubiquinone reductase complex I is nuclear [] and is found in plants [], insects, fungi and higher metazoans []. It appears to act within the membrane and, in mammals, is highly expressed in muscle and neural tissue, indicative of a role in ATP generation [].
Probab=35.15 E-value=35 Score=24.32 Aligned_cols=26 Identities=31% Similarity=0.825 Sum_probs=15.0
Q ss_pred ehhhhHHHHHHHHHhHhhhhhhhccCC
Q 028870 63 YSLIILAGLGVAGAAAYAVFKELIFEP 89 (202)
Q Consensus 63 ~~~vIl~G~gltg~v~Y~l~~ELf~~~ 89 (202)
|=+++++|+|+++ ++|+++.-|+..|
T Consensus 7 ~PL~~~vg~a~~~-a~~~~~r~l~~~P 32 (73)
T PF06522_consen 7 YPLFVIVGVAVGG-ATFYLYRLLLTNP 32 (73)
T ss_pred cchHHHHHHHHHH-HHHHHHHHHhcCC
Confidence 3456677777744 4555556654443
No 19
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=30.94 E-value=1.2e+02 Score=20.72 Aligned_cols=14 Identities=43% Similarity=0.582 Sum_probs=10.3
Q ss_pred chhhHhhhCCCcee
Q 028870 105 DGQVRVRIGSPITG 118 (202)
Q Consensus 105 d~~V~~~LG~PI~a 118 (202)
-.+|+.+||.|..-
T Consensus 18 k~qV~~lLG~P~~~ 31 (71)
T PF04355_consen 18 KDQVRALLGSPSLR 31 (71)
T ss_dssp HHHHHHHHTS-SEE
T ss_pred HHHHHHhcCCCCcc
Confidence 36899999999664
No 20
>PF14927 Neurensin: Neurensin
Probab=30.11 E-value=61 Score=26.37 Aligned_cols=52 Identities=25% Similarity=0.330 Sum_probs=30.6
Q ss_pred eehhhhHHHHHHHH-HhHhhhh---------hhhccCCcchHHHHHHHHHHhcchhhHhhhC
Q 028870 62 SYSLIILAGLGVAG-AAAYAVF---------KELIFEPKEYKIFNKALKRIQDDGQVRVRIG 113 (202)
Q Consensus 62 ~~~~vIl~G~gltg-~v~Y~l~---------~ELf~~~s~~~iy~~Al~~ik~d~~V~~~LG 113 (202)
+-.++++.-+|++. .+.|++= .|++.-.+....||.+|++|+----+.=-+|
T Consensus 48 ~i~g~l~Ll~Gi~~l~vgY~vP~~~e~~~~~~~~~~vD~~a~~~n~~Ld~c~laG~~L~~lG 109 (140)
T PF14927_consen 48 FISGLLLLLLGIVALTVGYLVPPKIEVFGEAGEFVVVDSQAARFNNALDTCKLAGLILLCLG 109 (140)
T ss_pred HHHHHHHHHHHHHHHHhhcccCCcceeccccccccccchHHHHHhhhHHHHHHHHHHHHHHH
Confidence 33444444455544 4457663 3333333456789999999987666655555
No 21
>cd06574 TM_PBP1_branched-chain-AA_like Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of monosaccharides including ribose, galactose, and arabinose. These transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. This group includes Escherichia coli LivM and LivH, two TMs which heterodimerize to form the translocation pathway of the E. coli branched-chain AA LIV-1/LS transporter. This transporter is comprised of two TMs (LivM and LivH), two ABCs (LivG and LivF), and one of two alternative PBP
Probab=28.99 E-value=57 Score=28.19 Aligned_cols=23 Identities=13% Similarity=0.303 Sum_probs=21.0
Q ss_pred HHHHHHHHhcchhhHhhhCCCce
Q 028870 95 FNKALKRIQDDGQVRVRIGSPIT 117 (202)
Q Consensus 95 y~~Al~~ik~d~~V~~~LG~PI~ 117 (202)
+.+++..+.+||++.+.+|-+.+
T Consensus 145 ~G~~lrAv~~n~~~A~~~Gi~v~ 167 (266)
T cd06574 145 LGLAMRATGDNPDMARSLGINVD 167 (266)
T ss_pred hchhhhhccCCHHHHHHcCCCHH
Confidence 89999999999999999997643
No 22
>COG4177 LivM ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]
Probab=28.26 E-value=46 Score=30.23 Aligned_cols=26 Identities=27% Similarity=0.471 Sum_probs=22.7
Q ss_pred CcchHHHHHHHHHHhcchhhHhhhCCCce
Q 028870 89 PKEYKIFNKALKRIQDDGQVRVRIGSPIT 117 (202)
Q Consensus 89 ~s~~~iy~~Al~~ik~d~~V~~~LG~PI~ 117 (202)
+|| |.++++-+++|++..+.+|-+..
T Consensus 179 ~S~---~Gr~l~AiRedE~~a~alG~n~~ 204 (314)
T COG4177 179 RSP---FGRALRAIREDEIAARALGINVT 204 (314)
T ss_pred cCC---cchhHhhhccCHHHHHHcCCCHH
Confidence 456 99999999999999999997643
No 23
>PF02982 Scytalone_dh: Scytalone dehydratase; InterPro: IPR004235 Scytalone dehydratase is a member of the group of enzymes involved in fungal melanin biosynthesis. It was first identified in a phytopathogenic fungus, Magnaporthe grisea (Rice blast fungus), which causes rice blast disease. Scytalone dehydratase is a molecular target of inhibitor design efforts aimed at protecting rice plants from fungal disease [, ].; GO: 0030411 scytalone dehydratase activity, 0006582 melanin metabolic process; PDB: 4STD_A 3STD_A 6STD_A 7STD_C 1STD_A 5STD_C 1IDP_B 2STD_A.
Probab=27.63 E-value=1.2e+02 Score=25.26 Aligned_cols=46 Identities=37% Similarity=0.481 Sum_probs=30.2
Q ss_pred ccccceEEECCCCceEEEEEEEEEcCCCceEEEEEEEEcCCCCceEEEEEEEEE
Q 028870 130 QRIPNRVYTDEFGIEHVEVNFYIRGPHGAGKVFTEMFKDKEDKQWKFTYLIVEI 183 (202)
Q Consensus 130 ~rI~~~~~~d~~G~eh~~m~F~V~Gp~g~G~V~le~~k~~~~g~wey~yL~VdV 183 (202)
.|++|++|+|.+..+ +..+ | .|.|+....-+| .+|.|.|.=|.-+|
T Consensus 97 lRaaHqry~D~~~~~-V~~k----G-h~h~~~~h~Y~K--vdG~WK~agl~P~v 142 (160)
T PF02982_consen 97 LRAAHQRYTDDSLTE-VKAK----G-HGHGTNTHWYRK--VDGVWKFAGLKPEV 142 (160)
T ss_dssp EEEEEEEESSTT--S-EEEE----E-EEEEEEEEEEEE--ETTEEEEEEEEEEE
T ss_pred EEeeeeeeeCCCccE-EEee----e-ccceeEEEEEEE--eCCEEEEeeeccce
Confidence 348999997655443 4432 2 356666666666 48999998887766
No 24
>cd06974 TerD_like Uncharacterized proteins involved in stress response, similar to tellurium resistance terD. Tellurium resistance terD like proteins. This family is composed of uncharacterized proteins involved in stress response, such as the tellurium resistance proteins, chemical-damaging agent resistance proteins, and general stress proteins from a variety of organisms. The tellurium resistance proteins are homologous terA,-D,-E,-F,-Z,-X gene products, which confer tellurium resistance mediated by plasmids. Currently, the biochemical mechanism of tellurium resistance remains unknown. The family also contains several ter gene homologues, YceC, YceD, YceE, for which there is no clear evidence for any involvement in the tellurium resistance. A putative cAMP-binding protin CABP1 shows a significant similarity to the terD protein and is also included in this family.
Probab=27.35 E-value=2.4e+02 Score=22.21 Aligned_cols=46 Identities=13% Similarity=0.320 Sum_probs=32.6
Q ss_pred EECCCCceEEEEEEEEEcC-CCceEEEEEEEEcCCCCceEEEEEEEEECC
Q 028870 137 YTDEFGIEHVEVNFYIRGP-HGAGKVFTEMFKDKEDKQWKFTYLIVEITS 185 (202)
Q Consensus 137 ~~d~~G~eh~~m~F~V~Gp-~g~G~V~le~~k~~~~g~wey~yL~VdV~g 185 (202)
..+.++ ....++|.+... ..++.+.+|..+. .+.|+|+.+---.++
T Consensus 106 l~~~~~-~~~~~~~~l~~~~~~~a~i~~elyr~--~~~Wk~~avg~g~~~ 152 (162)
T cd06974 106 LVDAGG-NTELARYDLTEDSGETALILAELYRR--NGEWKFRAVGQGFNG 152 (162)
T ss_pred EEECCC-CeEEEEEECCCCCCcEEEEEEEEEEE--CCeEEEEEeccccCC
Confidence 434443 345666777775 7899999999996 699999877554443
No 25
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=26.28 E-value=1e+02 Score=25.13 Aligned_cols=21 Identities=43% Similarity=0.512 Sum_probs=13.7
Q ss_pred hhhHHHHHHHHHhHhhhhhhh
Q 028870 65 LIILAGLGVAGAAAYAVFKEL 85 (202)
Q Consensus 65 ~vIl~G~gltg~v~Y~l~~EL 85 (202)
.++++++.+.++++|+++..|
T Consensus 10 ~~~~~~~~~~~~~~~L~~~a~ 30 (148)
T PRK13254 10 LIILGALAALGLAVALVLYAL 30 (148)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 455566666667777777765
No 26
>PF15050 SCIMP: SCIMP protein
Probab=25.76 E-value=51 Score=26.44 Aligned_cols=26 Identities=27% Similarity=0.345 Sum_probs=19.8
Q ss_pred hhhHHHHHHHHHhHhhhhhhhccCCcc
Q 028870 65 LIILAGLGVAGAAAYAVFKELIFEPKE 91 (202)
Q Consensus 65 ~vIl~G~gltg~v~Y~l~~ELf~~~s~ 91 (202)
.||+++++| |+++|++.+-+|-.-+.
T Consensus 15 aII~vS~~l-glIlyCvcR~~lRqGkk 40 (133)
T PF15050_consen 15 AIILVSVVL-GLILYCVCRWQLRQGKK 40 (133)
T ss_pred HHHHHHHHH-HHHHHHHHHHHHHcccc
Confidence 367778887 89999999988655444
No 27
>PRK05113 electron transport complex protein RnfB; Provisional
Probab=25.65 E-value=58 Score=27.28 Aligned_cols=24 Identities=13% Similarity=0.033 Sum_probs=16.8
Q ss_pred ehhhhHHHHHHHHHhHhhhhhhhc
Q 028870 63 YSLIILAGLGVAGAAAYAVFKELI 86 (202)
Q Consensus 63 ~~~vIl~G~gltg~v~Y~l~~ELf 86 (202)
..++++.++|+..+++-.+.+..|
T Consensus 6 ~~~~~~~~lg~~~g~~l~~a~~~~ 29 (191)
T PRK05113 6 IAVAALSLLALVFGAILGFASRRF 29 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCc
Confidence 345677778877777777777765
No 28
>PF09604 Potass_KdpF: F subunit of K+-transporting ATPase (Potass_KdpF); InterPro: IPR011726 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the F subunit (KdpF) of a P-type K+-translocating ATPase (Kdp). KdpF is a very small integral membrane peptide. The kdpABC operon of Escherichia coli codes for the high affinity K+-translocating Kdp complex []. KdpF is found upstream of the KdpA subunit (IPR004623 from INTERPRO). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation. More information about this protein can be found at Protein of the Month: ATP Synthases [].
Probab=25.49 E-value=73 Score=18.50 Aligned_cols=10 Identities=10% Similarity=0.192 Sum_probs=4.5
Q ss_pred HHhHhhhhhh
Q 028870 75 GAAAYAVFKE 84 (202)
Q Consensus 75 g~v~Y~l~~E 84 (202)
+.++|+++.=
T Consensus 10 ~L~~YL~~aL 19 (25)
T PF09604_consen 10 ALFVYLFYAL 19 (25)
T ss_pred HHHHHHHHHH
Confidence 4444544443
No 29
>COG2310 TerZ Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms]
Probab=25.48 E-value=2.4e+02 Score=24.02 Aligned_cols=37 Identities=14% Similarity=0.385 Sum_probs=28.6
Q ss_pred EEEEEEEEc--CCCceEEEEEEEEcCCCCceEEEEEEEEEC
Q 028870 146 VEVNFYIRG--PHGAGKVFTEMFKDKEDKQWKFTYLIVEIT 184 (202)
Q Consensus 146 ~~m~F~V~G--p~g~G~V~le~~k~~~~g~wey~yL~VdV~ 184 (202)
...+|.+.+ ...++++.+|..+. +++|+|+-+--=..
T Consensus 133 el~ry~Ls~d~~~etavi~~eLyR~--~~~Wkf~AvGqg~~ 171 (182)
T COG2310 133 ELARYDLSEDFSQETAVILGELYRH--NGEWKFTAVGQGFN 171 (182)
T ss_pred EEEEEEccccccceeeEEEEEEEEc--CCeEEEEEEeeccC
Confidence 345577887 56799999999996 79999988765443
No 30
>cd06263 MAM Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region.
Probab=25.21 E-value=3.2e+02 Score=20.96 Aligned_cols=52 Identities=13% Similarity=0.235 Sum_probs=29.6
Q ss_pred CceEEEEEEEEEcCCCceEEEEEEEEcCC-------------CCceEEEEEEEEECCC-CeeEEEecCC
Q 028870 142 GIEHVEVNFYIRGPHGAGKVFTEMFKDKE-------------DKQWKFTYLIVEITSP-YKAQLMLESY 196 (202)
Q Consensus 142 G~eh~~m~F~V~Gp~g~G~V~le~~k~~~-------------~g~wey~yL~VdV~g~-~r~~Iile~~ 196 (202)
+.--+.+.+|..|+. .|.+.|.+..+.. ...|. ...|++... ++-+|++|-.
T Consensus 71 ~~~Cl~F~y~~~g~~-~g~L~V~v~~~~~~~~~~lw~~~~~~~~~W~--~~~v~l~~~~~~fqi~fe~~ 136 (157)
T cd06263 71 SSHCLSFWYHMYGSG-VGTLNVYVREEGGGLGTLLWSASGGQGNQWQ--EAEVTLSASSKPFQVVFEGV 136 (157)
T ss_pred CCeEEEEEEEecCCC-CCeEEEEEEeCCCCcceEEEEEECCCCCeeE--EEEEEECCCCCceEEEEEEE
Confidence 333456666666764 5666666655422 13344 455666654 6777877654
No 31
>KOG4056 consensus Translocase of outer mitochondrial membrane complex, subunit TOM20 [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.20 E-value=93 Score=25.47 Aligned_cols=22 Identities=18% Similarity=0.377 Sum_probs=18.6
Q ss_pred hhhhHHHHHHHHHhHhhhhhhh
Q 028870 64 SLIILAGLGVAGAAAYAVFKEL 85 (202)
Q Consensus 64 ~~vIl~G~gltg~v~Y~l~~EL 85 (202)
.++|++|++.+.++.|+|+.+-
T Consensus 10 ~~vI~agiag~af~gYciYFd~ 31 (143)
T KOG4056|consen 10 TSVIAAGIAGLAFIGYCIYFDK 31 (143)
T ss_pred hHHHHHHHHHHHHHHHHhhccc
Confidence 4688889888899999999874
No 32
>TIGR03409 urea_trans_UrtB urea ABC transporter, permease protein UrtB. Members of this protein family are ABC transporter permease proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.
Probab=24.80 E-value=57 Score=28.61 Aligned_cols=23 Identities=4% Similarity=0.200 Sum_probs=21.0
Q ss_pred HHHHHHHHhcchhhHhhhCCCce
Q 028870 95 FNKALKRIQDDGQVRVRIGSPIT 117 (202)
Q Consensus 95 y~~Al~~ik~d~~V~~~LG~PI~ 117 (202)
+.+++..+.+||+..+++|-+.+
T Consensus 167 ~G~~lrAi~~n~~aA~~~Gi~v~ 189 (291)
T TIGR03409 167 LGLRVRAVTQNRVMAAALGINTR 189 (291)
T ss_pred hhHhheeeeCCHHHHHHcCCCHH
Confidence 89999999999999999998643
No 33
>TIGR01006 polys_exp_MPA1 polysaccharide export protein, MPA1 family, Gram-positive type. This family contains members from Low GC Gram-positive bacteria; they are proposed to have a function in the export of complex polysaccharides.
Probab=24.76 E-value=60 Score=27.21 Aligned_cols=39 Identities=26% Similarity=0.353 Sum_probs=27.4
Q ss_pred HHHHHHHHHhHhhhhhhhccCCcchHHHHHHHHHHhcchhhHhhhCCCcee
Q 028870 68 LAGLGVAGAAAYAVFKELIFEPKEYKIFNKALKRIQDDGQVRVRIGSPITG 118 (202)
Q Consensus 68 l~G~gltg~v~Y~l~~ELf~~~s~~~iy~~Al~~ik~d~~V~~~LG~PI~a 118 (202)
-+.+|+..+++++++.|+| + +++++..++.+.+|-|+=|
T Consensus 181 g~~~G~~~~~~~~~~~~~~---------d---~~i~~~~d~~~~~~~~vlg 219 (226)
T TIGR01006 181 GFLLGLVVALIIVLLKELL---------D---TRVKRPEDVEDVLGMTLLG 219 (226)
T ss_pred HHHHHHHHHHHHHHHHHHH---------h---CCcCCHHHHHHHcCCCeEE
Confidence 3345666677888889985 1 3567788888889888643
No 34
>PF09315 DUF1973: Domain of unknown function (DUF1973); InterPro: IPR015394 These functionally uncharacterised domains are found in various eukaryotic calcium-dependent chloride channels.
Probab=24.65 E-value=2.8e+02 Score=23.08 Aligned_cols=41 Identities=15% Similarity=0.189 Sum_probs=24.8
Q ss_pred ceEEECCCCceEEEEEEEEEcCCCceEEEEEEEEcCCCCceEEEE
Q 028870 134 NRVYTDEFGIEHVEVNFYIRGPHGAGKVFTEMFKDKEDKQWKFTY 178 (202)
Q Consensus 134 ~~~~~d~~G~eh~~m~F~V~Gp~g~G~V~le~~k~~~~g~wey~y 178 (202)
.....|++|..+.. |.+.-. ..++++.+-...+.|.|.|..
T Consensus 44 ~i~L~~P~G~~~~~--~~~d~~--~~~~~i~ipg~ae~G~W~y~i 84 (179)
T PF09315_consen 44 SITLTDPSGTVYTT--FTTDSN--SKTARIQIPGTAEVGTWTYSI 84 (179)
T ss_pred eEEEECCCCCEEee--eEEccc--ccEEEEECCCCcccccEEEEE
Confidence 34566788887766 555533 344444442223579999977
No 35
>PLN00063 photosystem II core complex proteins psbY; Provisional
Probab=24.24 E-value=2.7e+02 Score=23.86 Aligned_cols=61 Identities=18% Similarity=0.126 Sum_probs=32.7
Q ss_pred CCCCCceeeeecceehhhhHHHHHHHHHhHhhhhhhhccCCcchHHHHHHHHHHhcchhhHhhhCC
Q 028870 49 NIPEKPVTFTEGASYSLIILAGLGVAGAAAYAVFKELIFEPKEYKIFNKALKRIQDDGQVRVRIGS 114 (202)
Q Consensus 49 ~~~eK~~~at~~~~~~~vIl~G~gltg~v~Y~l~~ELf~~~s~~~iy~~Al~~ik~d~~V~~~LG~ 114 (202)
++.+|++..+-.....--.++|++++|.++ +-| .++.+-..-.+..+....|-|+.-+|..
T Consensus 34 ~~~~~pk~~~~~~~~~~~~v~~~~laga~~----s~l-~~~~~A~AAq~ia~~A~~D~R~liVl~P 94 (194)
T PLN00063 34 SMQNKPKGLTISKSADNTNVAGTAIAGAIF----SAL-SSSEPALAAQQIAELAEGDNRGLALLLP 94 (194)
T ss_pred cccccccccccccccchhHHHHHHHHHHHH----Hhh-cCCcHHHHHHHHHHHhccCcccchhHHH
Confidence 445555543322222323578899877543 334 2333333334555556678888777743
No 36
>TIGR00985 3a0801s04tom mitochondrial import receptor subunit translocase of outer membrane 20 kDa subunit.
Probab=23.78 E-value=1.1e+02 Score=25.16 Aligned_cols=35 Identities=29% Similarity=0.534 Sum_probs=22.8
Q ss_pred hhhHHHHHHHHHhHhhhhhhhccCCcchHHHHHHHHH
Q 028870 65 LIILAGLGVAGAAAYAVFKELIFEPKEYKIFNKALKR 101 (202)
Q Consensus 65 ~vIl~G~gltg~v~Y~l~~ELf~~~s~~~iy~~Al~~ 101 (202)
..+++|++.++++.|+|+-+= .-....-|.+-|.+
T Consensus 9 ~~~~ag~a~~~flgYciYFD~--KRR~dPdFRkkLr~ 43 (148)
T TIGR00985 9 VVIAAGIAAAAFLGYAIYFDY--KRRNDPDFRKKLRR 43 (148)
T ss_pred HHHHHHHHHHHHHHHHHhhhh--hhccCHHHHHHHHH
Confidence 456677788888889998663 22234457666643
No 37
>PF06724 DUF1206: Domain of Unknown Function (DUF1206); InterPro: IPR009597 This region consists of two a pair of transmembrane helices and occurs three times in each of the family member proteins.
Probab=23.28 E-value=66 Score=22.43 Aligned_cols=25 Identities=24% Similarity=0.343 Sum_probs=18.6
Q ss_pred ceehhhhHHHHHHHHHhHhhhhhhh
Q 028870 61 ASYSLIILAGLGVAGAAAYAVFKEL 85 (202)
Q Consensus 61 ~~~~~vIl~G~gltg~v~Y~l~~EL 85 (202)
.+..+++++|+|+.+..+|.++.-+
T Consensus 45 ~G~~ll~~vg~gli~~gi~~~~~a~ 69 (73)
T PF06724_consen 45 FGRWLLGAVGLGLIGYGIWQFVKAV 69 (73)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4446788889999888888876543
No 38
>PF10661 EssA: WXG100 protein secretion system (Wss), protein EssA; InterPro: IPR018920 The Wss (WXG100 protein secretion system) in Staphylococcus aureus seems to be encoded by a locus of eight ORFs, called ess (eSAT-6 secretion system) []. This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with YukC and YukAB. Proteins homologous to EssA, YukC, EsaA and YukD were absent from mycobacteria []. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions.
Probab=23.23 E-value=53 Score=26.65 Aligned_cols=17 Identities=18% Similarity=0.194 Sum_probs=11.8
Q ss_pred HHHHHHHhHhhhhhhhc
Q 028870 70 GLGVAGAAAYAVFKELI 86 (202)
Q Consensus 70 G~gltg~v~Y~l~~ELf 86 (202)
.+.+.++++|.+++-+|
T Consensus 128 ~ll~i~~giy~~~r~~~ 144 (145)
T PF10661_consen 128 ILLAICGGIYVVLRKVW 144 (145)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 34455788899888764
No 39
>cd01324 cbb3_Oxidase_CcoQ Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Found exclusively in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized function in microaerobic energy metabolism. The cbb3 operon contains four genes (ccoNOQP or fixNOQP), with ccoN coding for subunit I. Instead of a CuA-containing subunit II analogous to other cytochrome oxidases, cbb3 utilizes subunits ccoO and ccoP, which contain one and two hemes, respectively, to transfer electrons to the binuclear center. ccoQ, the fourth subunit, is a single transmembrane helix protein. It has been shown to protect the core complex from proteolytic degradation by serine proteases. See cd00919, cd01322
Probab=22.77 E-value=99 Score=20.43 Aligned_cols=31 Identities=26% Similarity=0.381 Sum_probs=18.1
Q ss_pred hhhhHHHHHHHHHhHhhhhhhhccCCcchHHHHHHHH
Q 028870 64 SLIILAGLGVAGAAAYAVFKELIFEPKEYKIFNKALK 100 (202)
Q Consensus 64 ~~vIl~G~gltg~v~Y~l~~ELf~~~s~~~iy~~Al~ 100 (202)
++++++.+...|+++|+ +.|+....|++|-.
T Consensus 14 ~~l~~~~~~Figiv~wa------~~p~~k~~f~eaa~ 44 (48)
T cd01324 14 WGLLYLALFFLGVVVWA------FRPGRKKAFDEAAN 44 (48)
T ss_pred HHHHHHHHHHHHHHHHH------hCCCcchhHHHHHc
Confidence 34444445555666666 45666677777743
No 40
>PHA03048 IMV membrane protein; Provisional
Probab=22.58 E-value=1.3e+02 Score=22.85 Aligned_cols=52 Identities=19% Similarity=0.197 Sum_probs=32.2
Q ss_pred eehhhhHHHHHHHHHhHhhhhhhhccCCcchHHHHHHHHHHhcchhhHhhhCC
Q 028870 62 SYSLIILAGLGVAGAAAYAVFKELIFEPKEYKIFNKALKRIQDDGQVRVRIGS 114 (202)
Q Consensus 62 ~~~~vIl~G~gltg~v~Y~l~~ELf~~~s~~~iy~~Al~~ik~d~~V~~~LG~ 114 (202)
-|++++++|+.|..+..-+-|-|+ ++++++..-=||+..+-==--..-.||-
T Consensus 10 y~S~vli~GIiLL~~aCIfAfidf-sK~k~~~~~wRalsii~FIlgivl~lG~ 61 (93)
T PHA03048 10 YFSTALIGGIILLAASCIFAFVDF-SKNKATVTVWRALSGIAFVLGIVMTIGM 61 (93)
T ss_pred ccchHHHHHHHHHHHHHHHhhhhh-hcCCCcchhHHHHHHHHHHHHHHHHHHH
Confidence 356678888887777777777886 7777765445666655433333334443
No 41
>cd00226 PRCH Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce ATP by ATP synthase. Subunit H is positioned mainly in the cytoplasm with one transmembrane alpha helix. Provides proton transfer pathway (water channels) connecting the terminal quinone electron acceptor of RC, to the aqueous phase. Found in photosynthetic bacteria: alpha, beta, and gamma proteobacteria.
Probab=22.10 E-value=1.9e+02 Score=25.73 Aligned_cols=30 Identities=30% Similarity=0.342 Sum_probs=20.1
Q ss_pred eEEEEEEEEcCCCCceEEEEEEEEECCCCeeEE
Q 028870 159 GKVFTEMFKDKEDKQWKFTYLIVEITSPYKAQL 191 (202)
Q Consensus 159 G~V~le~~k~~~~g~wey~yL~VdV~g~~r~~I 191 (202)
|+|.=-.+. .++|..|||.||+.+..|+.+
T Consensus 162 GtV~Dv~vD---~~e~~iRYLeVdtg~~gkkVL 191 (246)
T cd00226 162 GKVTDLWVD---RPEQLFRYLEVELAGGGRTVL 191 (246)
T ss_pred EEEEEEEEc---CCcceEEEEEEEcCCCCCEEE
Confidence 555544444 589999999999964234433
No 42
>PF14167 YfkD: YfkD-like protein
Probab=21.98 E-value=1.9e+02 Score=25.32 Aligned_cols=40 Identities=10% Similarity=0.117 Sum_probs=31.9
Q ss_pred EcCCCceEEEEEEEEcCCCCceEEEEEEEEECCCCeeEEE
Q 028870 153 RGPHGAGKVFTEMFKDKEDKQWKFTYLIVEITSPYKAQLM 192 (202)
Q Consensus 153 ~Gp~g~G~V~le~~k~~~~g~wey~yL~VdV~g~~r~~Ii 192 (202)
--|+..|..|+.+-.-++.|+-.|--.|++++|.++..+|
T Consensus 164 v~pk~~GyL~aYaPAVnEkGkvtyGEVYl~lKG~kk~lvv 203 (232)
T PF14167_consen 164 VPPKKLGYLYAYAPAVNEKGKVTYGEVYLVLKGNKKKLVV 203 (232)
T ss_pred cCccceeeEEEechhhcccCceeEEEEEEEEeCCccEEEE
Confidence 3577888888887666678999999999999998766655
No 43
>PRK10692 hypothetical protein; Provisional
Probab=21.96 E-value=1.3e+02 Score=22.80 Aligned_cols=37 Identities=16% Similarity=0.064 Sum_probs=21.8
Q ss_pred ehhhhHHHHHHHHHhHhhhhhhhccCCcchHHHHHHH
Q 028870 63 YSLIILAGLGVAGAAAYAVFKELIFEPKEYKIFNKAL 99 (202)
Q Consensus 63 ~~~vIl~G~gltg~v~Y~l~~ELf~~~s~~~iy~~Al 99 (202)
|..+.|.=+.+.+++.|.|++++|.=+=|.-..+-|+
T Consensus 11 N~lMglGmv~Mv~gigysi~~~i~~L~Lp~~~~~gal 47 (92)
T PRK10692 11 NVLMGLGLVVMVVGVGYSILNQLPQLNLPQFFAHGAL 47 (92)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhcccCCchHHHHhhHH
Confidence 3333333344457889999999954333655545444
No 44
>TIGR03622 urea_t_UrtB_arc urea ABC transporter, permease protein UrtB. Members of this protein family are ABC transporter permease subunits restricted to the Archaea. Several lines of evidence suggest this protein is functionally analogous, as well as homologous, to the UrtB subunit of the Corynebacterium glutamicum urea transporter. All members of the operon show sequence similarity to urea transport subunits, the gene is located near the urease structural subunits in two of three species, and partial phylogenetic profiling identifies this permease subunit as closely matching the profile of urea utilization.
Probab=21.62 E-value=72 Score=27.87 Aligned_cols=23 Identities=13% Similarity=0.187 Sum_probs=21.0
Q ss_pred HHHHHHHHhcchhhHhhhCCCce
Q 028870 95 FNKALKRIQDDGQVRVRIGSPIT 117 (202)
Q Consensus 95 y~~Al~~ik~d~~V~~~LG~PI~ 117 (202)
+.+++.-+.+||+..+.+|-+.+
T Consensus 157 ~Gr~lrAv~~n~~aA~~~Gi~v~ 179 (283)
T TIGR03622 157 FGVRARATIQDPETARAMGVDTD 179 (283)
T ss_pred HhHhheeeeCCHHHHHHcCCCHH
Confidence 89999999999999999998743
No 45
>TIGR03408 urea_trans_UrtC urea ABC transporter, permease protein UrtC. Members of this protein family are ABC transporter permease proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.
Probab=21.59 E-value=64 Score=28.69 Aligned_cols=22 Identities=23% Similarity=0.249 Sum_probs=20.6
Q ss_pred HHHHHHHHhcchhhHhhhCCCc
Q 028870 95 FNKALKRIQDDGQVRVRIGSPI 116 (202)
Q Consensus 95 y~~Al~~ik~d~~V~~~LG~PI 116 (202)
+.+++..+++||+..+.+|-+.
T Consensus 191 ~Gr~l~Ai~~n~~aA~~~Gi~v 212 (313)
T TIGR03408 191 FGRVLIAIRDAENRVRFLGYDP 212 (313)
T ss_pred hhhhheeecCCHHHHHHcCCCH
Confidence 8999999999999999999764
No 46
>PRK01741 cell division protein ZipA; Provisional
Probab=21.48 E-value=65 Score=29.81 Aligned_cols=33 Identities=24% Similarity=0.331 Sum_probs=23.5
Q ss_pred hhhHHHHHHHHHhHhhhhhhhccCCcchHHHHHHHH
Q 028870 65 LIILAGLGVAGAAAYAVFKELIFEPKEYKIFNKALK 100 (202)
Q Consensus 65 ~vIl~G~gltg~v~Y~l~~ELf~~~s~~~iy~~Al~ 100 (202)
++||++++|.++|++.||+-= -..+++|+.|..
T Consensus 7 liILg~lal~~Lv~hgiWsnR---rEKSqyF~n~~t 39 (332)
T PRK01741 7 LIILGILALVALVAHGIWSNR---REKSQYFSNANT 39 (332)
T ss_pred HHHHHHHHHHHHHHhhhhhhh---hHHHHhhhcccc
Confidence 478888999999988887642 114677776665
No 47
>PF14029 DUF4244: Protein of unknown function (DUF4244)
Probab=20.92 E-value=56 Score=22.60 Aligned_cols=23 Identities=35% Similarity=0.469 Sum_probs=14.4
Q ss_pred cceehhhhHHHHHHHHHhHhhhhh
Q 028870 60 GASYSLIILAGLGVAGAAAYAVFK 83 (202)
Q Consensus 60 ~~~~~~vIl~G~gltg~v~Y~l~~ 83 (202)
++=|.+..+++++++|+ +|.+.+
T Consensus 17 TaEYAvgtlAA~afA~v-L~~vvt 39 (56)
T PF14029_consen 17 TAEYAVGTLAAAAFAGV-LYKVVT 39 (56)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHhc
Confidence 44566777788888554 555543
No 48
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.90 E-value=1e+02 Score=20.79 Aligned_cols=12 Identities=25% Similarity=0.576 Sum_probs=5.3
Q ss_pred HHHHHHHHHHhc
Q 028870 93 KIFNKALKRIQD 104 (202)
Q Consensus 93 ~iy~~Al~~ik~ 104 (202)
.-.++.++++++
T Consensus 51 ~~~~k~l~~le~ 62 (68)
T PF06305_consen 51 RRLRKELKKLEK 62 (68)
T ss_pred HHHHHHHHHHHH
Confidence 334444444443
No 49
>PF06422 PDR_CDR: CDR ABC transporter; InterPro: IPR010929 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). In yeast, the PDR and CDR ABC transporters display extensive sequence homology, and confer resistance to several anti-fungal compounds by actively transporting their substrates out of the cell. These transporters have two homologous halves, each with an N-terminal intracellular hydrophilic region that contains an ATP-binding site, followed by a C-terminal membrane-associated region containing six transmembrane segments []. This entry represents a domain of the PDR/CDR ABC transporter comprising extracellular loop 3, transmembrane segment 6 and a linker region.; GO: 0005524 ATP binding, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0006810 transport, 0016021 integral to membrane
Probab=20.58 E-value=92 Score=23.46 Aligned_cols=25 Identities=20% Similarity=-0.044 Sum_probs=20.4
Q ss_pred hhHHHHHHHHHhHhhhhhhhccCCc
Q 028870 66 IILAGLGVAGAAAYAVFKELIFEPK 90 (202)
Q Consensus 66 vIl~G~gltg~v~Y~l~~ELf~~~s 90 (202)
.||+|+.++-.++++++.|++...+
T Consensus 53 GIli~f~i~f~~~~~~~~e~~~~~~ 77 (103)
T PF06422_consen 53 GILIAFWIFFIVLTLLATEFIKFEK 77 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcccC
Confidence 5778888888899999999975554
No 50
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=20.48 E-value=1.6e+02 Score=22.10 Aligned_cols=46 Identities=15% Similarity=0.173 Sum_probs=26.9
Q ss_pred hhhhHHHHHHHHHhHhhhhhhhccCCcchHHHHHHHHHHhcchhhHhh
Q 028870 64 SLIILAGLGVAGAAAYAVFKELIFEPKEYKIFNKALKRIQDDGQVRVR 111 (202)
Q Consensus 64 ~~vIl~G~gltg~v~Y~l~~ELf~~~s~~~iy~~Al~~ik~d~~V~~~ 111 (202)
++++++.+++.|++.+.-.+.+- ..-..+|+..+..+..=.++...
T Consensus 12 f~~~~~l~~~~~~~~~~~l~~~~--~~~~~i~~~~~~~~~~~~~~~~~ 57 (181)
T PF12729_consen 12 FGLIILLLLIVGIVGLYSLSQIN--QNVEEIYENNLPSIELLNDIRSN 57 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhhhHHHHHHHHHHHH
Confidence 45566666666777777777761 12356677766665544444433
No 51
>PRK10740 branched-chain amino acid transporter permease subunit LivH; Reviewed
Probab=20.07 E-value=56 Score=29.17 Aligned_cols=22 Identities=14% Similarity=0.226 Sum_probs=20.6
Q ss_pred HHHHHHHHhcchhhHhhhCCCc
Q 028870 95 FNKALKRIQDDGQVRVRIGSPI 116 (202)
Q Consensus 95 y~~Al~~ik~d~~V~~~LG~PI 116 (202)
|.+++..+++||+..+.+|-+.
T Consensus 180 ~G~~lrAv~~n~~aA~~~Gin~ 201 (308)
T PRK10740 180 MGRACRACAEDLKMASLLGINT 201 (308)
T ss_pred hhheeeeeeCCHHHHHHcCCCH
Confidence 9999999999999999999764
Done!