Query 018859
Match_columns 349
No_of_seqs 16 out of 18
Neff 1.7
Searched_HMMs 46136
Date Fri Mar 29 04:38:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018859.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018859hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14575 EphA2_TM: Ephrin type 80.4 1.7 3.8E-05 33.7 2.9 8 155-162 55-62 (75)
2 PF05977 MFS_3: Transmembrane 55.9 52 0.0011 32.9 7.8 78 179-283 426-508 (524)
3 KOG3647 Predicted coiled-coil 54.8 8.9 0.00019 37.9 2.3 29 265-301 144-172 (338)
4 PF12669 P12: Virus attachment 43.0 20 0.00043 27.0 2.1 24 105-128 1-24 (58)
5 PF05597 Phasin: Poly(hydroxya 42.1 19 0.00042 31.0 2.2 27 254-282 97-123 (132)
6 PF01299 Lamp: Lysosome-associ 41.2 26 0.00056 32.4 3.0 26 107-133 276-301 (306)
7 COG5665 NOT5 CCR4-NOT transcri 38.4 33 0.00072 35.6 3.5 81 214-306 91-177 (548)
8 PRK14126 cell division protein 36.5 29 0.00062 27.6 2.2 19 170-188 4-22 (85)
9 PF03242 LEA_3: Late embryogen 36.5 17 0.00036 30.0 0.9 13 227-239 67-79 (93)
10 TIGR03141 cytochro_ccmD heme e 34.1 19 0.00042 25.5 0.8 38 106-143 6-43 (45)
11 KOG3400 RNA polymerase subunit 34.0 20 0.00042 32.3 1.0 12 176-187 88-99 (143)
12 PF06390 NESP55: Neuroendocrin 32.2 12 0.00025 36.0 -0.7 22 201-224 2-23 (257)
13 PF06874 FBPase_2: Firmicute f 32.0 34 0.00074 36.6 2.5 34 167-200 330-374 (640)
14 PF13600 DUF4140: N-terminal d 31.5 88 0.0019 24.3 4.1 16 221-236 30-45 (104)
15 COG2929 Uncharacterized protei 31.1 18 0.00039 30.3 0.3 18 246-264 5-22 (93)
16 COG4391 Uncharacterized protei 30.4 41 0.0009 26.7 2.1 29 160-188 31-62 (62)
17 PF06781 UPF0233: Uncharacteri 30.2 36 0.00077 28.0 1.8 21 102-122 65-85 (87)
18 PRK02251 putative septation in 28.7 41 0.0009 27.8 2.0 21 102-122 65-85 (87)
19 KOG0250 DNA repair protein RAD 28.2 36 0.00077 38.4 1.9 50 99-148 59-110 (1074)
20 PRK00159 putative septation in 27.3 44 0.00096 27.7 1.9 24 99-122 62-85 (87)
21 PF14698 ASL_C2: Argininosucci 27.3 21 0.00045 27.2 0.0 21 242-268 2-22 (70)
22 PF07225 NDUF_B4: NADH-ubiquin 27.2 68 0.0015 27.8 3.1 43 100-150 77-119 (125)
23 PF00280 potato_inhibit: Potat 26.8 22 0.00049 27.3 0.1 20 213-232 28-47 (63)
24 cd08153 srpA_like Catalase-lik 25.9 92 0.002 28.8 3.9 72 165-244 158-243 (295)
25 PF11511 RhodobacterPufX: Intr 25.4 58 0.0013 26.1 2.2 38 79-124 11-48 (67)
26 KOG3591 Alpha crystallins [Pos 25.0 33 0.00071 30.5 0.8 12 221-232 122-133 (173)
27 PF11935 DUF3453: Domain of un 24.4 31 0.00068 31.1 0.6 15 230-244 92-106 (239)
28 COG2975 Uncharacterized protei 24.4 36 0.00077 27.2 0.8 9 224-232 18-26 (64)
29 PF13908 Shisa: Wnt and FGF in 23.4 50 0.0011 28.2 1.6 26 100-125 74-99 (179)
30 COG1006 MnhC Multisubunit Na+/ 22.4 85 0.0018 26.9 2.8 34 86-125 66-99 (115)
31 PF15050 SCIMP: SCIMP protein 22.3 96 0.0021 27.7 3.1 42 104-158 6-48 (133)
32 PHA03152 hypothetical protein; 22.1 89 0.0019 28.0 2.9 36 268-304 98-133 (138)
33 PF07407 Seadorna_VP6: Seadorn 22.0 81 0.0018 32.2 3.0 42 236-285 22-63 (420)
34 PF04995 CcmD: Heme exporter p 21.9 40 0.00088 23.9 0.7 40 106-145 5-44 (46)
35 PF13874 Nup54: Nucleoporin co 21.2 28 0.00061 29.2 -0.3 29 252-282 93-121 (141)
36 TIGR01837 PHA_granule_1 poly(h 20.4 68 0.0015 26.7 1.8 32 254-289 84-115 (118)
37 PF08492 SRP72: SRP72 RNA-bind 20.2 54 0.0012 25.3 1.1 13 224-236 39-51 (59)
No 1
>PF14575 EphA2_TM: Ephrin type-A receptor 2 transmembrane domain; PDB: 3KUL_A 2XVD_A 2VX1_A 2VWV_A 2VX0_A 2VWY_A 2VWZ_A 2VWW_A 2VWU_A 2VWX_A ....
Probab=80.42 E-value=1.7 Score=33.73 Aligned_cols=8 Identities=63% Similarity=1.215 Sum_probs=3.9
Q ss_pred CCCccCCC
Q 018859 155 RPLKYEDP 162 (349)
Q Consensus 155 kplkYeDP 162 (349)
-|-+||||
T Consensus 55 DP~TYEDP 62 (75)
T PF14575_consen 55 DPHTYEDP 62 (75)
T ss_dssp -GGGSSSH
T ss_pred CcccccCH
Confidence 45555555
No 2
>PF05977 MFS_3: Transmembrane secretion effector; InterPro: IPR010290 This family consists of the enterobactin exporter EntS proteins and putative permeases all belonging to the major facilitator superfamily. EntS exports the siderophore enterobactin out of the cell. The genetic locus entS was changed from ybdA so as to reflect its relevant biological function [].
Probab=55.94 E-value=52 Score=32.93 Aligned_cols=78 Identities=31% Similarity=0.527 Sum_probs=49.5
Q ss_pred ecceeeeeccccccHHHHHHHHhhhhc----cccccCceEeeccCCCCCCCC-CCCceeeecCCCCcccccccccHHHHh
Q 018859 179 MCGKVYRLAPITLTKEQQTIHQKRRSR----AYQWKRPTIFLKEGDLIPPDV-DPDTVRWIPANHPFATTANDIDEDLAQ 253 (349)
Q Consensus 179 M~GK~yRLaPvtLT~Eqq~~HQkRRsr----AYqWKRPtvFLkEGdsvPpdV-DPdtVRWIPaNHPFAtt~s~iDEdlAq 253 (349)
|---+||++|=.-.+=..+||+.||+| ||+|. +| .|+ ||+ ||+-.=| .|.-++
T Consensus 426 ~v~~~y~i~~~~~~~f~~~~~~~~~~r~r~ga~~w~---~~--------~d~~~~~--~~~e~~~---------~~~w~~ 483 (524)
T PF05977_consen 426 MVTIEYRIAPEDAAAFLAAMRELRRIRRRDGARRWG---LF--------RDLEDPG--RWVERFH---------VESWLE 483 (524)
T ss_pred EEEEEEEECcccHHHHHHHHHHHHHHHhhcChhhce---ee--------eccCCCC--eEEEEEe---------CCCHHH
Confidence 455799999988877777888776665 99994 33 222 233 7775422 222221
Q ss_pred cccccccCCccchhhhHHHHHHHHHHhhhH
Q 018859 254 NNVYQKQGVPFRIRAEHEALQKKLEALQNE 283 (349)
Q Consensus 254 ~NVyQk~GVP~RikAEHEALq~klea~qne 283 (349)
|..|- -|+.+...++|+++.++...
T Consensus 484 ---~~r~~--~r~t~~d~~~~~~~~~~~~~ 508 (524)
T PF05977_consen 484 ---HLRQH--ERVTQADRELQERLRAFHRG 508 (524)
T ss_pred ---HHHHh--ccCCHhhHHHHHHHHHhcCC
Confidence 22221 37888888888888887763
No 3
>KOG3647 consensus Predicted coiled-coil protein [General function prediction only]
Probab=54.81 E-value=8.9 Score=37.94 Aligned_cols=29 Identities=41% Similarity=0.611 Sum_probs=23.6
Q ss_pred chhhhHHHHHHHHHHhhhHhhhcccccCCcchhhhhh
Q 018859 265 RIRAEHEALQKKLEALQNEQKLNKLVIDSSNAKDFER 301 (349)
Q Consensus 265 RikAEHEALq~klea~qneqklnkl~~d~~nak~~eR 301 (349)
|-|+|.|.+|++||+||. |-|.-|.+||+
T Consensus 144 rrk~ElEr~rkRle~Lqs--------iRP~~MdEyE~ 172 (338)
T KOG3647|consen 144 RRKAELERTRKRLEALQS--------IRPAHMDEYED 172 (338)
T ss_pred HHHHHHHHHHHHHHHHHh--------cchHHHHHHHH
Confidence 568999999999999997 56666666664
No 4
>PF12669 P12: Virus attachment protein p12 family
Probab=43.01 E-value=20 Score=26.99 Aligned_cols=24 Identities=25% Similarity=0.516 Sum_probs=15.3
Q ss_pred chhhHHHHHHHHHHHHHHhhheec
Q 018859 105 SFAIGLSLSTAFLVIVVRAFIVRR 128 (349)
Q Consensus 105 nf~~g~cv~~a~l~~~~R~~v~r~ 128 (349)
|+++++.|+++++.+++|.++.++
T Consensus 1 tiII~~Ii~~~~~~v~~r~~~k~~ 24 (58)
T PF12669_consen 1 TIIIGIIILAAVAYVAIRKFIKDK 24 (58)
T ss_pred CeeHHHHHHHHHHHHHHHHHHHHh
Confidence 567777766666655667766443
No 5
>PF05597 Phasin: Poly(hydroxyalcanoate) granule associated protein (phasin); InterPro: IPR008769 Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.
Probab=42.07 E-value=19 Score=30.97 Aligned_cols=27 Identities=30% Similarity=0.534 Sum_probs=23.8
Q ss_pred cccccccCCccchhhhHHHHHHHHHHhhh
Q 018859 254 NNVYQKQGVPFRIRAEHEALQKKLEALQN 282 (349)
Q Consensus 254 ~NVyQk~GVP~RikAEHEALq~klea~qn 282 (349)
++...+-|||+ +.|.+||..|+.+|..
T Consensus 97 ~~aL~rLgvPs--~~dv~~L~~rId~L~~ 123 (132)
T PF05597_consen 97 ARALNRLGVPS--RKDVEALSARIDQLTA 123 (132)
T ss_pred HHHHHhcCCCC--HHHHHHHHHHHHHHHH
Confidence 46788999999 6899999999999987
No 6
>PF01299 Lamp: Lysosome-associated membrane glycoprotein (Lamp); InterPro: IPR002000 Lysosome-associated membrane glycoproteins (lamp) [] are integral membrane proteins, specific to lysosomes, and whose exact biological function is not yet clear. Structurally, the lamp proteins consist of two internally homologous lysosome-luminal domains separated by a proline-rich hinge region; at the C-terminal extremity there is a transmembrane region (TM) followed by a very short cytoplasmic tail (C). In each of the duplicated domains, there are two conserved disulphide bonds. This structure is schematically represented in the figure below. +-----+ +-----+ +-----+ +-----+ | | | | | | | | xCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxxxCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxx +--------------------------++Hinge++--------------------------++TM++C+ In mammals, there are two closely related types of lamp: lamp-1 and lamp-2, which form major components of the lysosome membrane. In chicken lamp-1 is known as LEP100. Also included in this entry is the macrophage protein CD68 (or macrosialin) [] is a heavily glycosylated integral membrane protein whose structure consists of a mucin-like domain followed by a proline-rich hinge; a single lamp-like domain; a transmembrane region and a short cytoplasmic tail. Similar to CD68, mammalian lamp-3, which is expressed in lymphoid organs, dendritic cells and in lung, contains all the C-terminal regions but lacks the N-terminal lamp-like region []. In a lamp-family protein from nematodes [] only the part C-terminal to the hinge is conserved. ; GO: 0016020 membrane
Probab=41.21 E-value=26 Score=32.43 Aligned_cols=26 Identities=27% Similarity=0.563 Sum_probs=12.1
Q ss_pred hhHHHHHHHHHHHHHHhhheecccCCC
Q 018859 107 AIGLSLSTAFLVIVVRAFIVRRSRYNR 133 (349)
Q Consensus 107 ~~g~cv~~a~l~~~~R~~v~r~~~~~~ 133 (349)
++|.+++..+|+++ =+|++.+||...
T Consensus 276 aVG~~La~lvlivL-iaYli~Rrr~~~ 301 (306)
T PF01299_consen 276 AVGAALAGLVLIVL-IAYLIGRRRSRA 301 (306)
T ss_pred HHHHHHHHHHHHHH-HhheeEeccccc
Confidence 34444444444433 356665555443
No 7
>COG5665 NOT5 CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=38.41 E-value=33 Score=35.63 Aligned_cols=81 Identities=28% Similarity=0.336 Sum_probs=56.0
Q ss_pred EeeccCCCCCCCCCC------CceeeecCCCCcccccccccHHHHhcccccccCCccchhhhHHHHHHHHHHhhhHhhhc
Q 018859 214 IFLKEGDLIPPDVDP------DTVRWIPANHPFATTANDIDEDLAQNNVYQKQGVPFRIRAEHEALQKKLEALQNEQKLN 287 (349)
Q Consensus 214 vFLkEGdsvPpdVDP------dtVRWIPaNHPFAtt~s~iDEdlAq~NVyQk~GVP~RikAEHEALq~klea~qneqkln 287 (349)
-|-|||=++|.-+|| |+|-||- +-+||---|--.|...-.-+|+. -||--|.+||-.-. ||.
T Consensus 91 ~fske~ls~~~~~dpke~~k~d~i~~i~---------~~~~el~~q~e~~ea~e~e~~~e-rh~~h~~~le~i~~--~l~ 158 (548)
T COG5665 91 QFSKEALTNPDIIDPKELKKRDQVLFIH---------DCLDELQKQLEQYEAQENEEQTE-RHEFHIANLENILK--KLQ 158 (548)
T ss_pred HhhHhhccCcccCChhHhccccceehHH---------HHHHHHHHHHHHHHHHHhHHHHH-HHHHHHHHHHHHHH--HHh
Confidence 488999999999999 7899993 44666555555666555555543 36666777765432 455
Q ss_pred ccccCCcchhhhhhhhccC
Q 018859 288 KLVIDSSNAKDFERAFKLN 306 (349)
Q Consensus 288 kl~~d~~nak~~eRp~~~~ 306 (349)
.--|||.-..+|.--...-
T Consensus 159 n~~~~pe~v~~~q~di~yy 177 (548)
T COG5665 159 NNEMDPEPVEEFQDDIKYY 177 (548)
T ss_pred ccCCChhhHHHHHHHHHHH
Confidence 5678888888887766543
No 8
>PRK14126 cell division protein ZapA; Provisional
Probab=36.53 E-value=29 Score=27.56 Aligned_cols=19 Identities=21% Similarity=0.387 Sum_probs=15.3
Q ss_pred ecCCCcceeecceeeeecc
Q 018859 170 VGKSNSTMEMCGKVYRLAP 188 (349)
Q Consensus 170 i~k~~Stv~M~GK~yRLaP 188 (349)
-.|..-.|+++|+.|+|++
T Consensus 4 ~~k~~v~V~I~G~~Y~i~~ 22 (85)
T PRK14126 4 GKKTRINVEIYGQQYTIVG 22 (85)
T ss_pred CCCceEEEEECCEEEEecC
Confidence 3455568999999999996
No 9
>PF03242 LEA_3: Late embryogenesis abundant protein; InterPro: IPR004926 Late-embryogenesis abundant (LEA) genes encode a diverse group of proteins that accumulate to high levels during the maturation phase of seed development []. This group includes LEA-5 [], whose expression is induced by salt, drought and heat stress [], and related proteins. ; GO: 0006950 response to stress
Probab=36.50 E-value=17 Score=29.99 Aligned_cols=13 Identities=46% Similarity=0.567 Sum_probs=12.0
Q ss_pred CCCceeeecCCCC
Q 018859 227 DPDTVRWIPANHP 239 (349)
Q Consensus 227 DPdtVRWIPaNHP 239 (349)
||.|=-|||.||-
T Consensus 67 DPvTGyyrPen~~ 79 (93)
T PF03242_consen 67 DPVTGYYRPENHF 79 (93)
T ss_pred CCCCccccCCCCC
Confidence 8999999999993
No 10
>TIGR03141 cytochro_ccmD heme exporter protein CcmD. The model for this protein family describes a small, hydrophobic, and only moderately well-conserved protein, tricky to identify accurately for all of these reasons. However, members are found as part of large operons involved in heme export across the inner membrane for assembly of c-type cytochromes in a large number of bacteria. The gray zone between the trusted cutoff (13.0) and noise cutoff (4.75) includes both low-scoring examples and false-positive matches to hydrophobic domains of longer proteins.
Probab=34.14 E-value=19 Score=25.54 Aligned_cols=38 Identities=18% Similarity=0.111 Sum_probs=21.3
Q ss_pred hhhHHHHHHHHHHHHHHhhheecccCCCCCchHHHHHh
Q 018859 106 FAIGLSLSTAFLVIVVRAFIVRRSRYNRPGSVEDLVRR 143 (349)
Q Consensus 106 f~~g~cv~~a~l~~~~R~~v~r~~~~~~~GSVaDLvRR 143 (349)
+-+|.+.+++++++++-.+....+++...-.++.+-+|
T Consensus 6 ~yVW~sYg~t~l~l~~li~~~~~~~r~~~~~l~~~~~r 43 (45)
T TIGR03141 6 FYVWLAYGITALVLAGLILWSLLDRRRLLRELRRLEAR 43 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 55777777777777665555444443333344444444
No 11
>KOG3400 consensus RNA polymerase subunit 8 [Transcription]
Probab=34.01 E-value=20 Score=32.25 Aligned_cols=12 Identities=50% Similarity=0.836 Sum_probs=9.7
Q ss_pred ceeecceeeeec
Q 018859 176 TMEMCGKVYRLA 187 (349)
Q Consensus 176 tv~M~GK~yRLa 187 (349)
---||||+||+-
T Consensus 88 eYvMyGkvYriE 99 (143)
T KOG3400|consen 88 EYVMYGKVYRIE 99 (143)
T ss_pred eEEEeeEEEEEe
Confidence 356999999984
No 12
>PF06390 NESP55: Neuroendocrine-specific golgi protein P55 (NESP55); InterPro: IPR009434 This family consists of several mammalian neuroendocrine-specific golgi protein P55 (NESP55) sequences. NESP55 is a novel member of the chromogranin family and is a soluble, acidic, heat-stable secretory protein that is expressed exclusively in endocrine and nervous tissues, although less widely than chromogranins [].
Probab=32.18 E-value=12 Score=36.05 Aligned_cols=22 Identities=55% Similarity=0.865 Sum_probs=14.8
Q ss_pred hhhhccccccCceEeeccCCCCCC
Q 018859 201 KRRSRAYQWKRPTIFLKEGDLIPP 224 (349)
Q Consensus 201 kRRsrAYqWKRPtvFLkEGdsvPp 224 (349)
-|||||+||.|-.-- =.|..||
T Consensus 2 drrsra~~~rrarh~--y~dlcpp 23 (257)
T PF06390_consen 2 DRRSRAQQWRRARHN--YNDLCPP 23 (257)
T ss_pred cchhHHHHHHHhhhc--ccccCCc
Confidence 489999999986532 2355554
No 13
>PF06874 FBPase_2: Firmicute fructose-1,6-bisphosphatase; InterPro: IPR009164 Fructose 1,6-bisphosphatase catalyses the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate []. This is an essential reaction in the process of gluconeogenesis, the process by which non-carbohydrate precursors are converted to glucose, and hence this enzyme is found almost universally. Enzyme activity can be regulated by a number of different mechanisms including AMP inhibition, cylic AMP-dependent phosphorylation and light-dependent-activation. This entry represents a group of fructose 1,6-bisphosphatases found within the Firmicutes (low GC Gram-positive bacteria) which do not show any significant sequence similarity to the enzymes from other organisms. The Bacillus subtilis enzyme is inhibited by AMP, though this can be overcome by phosphoenolpyruvate, and is dependent on Mn(2+) [, ]. Mutants lacking this enzyme are apparently still able to grow on gluconeogenic growth substrates such as malate and glycerol.; GO: 0042132 fructose 1,6-bisphosphate 1-phosphatase activity, 0006094 gluconeogenesis
Probab=31.97 E-value=34 Score=36.61 Aligned_cols=34 Identities=32% Similarity=0.517 Sum_probs=29.2
Q ss_pred ceeecCCCcceeecceeeee-----------ccccccHHHHHHHH
Q 018859 167 LVKVGKSNSTMEMCGKVYRL-----------APITLTKEQQTIHQ 200 (349)
Q Consensus 167 lVKi~k~~Stv~M~GK~yRL-----------aPvtLT~Eqq~~HQ 200 (349)
|=|||-.+.||.+-||+|-| .|-.||+|++++=+
T Consensus 330 L~kId~~~gti~i~gk~y~L~d~~FPTiDp~~Py~LT~eE~~vi~ 374 (640)
T PF06874_consen 330 LDKIDYEKGTITIDGKEYPLNDTNFPTIDPEDPYELTEEEEEVID 374 (640)
T ss_pred HhhcCccCCEEEECCEEEeecCCCCCCCCCCCcccCCHHHHHHHH
Confidence 44999999999999999998 48899999887543
No 14
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=31.48 E-value=88 Score=24.31 Aligned_cols=16 Identities=38% Similarity=0.727 Sum_probs=12.8
Q ss_pred CCCCCCCCCceeeecC
Q 018859 221 LIPPDVDPDTVRWIPA 236 (349)
Q Consensus 221 svPpdVDPdtVRWIPa 236 (349)
.||+.+||+++|==..
T Consensus 30 ~Lp~~~d~~Sl~V~~~ 45 (104)
T PF13600_consen 30 GLPPSLDPDSLRVSGE 45 (104)
T ss_pred CCCcccCCCcEEEEec
Confidence 5899999999986433
No 15
>COG2929 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.10 E-value=18 Score=30.30 Aligned_cols=18 Identities=44% Similarity=0.800 Sum_probs=15.6
Q ss_pred cccHHHHhcccccccCCcc
Q 018859 246 DIDEDLAQNNVYQKQGVPF 264 (349)
Q Consensus 246 ~iDEdlAq~NVyQk~GVP~ 264 (349)
+-||+-|+-|. |||||+|
T Consensus 5 ewDe~Ka~sNl-~KHGv~F 22 (93)
T COG2929 5 EWDENKARSNL-EKHGVSF 22 (93)
T ss_pred EeCchHhhhhH-HHcCCCH
Confidence 45888899995 9999999
No 16
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.37 E-value=41 Score=26.66 Aligned_cols=29 Identities=34% Similarity=0.710 Sum_probs=19.7
Q ss_pred CCCCCCcce--eecCCCc-ceeecceeeeecc
Q 018859 160 EDPFNNPLV--KVGKSNS-TMEMCGKVYRLAP 188 (349)
Q Consensus 160 eDPFNNPlV--Ki~k~~S-tv~M~GK~yRLaP 188 (349)
+-||..|=| -+++.+. +---||++|||+|
T Consensus 31 ~~p~~HPrV~L~mg~~gev~CPYC~t~y~l~~ 62 (62)
T COG4391 31 EPPNDHPRVFLDMGDEGEVVCPYCSTRYRLNP 62 (62)
T ss_pred CCCCCCCEEEEEcCCCCcEecCccccEEEecC
Confidence 446888877 4444333 3357999999986
No 17
>PF06781 UPF0233: Uncharacterised protein family (UPF0233); InterPro: IPR009619 This is a group of proteins of unknown function.
Probab=30.24 E-value=36 Score=27.97 Aligned_cols=21 Identities=24% Similarity=0.377 Sum_probs=17.0
Q ss_pred CCcchhhHHHHHHHHHHHHHH
Q 018859 102 TRSSFAIGLSLSTAFLVIVVR 122 (349)
Q Consensus 102 ~g~nf~~g~cv~~a~l~~~~R 122 (349)
..-|++|||++.++-++++.|
T Consensus 65 G~WN~~IGfg~~~~Gf~mt~r 85 (87)
T PF06781_consen 65 GNWNLAIGFGLMIVGFLMTMR 85 (87)
T ss_pred cchHHHHHHHHHHHHHHHHcc
Confidence 356999999999888887755
No 18
>PRK02251 putative septation inhibitor protein; Reviewed
Probab=28.74 E-value=41 Score=27.82 Aligned_cols=21 Identities=19% Similarity=0.200 Sum_probs=17.3
Q ss_pred CCcchhhHHHHHHHHHHHHHH
Q 018859 102 TRSSFAIGLSLSTAFLVIVVR 122 (349)
Q Consensus 102 ~g~nf~~g~cv~~a~l~~~~R 122 (349)
.+-|++|||++.++-++++.|
T Consensus 65 G~WN~~IGfg~~~~G~~mt~r 85 (87)
T PRK02251 65 GAWNLVIGFGLIMAGFGMTTQ 85 (87)
T ss_pred cchhHHHHHHHHHHHHHHHcc
Confidence 456999999999988887765
No 19
>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]
Probab=28.19 E-value=36 Score=38.37 Aligned_cols=50 Identities=28% Similarity=0.312 Sum_probs=37.7
Q ss_pred hccCCcchhhH--HHHHHHHHHHHHHhhheecccCCCCCchHHHHHhccccc
Q 018859 99 KRHTRSSFAIG--LSLSTAFLVIVVRAFIVRRSRYNRPGSVEDLVRRGQLRS 148 (349)
Q Consensus 99 ~k~~g~nf~~g--~cv~~a~l~~~~R~~v~r~~~~~~~GSVaDLvRRGQLrS 148 (349)
.=+...||+.| ..-=-|+|+|..-++--|-+..+|+.|+-|||+.|+--.
T Consensus 59 eFg~~vNfI~G~NGSGKSAIltAl~lglG~rAs~tnRgsslK~lIK~G~~~A 110 (1074)
T KOG0250|consen 59 EFGPRVNFIVGNNGSGKSAILTALTLGLGGRASATNRGSSLKDLIKDGCSSA 110 (1074)
T ss_pred ccCCCceEeecCCCCcHHHHHHHHHHhhccccccccchhhHHHHHhCCCcce
Confidence 33455677777 444456777777778888899999999999999998543
No 20
>PRK00159 putative septation inhibitor protein; Reviewed
Probab=27.31 E-value=44 Score=27.69 Aligned_cols=24 Identities=25% Similarity=0.365 Sum_probs=18.6
Q ss_pred hccCCcchhhHHHHHHHHHHHHHH
Q 018859 99 KRHTRSSFAIGLSLSTAFLVIVVR 122 (349)
Q Consensus 99 ~k~~g~nf~~g~cv~~a~l~~~~R 122 (349)
..-.+-|++|||++.++-++++.|
T Consensus 62 ~~lG~WN~~IGFg~~i~G~lmt~r 85 (87)
T PRK00159 62 ADLGPWNYAIGFALMITGLLMTMR 85 (87)
T ss_pred cccCchhHHHHHHHHHHHHHHhcc
Confidence 334456999999999998888765
No 21
>PF14698 ASL_C2: Argininosuccinate lyase C-terminal; PDB: 1XWO_A 2E9F_A 1TJW_C 1TJU_A 1DCN_B 1K7W_B 1HY1_C 1TJV_B 1AUW_A 1U15_B ....
Probab=27.25 E-value=21 Score=27.19 Aligned_cols=21 Identities=43% Similarity=0.757 Sum_probs=12.1
Q ss_pred cccccccHHHHhcccccccCCccchhh
Q 018859 242 TTANDIDEDLAQNNVYQKQGVPFRIRA 268 (349)
Q Consensus 242 tt~s~iDEdlAq~NVyQk~GVP~RikA 268 (349)
+|++|+-+-|. ++ |+|||---
T Consensus 2 ~~ATdlAD~LV-----r~-GipFR~AH 22 (70)
T PF14698_consen 2 STATDLADYLV-----RK-GIPFREAH 22 (70)
T ss_dssp GGHHHHHHHHH-----HT-TS-HHHHH
T ss_pred ccHHHHHHHHH-----Hc-CCCHHHHH
Confidence 34566655554 34 99999643
No 22
>PF07225 NDUF_B4: NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4); InterPro: IPR009866 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 family contains human NADH-ubiquinone oxidoreductase subunit NDUFB4 and related sequences.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=27.17 E-value=68 Score=27.79 Aligned_cols=43 Identities=28% Similarity=0.539 Sum_probs=26.7
Q ss_pred ccCCcchhhHHHHHHHHHHHHHHhhheecccCCCCCchHHHHHhcccccCC
Q 018859 100 RHTRSSFAIGLSLSTAFLVIVVRAFIVRRSRYNRPGSVEDLVRRGQLRSDR 150 (349)
Q Consensus 100 k~~g~nf~~g~cv~~a~l~~~~R~~v~r~~~~~~~GSVaDLvRRGQLrSdr 150 (349)
|-.+-+..+|++++++ .+++-.++++..++ .-.+++|-||| ||
T Consensus 77 RpTPktsllg~~~~v~--P~i~~~~~~KtdRD----~~E~~~r~G~~--dR 119 (125)
T PF07225_consen 77 RPTPKTSLLGLGFGVV--PLIFYYYVLKTDRD----RKEKLIRTGKL--DR 119 (125)
T ss_pred ccCchHHHHHHHHHHH--HHHHHHhhhccchh----HHHHHHhcCcc--ce
Confidence 3456677777655444 33444455544444 35799999999 65
No 23
>PF00280 potato_inhibit: Potato inhibitor I family; InterPro: IPR000864 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This family of proteinase inhibitors belong to MEROPS inhibitor family I13, clan IG. They inhibit peptidases of the S1 (IPR001254 from INTERPRO) and S8 (IPR000209 from INTERPRO) families []. Potato inhibitor type I sequences are not solely restricted to potatoes but are found in other plant species for example: barley endosperm chymotrypsin inhibitor [], and pumpkin trypsin inhibitor. Exceptions are found in leech's, e.g.Hirudo medicinalis (Medicinal leech), but not other metazoa []. In general, the proteins have retained a specificity towards chymotrypsin-like and elastase-like proteases []. Structurally these inhibitors are small (60 to 90 residues) and in contrast with other families of protease inhibitors, they lack disulphide bonds. The inhibitor is a wedge-shaped molecule, its pointed edge formed by the protease-binding loop, which contains the scissile bond. The loop binds tightly to the protease active site, subsequent cleavage of the scissile bond causing inhibition of the enzyme []. The inhibitors (designated type I and II) are synthesised in potato tubers, increasing in concentration as the tuber develops. Synthesis of the inhibitors throughout the plant is also induced by leaf damage; this systemic response being triggered by the release of a putative plant hormone []. Examples found in the bacteria and archaea are probable false positives.; GO: 0004867 serine-type endopeptidase inhibitor activity, 0009611 response to wounding; PDB: 1TEC_I 1SBN_I 1ACB_I 1EGP_A 3TEC_I 2SEC_I 1EGL_A 2TEC_I 1SIB_I 1MEE_I ....
Probab=26.78 E-value=22 Score=27.27 Aligned_cols=20 Identities=35% Similarity=0.497 Sum_probs=18.7
Q ss_pred eEeeccCCCCCCCCCCCcee
Q 018859 213 TIFLKEGDLIPPDVDPDTVR 232 (349)
Q Consensus 213 tvFLkEGdsvPpdVDPdtVR 232 (349)
.++|.+|..+|.|.++|-||
T Consensus 28 v~vlp~gs~vt~df~~~RVr 47 (63)
T PF00280_consen 28 VVVLPEGSPVTMDFRCDRVR 47 (63)
T ss_dssp EEEEETTSEEESSBETTEEE
T ss_pred EEEEeCCCCcCCCcCCCEEE
Confidence 46999999999999999998
No 24
>cd08153 srpA_like Catalase-like heme-binding proteins similar to the uncharacterized srpA. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity. This family contains uncharacterized proteins similar to the Synechococcus elongatus PCC 7942 periplasmic protein srpA, of mostly bacterial origin. The plasmid-encoded srpA is regulated by sulfate, but does not seem to function in its uptake or metabolism.
Probab=25.91 E-value=92 Score=28.81 Aligned_cols=72 Identities=19% Similarity=0.342 Sum_probs=44.9
Q ss_pred CcceeecCCCcceeecceeeeeccc----cccHHH----------HHHHHhhhhccccccCceEeeccCCCCCCCCCCCc
Q 018859 165 NPLVKVGKSNSTMEMCGKVYRLAPI----TLTKEQ----------QTIHQKRRSRAYQWKRPTIFLKEGDLIPPDVDPDT 230 (349)
Q Consensus 165 NPlVKi~k~~Stv~M~GK~yRLaPv----tLT~Eq----------q~~HQkRRsrAYqWKRPtvFLkEGdsvPpdVDPdt 230 (349)
|||.=+++.+.+ .+.| ||+.|. .|++|+ +++.|.=+...+.|.==.-...+||+ ++--|
T Consensus 158 ~~f~f~~~~G~~--~~vk-~~~~P~~g~~~l~~~~~~~~~~d~l~~~l~~~l~~g~~~f~l~vQl~~~~d~----i~D~t 230 (295)
T cd08153 158 NAFYFTNANGKR--QPVR-WRFVPEDGVKYLSDEEAAKLGPDFLFDELAQRLAQGPVRWDLVLQLAEPGDP----TDDPT 230 (295)
T ss_pred eeEEEECCCCCE--EEEE-EEEEECCCCCCCCHHHhccCCcchhHHHHHHHHHhCCceEEEEEEEcCCCCc----CCCCC
Confidence 555544443322 2233 788885 366655 34566665667788777777788883 45568
Q ss_pred eeeecCCCCccccc
Q 018859 231 VRWIPANHPFATTA 244 (349)
Q Consensus 231 VRWIPaNHPFAtt~ 244 (349)
+.| |..|||-+-+
T Consensus 231 ~~W-pe~~p~~~vg 243 (295)
T cd08153 231 KPW-PADRKEVDAG 243 (295)
T ss_pred ccC-CCCCceeEEE
Confidence 999 7779996544
No 25
>PF11511 RhodobacterPufX: Intrinsic membrane protein PufX; InterPro: IPR020169 PufX organises RC-LH1, the photosynthesis reaction centre-light harvesting complex 1 core complex of Rhodobacter sphaeroides []. It also facilitates the exchange of quinol for quinone between the reaction centre and cytochrome bc(1) complexes. In organic solvent, PufX contains two hydrophobic helices which are flanked by unstructured regions and connected by a helical bend [].; PDB: 2DW3_A 2ITA_A 2NRG_A.
Probab=25.38 E-value=58 Score=26.14 Aligned_cols=38 Identities=18% Similarity=0.313 Sum_probs=27.6
Q ss_pred CchhhHHHHhhccCchhhhhhccCCcchhhHHHHHHHHHHHHHHhh
Q 018859 79 DPVAKFQETLISLPPVAFVMKRHTRSSFAIGLSLSTAFLVIVVRAF 124 (349)
Q Consensus 79 ~sv~~~~~~v~s~Pp~vf~~~k~~g~nf~~g~cv~~a~l~~~~R~~ 124 (349)
++...|+..+ .+.|.|+.| .++.+|+++.|++++.+.+
T Consensus 11 ~~k~~L~~~~------~~qMlkGag--~Aav~~~~~~~~l~~~~~i 48 (67)
T PF11511_consen 11 NPKFRLRAWI------LFQMLKGAG--YAAVFFLGLWFLLVALYFI 48 (67)
T ss_dssp -HHHHHHHHH------HHHHHHHHH--HHHHHHHHHHHHHHHHHHH
T ss_pred CchhhHHHHH------HHHHHhccc--HHHHHHHHHHHHHHHHHHH
Confidence 4455666644 478888876 5777999999999888764
No 26
>KOG3591 consensus Alpha crystallins [Posttranslational modification, protein turnover, chaperones]
Probab=25.05 E-value=33 Score=30.51 Aligned_cols=12 Identities=58% Similarity=1.082 Sum_probs=10.7
Q ss_pred CCCCCCCCCcee
Q 018859 221 LIPPDVDPDTVR 232 (349)
Q Consensus 221 svPpdVDPdtVR 232 (349)
.||+||||++|+
T Consensus 122 ~LP~~vdp~~V~ 133 (173)
T KOG3591|consen 122 LLPEDVDPTSVT 133 (173)
T ss_pred cCCCCCChhheE
Confidence 499999999986
No 27
>PF11935 DUF3453: Domain of unknown function (DUF3453); InterPro: IPR021850 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 239 to 261 amino acids in length. ; PDB: 3ODS_A 3ODR_A 3O2Q_A 3O2T_A 3O2S_A 3GS3_A.
Probab=24.39 E-value=31 Score=31.11 Aligned_cols=15 Identities=27% Similarity=0.653 Sum_probs=9.1
Q ss_pred ceeeecCCCCccccc
Q 018859 230 TVRWIPANHPFATTA 244 (349)
Q Consensus 230 tVRWIPaNHPFAtt~ 244 (349)
.+-|||.||||-...
T Consensus 92 SL~~vp~~Hp~l~~~ 106 (239)
T PF11935_consen 92 SLSSVPPNHPLLNPQ 106 (239)
T ss_dssp -GGGS-TT-SSS-HH
T ss_pred CHHHcCCCCCcCCHH
Confidence 466999999998754
No 28
>COG2975 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.37 E-value=36 Score=27.23 Aligned_cols=9 Identities=89% Similarity=1.446 Sum_probs=8.5
Q ss_pred CCCCCCcee
Q 018859 224 PDVDPDTVR 232 (349)
Q Consensus 224 pdVDPdtVR 232 (349)
|||||-|||
T Consensus 18 pdvDPktvr 26 (64)
T COG2975 18 PDVDPKTVR 26 (64)
T ss_pred CCCCcceee
Confidence 899999997
No 29
>PF13908 Shisa: Wnt and FGF inhibitory regulator
Probab=23.36 E-value=50 Score=28.18 Aligned_cols=26 Identities=12% Similarity=0.220 Sum_probs=14.2
Q ss_pred ccCCcchhhHHHHHHHHHHHHHHhhh
Q 018859 100 RHTRSSFAIGLSLSTAFLVIVVRAFI 125 (349)
Q Consensus 100 k~~g~nf~~g~cv~~a~l~~~~R~~v 125 (349)
+....+++.|+.++++++|+++-.++
T Consensus 74 ~~~~~~iivgvi~~Vi~Iv~~Iv~~~ 99 (179)
T PF13908_consen 74 IYFITGIIVGVICGVIAIVVLIVCFC 99 (179)
T ss_pred ccceeeeeeehhhHHHHHHHhHhhhe
Confidence 44455666666555555555554443
No 30
>COG1006 MnhC Multisubunit Na+/H+ antiporter, MnhC subunit [Inorganic ion transport and metabolism]
Probab=22.42 E-value=85 Score=26.91 Aligned_cols=34 Identities=24% Similarity=0.407 Sum_probs=26.0
Q ss_pred HHhhccCchhhhhhccCCcchhhHHHHHHHHHHHHHHhhh
Q 018859 86 ETLISLPPVAFVMKRHTRSSFAIGLSLSTAFLVIVVRAFI 125 (349)
Q Consensus 86 ~~v~s~Pp~vf~~~k~~g~nf~~g~cv~~a~l~~~~R~~v 125 (349)
..+.-+|.|+-+. .++||||+.+.+|+.+.|.|-
T Consensus 66 ~~aDPlPQALILT------AIVIgfa~tal~L~l~~~~y~ 99 (115)
T COG1006 66 TYVDPLPQALILT------AIVIGFATTALALVLAYRAYK 99 (115)
T ss_pred ccCCchhHHHHHH------HHHHHHHHHHHHHHHHHHHHH
Confidence 3344567765554 589999999999999999885
No 31
>PF15050 SCIMP: SCIMP protein
Probab=22.33 E-value=96 Score=27.72 Aligned_cols=42 Identities=33% Similarity=0.473 Sum_probs=24.6
Q ss_pred cchhhHHHHHHHHHHHHHHhhheecccCCCCCchHHHHHhcccccCC-cCCCCCCc
Q 018859 104 SSFAIGLSLSTAFLVIVVRAFIVRRSRYNRPGSVEDLVRRGQLRSDR-RGISRPLK 158 (349)
Q Consensus 104 ~nf~~g~cv~~a~l~~~~R~~v~r~~~~~~~GSVaDLvRRGQLrSdr-RGiskplk 158 (349)
-||+|-++||+.++-++ ..+|+. -|-|-|||-|+ --|+||+|
T Consensus 6 ~nFWiiLAVaII~vS~~-lglIly------------CvcR~~lRqGkkweiakp~k 48 (133)
T PF15050_consen 6 DNFWIILAVAIILVSVV-LGLILY------------CVCRWQLRQGKKWEIAKPLK 48 (133)
T ss_pred hchHHHHHHHHHHHHHH-HHHHHH------------HHHHHHHHccccceeccchh
Confidence 48999998886554433 333321 23445565554 46777775
No 32
>PHA03152 hypothetical protein; Provisional
Probab=22.06 E-value=89 Score=28.04 Aligned_cols=36 Identities=36% Similarity=0.449 Sum_probs=31.7
Q ss_pred hhHHHHHHHHHHhhhHhhhcccccCCcchhhhhhhhc
Q 018859 268 AEHEALQKKLEALQNEQKLNKLVIDSSNAKDFERAFK 304 (349)
Q Consensus 268 AEHEALq~klea~qneqklnkl~~d~~nak~~eRp~~ 304 (349)
+|-+.|...|..+|| +=+.||.+++.|...|.|-+-
T Consensus 98 ~ee~~lln~l~~l~~-sf~s~~~~~tt~~~~f~~~~g 133 (138)
T PHA03152 98 AEEQNFKNHLITLQN-SFLSKLGPDTTGAIKFKRKHG 133 (138)
T ss_pred HHHHHHHHHHHHHHH-HHHHhcCcccccchhhhhhhc
Confidence 799999999999987 778999999999999988653
No 33
>PF07407 Seadorna_VP6: Seadornavirus VP6 protein; InterPro: IPR009982 This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.
Probab=22.00 E-value=81 Score=32.25 Aligned_cols=42 Identities=26% Similarity=0.360 Sum_probs=30.9
Q ss_pred CCCCcccccccccHHHHhcccccccCCccchhhhHHHHHHHHHHhhhHhh
Q 018859 236 ANHPFATTANDIDEDLAQNNVYQKQGVPFRIRAEHEALQKKLEALQNEQK 285 (349)
Q Consensus 236 aNHPFAtt~s~iDEdlAq~NVyQk~GVP~RikAEHEALq~klea~qneqk 285 (349)
.||-....+-|=.-+|-+.| .|+|+|.++|+.|+|+|.+|-+
T Consensus 22 ~~~~~~~~~~~e~~aLr~EN--------~~LKkEN~~Lk~eVerLE~e~l 63 (420)
T PF07407_consen 22 ENHELEGVSIDENFALRMEN--------HSLKKENNDLKIEVERLENEML 63 (420)
T ss_pred ccccccccchhhhhhHHHHh--------HHHHHHHHHHHHHHHHHHHHhh
Confidence 47777665533333455666 5899999999999999977765
No 34
>PF04995 CcmD: Heme exporter protein D (CcmD); InterPro: IPR007078 The CcmD protein is part of a C-type cytochrome biogenesis operon []. The exact function of this protein is uncertain. It has been proposed that CcmC, CcmD and CcmE interact directly with each other, establishing a cytoplasm to periplasm haem delivery pathway for cytochrome c maturation []. This protein is found fused to CcmE in P52224 from SWISSPROT. These proteins contain a predicted transmembrane helix.; GO: 0006810 transport, 0016021 integral to membrane
Probab=21.91 E-value=40 Score=23.88 Aligned_cols=40 Identities=23% Similarity=0.138 Sum_probs=21.7
Q ss_pred hhhHHHHHHHHHHHHHHhhheecccCCCCCchHHHHHhcc
Q 018859 106 FAIGLSLSTAFLVIVVRAFIVRRSRYNRPGSVEDLVRRGQ 145 (349)
Q Consensus 106 f~~g~cv~~a~l~~~~R~~v~r~~~~~~~GSVaDLvRRGQ 145 (349)
+-+|.|.+++++++++-.+....+++.-.-.++.+.+|+|
T Consensus 5 ~yVW~sYg~t~~~l~~l~~~~~~~~r~~~~~l~~~~~r~~ 44 (46)
T PF04995_consen 5 FYVWSSYGVTALVLAGLIVWSLRRRRRLRKELKRLEAREQ 44 (46)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHc
Confidence 4567777777766665555444443333344555555544
No 35
>PF13874 Nup54: Nucleoporin complex subunit 54; PDB: 3T97_B.
Probab=21.23 E-value=28 Score=29.24 Aligned_cols=29 Identities=31% Similarity=0.604 Sum_probs=5.7
Q ss_pred HhcccccccCCccchhhhHHHHHHHHHHhhh
Q 018859 252 AQNNVYQKQGVPFRIRAEHEALQKKLEALQN 282 (349)
Q Consensus 252 Aq~NVyQk~GVP~RikAEHEALq~klea~qn 282 (349)
++.-|+...|.| +..|-|.|..+||++..
T Consensus 93 ~~~eilr~~g~~--l~~eEe~L~~~le~l~~ 121 (141)
T PF13874_consen 93 RKQEILRNRGYA--LSPEEEELRKRLEALEA 121 (141)
T ss_dssp HHHHHHHH-----------------------
T ss_pred HHHHHHHHcCCC--CCHHHHHHHHHHHHHHH
Confidence 455688999998 77899999999999887
No 36
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=20.37 E-value=68 Score=26.65 Aligned_cols=32 Identities=31% Similarity=0.502 Sum_probs=25.0
Q ss_pred cccccccCCccchhhhHHHHHHHHHHhhhHhhhccc
Q 018859 254 NNVYQKQGVPFRIRAEHEALQKKLEALQNEQKLNKL 289 (349)
Q Consensus 254 ~NVyQk~GVP~RikAEHEALq~klea~qneqklnkl 289 (349)
+++..+-|+|++ .|.++|..|+.+|.. +|++|
T Consensus 84 ~~~L~~lg~~tk--~ev~~L~~RI~~Le~--~l~~l 115 (118)
T TIGR01837 84 EQALNRLNIPSR--EEIEALSAKIEQLAV--QVEEL 115 (118)
T ss_pred HHHHHHcCCCCH--HHHHHHHHHHHHHHH--HHHHH
Confidence 468889999985 789999999998865 45443
No 37
>PF08492 SRP72: SRP72 RNA-binding domain; InterPro: IPR013699 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the RNA binding domain of the SRP72 subunit. This domain is responsible for the binding of SRP72 to the 7S SRP RNA []. ; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle
Probab=20.16 E-value=54 Score=25.29 Aligned_cols=13 Identities=46% Similarity=1.163 Sum_probs=10.0
Q ss_pred CCCCCCceeeecC
Q 018859 224 PDVDPDTVRWIPA 236 (349)
Q Consensus 224 pdVDPdtVRWIPa 236 (349)
|++-||-=||||-
T Consensus 39 p~~~PDPERWLP~ 51 (59)
T PF08492_consen 39 PGKTPDPERWLPK 51 (59)
T ss_pred CCCCCCccccCch
Confidence 4566888899994
Done!