Query psy5788
Match_columns 204
No_of_seqs 20 out of 22
Neff 2.4
Searched_HMMs 46136
Date Fri Aug 16 17:58:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5788.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5788hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4512|consensus 100.0 2.9E-48 6.2E-53 363.2 6.8 137 1-137 486-624 (625)
2 PF08620 RPAP1_C: RPAP1-like, 71.0 5.6 0.00012 29.7 3.3 31 3-33 37-67 (73)
3 PF13728 TraF: F plasmid trans 70.7 5.9 0.00013 33.5 3.8 56 16-71 132-200 (215)
4 PRK11657 dsbG disulfide isomer 44.1 32 0.0007 29.6 3.8 44 25-69 26-71 (251)
5 smart00604 MD MD domain. 38.7 33 0.00072 28.9 3.0 26 62-87 4-30 (145)
6 TIGR02739 TraF type-F conjugat 37.1 46 0.001 29.6 3.8 54 16-69 162-228 (256)
7 COG3716 ManZ Phosphotransferas 36.8 27 0.00058 32.0 2.3 57 118-174 166-230 (269)
8 PRK10738 hypothetical protein; 36.7 32 0.00069 27.2 2.5 24 122-146 33-56 (134)
9 PF13691 Lactamase_B_4: tRNase 34.9 29 0.00063 25.1 1.8 44 56-107 13-63 (63)
10 smart00139 MyTH4 Domain in Myo 34.4 9.6 0.00021 30.5 -0.8 36 4-40 55-91 (144)
11 PRK13703 conjugal pilus assemb 30.7 75 0.0016 28.2 4.0 53 16-68 155-220 (248)
12 PF12308 Noelin-1: Neurogenesi 28.1 51 0.0011 26.5 2.3 30 121-150 68-97 (101)
13 KOG4312|consensus 26.8 71 0.0015 31.1 3.4 41 126-177 335-375 (449)
14 COG4967 PilV Tfp pilus assembl 25.2 2.1E+02 0.0045 24.4 5.5 59 11-71 37-95 (162)
15 PRK05406 LamB/YcsF family prot 23.8 1.3E+02 0.0028 27.1 4.3 42 2-48 76-117 (246)
16 PF03746 LamB_YcsF: LamB/YcsF 23.7 96 0.0021 27.8 3.5 41 3-48 75-115 (242)
17 KOG3725|consensus 23.6 97 0.0021 29.4 3.6 60 5-65 232-299 (375)
18 TIGR00828 EIID-AGA PTS system, 23.5 50 0.0011 29.7 1.7 57 118-174 162-232 (271)
19 PF02566 OsmC: OsmC-like prote 22.5 55 0.0012 22.9 1.4 15 124-138 7-21 (100)
20 PRK07027 cobalamin biosynthesi 22.5 74 0.0016 25.0 2.3 75 5-85 14-124 (126)
21 PF15337 Vasculin: Vascular pr 22.1 59 0.0013 26.1 1.7 22 18-39 4-25 (97)
22 PF07539 DRIM: Down-regulated 20.4 71 0.0015 25.8 1.8 31 5-36 13-45 (141)
23 PRK06804 flgA flagellar basal 20.2 6E+02 0.013 22.7 7.7 107 9-122 46-171 (261)
No 1
>KOG4512|consensus
Probab=100.00 E-value=2.9e-48 Score=363.17 Aligned_cols=137 Identities=42% Similarity=0.578 Sum_probs=132.0
Q ss_pred CcccCchHhHHHHHHHHHHHHHHHHHHHHHHHhceeecccCCccccCCCCccCCcceeEeecCCCCeeeEEeeCCCCce-
Q psy5788 1 MKLSYEPQELRDLIFCQIYQHQISAMEKLAKCMGWQFLSSSAHLGLGGVEPLGNASSCLLSSPMGDRMISVRCEPQAGI- 79 (204)
Q Consensus 1 vtLS~e~QELrDlil~Qi~QHQV~~vq~LAK~MGW~vLs~S~HvG~GpvE~lGnassillASP~gdr~IaVR~~p~~gI- 79 (204)
|+|||++|||||+|+|||.||||+++++|||+|+|+||++|||+|.|++|++||||+|.+|||++||+|+||..+..|+
T Consensus 486 i~lSy~~qelrd~ll~qi~qhqI~~~~~Lar~m~w~vls~Snh~g~g~~E~vgnas~~~~asp~~d~~i~vr~~~~~g~~ 565 (625)
T KOG4512|consen 486 IELSYPKQELRDMLLVQIVQHQIQSGNGLARDMKWKVLSYSNHYGEGDSEKVGNASWKDSASPAQDYTILVRDVFKTGEK 565 (625)
T ss_pred EEEecCHHHHHHHHHHHHHHHHHHHHHhHhhccCceEeecccccCCCcccccccchhhhccCcccCceEEEeeccCCcch
Confidence 6899999999999999999999999999999999999999999999999999999999999999999999987666666
Q ss_pred -EEEEcCCCCCCCCCcccccccccccCCCCceeeecccCCCChhHHHHHHHHHHhhhhh
Q psy5788 80 -QVAIAHSPRKDFFCGQLVKERKWENLGGPFKEVRWDKMEGKNFLNKMELLMASLTSLI 137 (204)
Q Consensus 80 -~V~I~rs~~~Df~~sdlv~D~KWe~Lgg~FKEV~w~kMeGrNFV~KMELLMa~Lt~~~ 137 (204)
+|.++|++++|||+|+++++.+|++|+|.||||+|+|||||+|+||||+||+.|++|+
T Consensus 566 ikv~f~r~~~kdlf~s~i~~~~~w~~l~g~fkeV~f~k~egk~f~~kme~lm~~L~~~~ 624 (625)
T KOG4512|consen 566 IKVDFSRKAQKDLFLSRIFNHYFWVLLFGIFKEVFFSKFEGKVFSHKMEILMKRLDFCL 624 (625)
T ss_pred hhhhcchhhhhccchhhhhhHHHHHHhccchheeehhhhccchhhhHHHHHHHhccccc
Confidence 7777999999999999999999999999999999999999999999999999999986
No 2
>PF08620 RPAP1_C: RPAP1-like, C-terminal; InterPro: IPR013929 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.
Probab=70.98 E-value=5.6 Score=29.67 Aligned_cols=31 Identities=23% Similarity=0.292 Sum_probs=29.1
Q ss_pred ccCchHhHHHHHHHHHHHHHHHHHHHHHHHh
Q psy5788 3 LSYEPQELRDLIFCQIYQHQISAMEKLAKCM 33 (204)
Q Consensus 3 LS~e~QELrDlil~Qi~QHQV~~vq~LAK~M 33 (204)
-+|..+||-.|.-+.+.+....++|.|++|+
T Consensus 37 aGYTi~El~~L~RSsv~~QR~~al~~L~~Il 67 (73)
T PF08620_consen 37 AGYTIQELFHLSRSSVPSQRCIALQTLGRIL 67 (73)
T ss_pred CCcCHHHHHHHHhcCcHHHHHHHHHHHHHHH
Confidence 4799999999999999999999999999986
No 3
>PF13728 TraF: F plasmid transfer operon protein
Probab=70.72 E-value=5.9 Score=33.54 Aligned_cols=56 Identities=18% Similarity=0.286 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHHHHHhceeecccCCc-------------cccCCCCccCCcceeEeecCCCCeeeEE
Q psy5788 16 CQIYQHQISAMEKLAKCMGWQFLSSSAH-------------LGLGGVEPLGNASSCLLSSPMGDRMISV 71 (204)
Q Consensus 16 ~Qi~QHQV~~vq~LAK~MGW~vLs~S~H-------------vG~GpvE~lGnassillASP~gdr~IaV 71 (204)
|..++.|.-+|+.+|+-.||.|+.-|.= -|...--.+...++++|..|++....-|
T Consensus 132 C~~C~~~~pil~~~~~~yg~~v~~vs~DG~~~~~fp~~~~~~g~~~~l~v~~~Pal~Lv~~~~~~~~pv 200 (215)
T PF13728_consen 132 CPYCQQQAPILQQFADKYGFSVIPVSLDGRPIPSFPNPRPDPGQAKRLGVKVTPALFLVNPNTKKWYPV 200 (215)
T ss_pred CchhHHHHHHHHHHHHHhCCEEEEEecCCCCCcCCCCCCCCHHHHHHcCCCcCCEEEEEECCCCeEEEE
Confidence 8889999999999999999999988862 1111112234667888888888555444
No 4
>PRK11657 dsbG disulfide isomerase/thiol-disulfide oxidase; Provisional
Probab=44.08 E-value=32 Score=29.61 Aligned_cols=44 Identities=16% Similarity=0.200 Sum_probs=34.0
Q ss_pred HHHHHHHHhceeeccc--CCccccCCCCccCCcceeEeecCCCCeee
Q psy5788 25 AMEKLAKCMGWQFLSS--SAHLGLGGVEPLGNASSCLLSSPMGDRMI 69 (204)
Q Consensus 25 ~vq~LAK~MGW~vLs~--S~HvG~GpvE~lGnassillASP~gdr~I 69 (204)
.|+.|.+. |-+|.+- .++-=.|-++-.++.+.++.+||+|+|.|
T Consensus 26 ~~~~l~~~-g~~v~~~~~~p~~l~g~~~~~~~~~~i~Y~t~dg~y~i 71 (251)
T PRK11657 26 PVKALEKQ-GITIIKTFDAPGGLKGYAAKYQDMGVTIYLTPDGKHAI 71 (251)
T ss_pred HHHHHHhC-CCEEEEeecCCCCceEEEEEeCCCceEEEEcCCCCEEE
Confidence 36777555 9999887 66544566677777777999999999998
No 5
>smart00604 MD MD domain.
Probab=38.71 E-value=33 Score=28.86 Aligned_cols=26 Identities=23% Similarity=0.415 Sum_probs=21.0
Q ss_pred cCCCCeeeEEeeCCCCceEEEE-cCCC
Q psy5788 62 SPMGDRMISVRCEPQAGIQVAI-AHSP 87 (204)
Q Consensus 62 SP~gdr~IaVR~~p~~gI~V~I-~rs~ 87 (204)
.|.|.+.|.||+.+..++.+.| .+|+
T Consensus 4 l~~G~w~l~v~s~~s~~C~l~vR~qS~ 30 (145)
T smart00604 4 LPPGTWTITVRANGSNSCTISVRSQSS 30 (145)
T ss_pred cCCceEEEEEecCCCCCEEEEEEeccc
Confidence 4789999999999888888888 4443
No 6
>TIGR02739 TraF type-F conjugative transfer system pilin assembly protein TraF. This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm. Unlike the related protein TrbB (TIGR02738), TraF does not contain a conserved pair of cysteines and has been shown not to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. Even more closely related than TrbB is a clade of genes (TIGR02740) which do contain the CXXC motif, but it is unclear whether these genes are involved in type-F conjugation systems per se.
Probab=37.07 E-value=46 Score=29.60 Aligned_cols=54 Identities=19% Similarity=0.210 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHHHHHhceeecccCCccc-----------cCCCCc--cCCcceeEeecCCCCeee
Q psy5788 16 CQIYQHQISAMEKLAKCMGWQFLSSSAHLG-----------LGGVEP--LGNASSCLLSSPMGDRMI 69 (204)
Q Consensus 16 ~Qi~QHQV~~vq~LAK~MGW~vLs~S~HvG-----------~GpvE~--lGnassillASP~gdr~I 69 (204)
|..++.|.-+|+++|+--||.|+.-|.==+ .|-.+- +-.-++++|..|++....
T Consensus 162 C~~C~~~apil~~fa~~ygi~v~~VS~DG~~~p~fp~~~~d~gqa~~l~v~~~Pal~Lv~~~t~~~~ 228 (256)
T TIGR02739 162 SPISQKMAPVIQAFAKEYGISVIPISVDGTLIPGLPNSRSDSGQAQHLGVKYFPALYLVNPKSQKMS 228 (256)
T ss_pred CchhHHHHHHHHHHHHHhCCeEEEEecCCCCCCCCCCccCChHHHHhcCCccCceEEEEECCCCcEE
Confidence 778899999999999999999998876311 111112 225678888888865543
No 7
>COG3716 ManZ Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IID [Carbohydrate transport and metabolism]
Probab=36.80 E-value=27 Score=32.03 Aligned_cols=57 Identities=30% Similarity=0.428 Sum_probs=40.1
Q ss_pred CCChhHHHHHH-HHHHhh--hhhhhHHHHHHHhhcchhhh-----hhhhcccchhhhhhhcCCCC
Q psy5788 118 EGKNFLNKMEL-LMASLT--SLIEGITVIAKLLSSRDRRE-----KEDRIGESNESILDKICPGR 174 (204)
Q Consensus 118 eGrNFV~KMEL-LMa~Lt--~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~ 174 (204)
.|.++++||.= .|..|| .+|=|++|++-|..+--+-. ..+.--.+-..+||+|+||-
T Consensus 166 ~G~~~i~~l~~g~l~~lt~~AsIlGl~ViGaLvat~v~i~~p~~~~~g~~~~~~Q~~LD~i~Pgl 230 (269)
T COG3716 166 VGVKAIDKLGGGNLQKLTEGASILGLTVIGALVATWVKINVPVSFAAGKVVATVQDILDKIFPGL 230 (269)
T ss_pred HhHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHheEEEEEEEEecCCceeehHHHHHHHHhhhH
Confidence 58999999998 888876 57889999999876532211 01112234568999999983
No 8
>PRK10738 hypothetical protein; Provisional
Probab=36.68 E-value=32 Score=27.19 Aligned_cols=24 Identities=21% Similarity=0.282 Sum_probs=18.4
Q ss_pred hHHHHHHHHHHhhhhhhhHHHHHHH
Q psy5788 122 FLNKMELLMASLTSLIEGITVIAKL 146 (204)
Q Consensus 122 FV~KMELLMa~Lt~~~~~~~~~~~~ 146 (204)
=.+=||||+++|.+|. ||++..-+
T Consensus 33 g~~P~EllL~aLg~Ct-~i~v~~~l 56 (134)
T PRK10738 33 APSPMEMVLMAAGGCS-AIDVVSIL 56 (134)
T ss_pred CCCHHHHHHHHHcCch-HHHHHHHH
Confidence 3467999999998885 77776544
No 9
>PF13691 Lactamase_B_4: tRNase Z endonuclease
Probab=34.87 E-value=29 Score=25.06 Aligned_cols=44 Identities=27% Similarity=0.425 Sum_probs=30.0
Q ss_pred ceeEeecCCCCeee-EE-----eeCCCCceEEEEcCCCCCCCCCcccccccc-cccCCC
Q psy5788 56 SSCLLSSPMGDRMI-SV-----RCEPQAGIQVAIAHSPRKDFFCGQLVKERK-WENLGG 107 (204)
Q Consensus 56 ssillASP~gdr~I-aV-----R~~p~~gI~V~I~rs~~~Df~~sdlv~D~K-We~Lgg 107 (204)
++++|..++..|.+ -+ |+=.+.+|++ ++..+. +++-.. |++.||
T Consensus 13 p~l~l~~d~~rYlFGn~gEGtQR~~~e~~ikl----~kl~~I----FlT~~~~w~~~GG 63 (63)
T PF13691_consen 13 PSLLLFFDSRRYLFGNCGEGTQRACNEHKIKL----SKLNDI----FLTGLSSWENIGG 63 (63)
T ss_pred CEEEEEeCCceEEeccCCcHHHHHHHHcCCCc----cccceE----EECCCCcccccCC
Confidence 78999999999998 45 6666666655 334444 344444 888876
No 10
>smart00139 MyTH4 Domain in Myosin and Kinesin Tails. Domain present twice in myosin-VIIa, and also present in 3 other myosins.
Probab=34.37 E-value=9.6 Score=30.53 Aligned_cols=36 Identities=31% Similarity=0.629 Sum_probs=23.0
Q ss_pred cCchHhHHHHHHHHHHHHHHHH-HHHHHHHhceeeccc
Q psy5788 4 SYEPQELRDLIFCQIYQHQISA-MEKLAKCMGWQFLSS 40 (204)
Q Consensus 4 S~e~QELrDlil~Qi~QHQV~~-vq~LAK~MGW~vLs~ 40 (204)
..+..+|||=|+||+.. |..- =..-+..-||++|+.
T Consensus 55 ~~~~~~LrDEiy~QLiK-Qtt~Np~~~s~~rgW~Ll~l 91 (144)
T smart00139 55 GLAHPELRDEIYCQLIK-QLTDNPSRQSEERGWELLYL 91 (144)
T ss_pred HhccHHHHHHHHHHHHH-HHhCCCCchHHHHHHHHHHH
Confidence 45678999999999864 2221 011234568988875
No 11
>PRK13703 conjugal pilus assembly protein TraF; Provisional
Probab=30.68 E-value=75 Score=28.23 Aligned_cols=53 Identities=15% Similarity=0.216 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHHHHhceeecccCCcc-----------ccCCCCccC--CcceeEeecCCCCee
Q psy5788 16 CQIYQHQISAMEKLAKCMGWQFLSSSAHL-----------GLGGVEPLG--NASSCLLSSPMGDRM 68 (204)
Q Consensus 16 ~Qi~QHQV~~vq~LAK~MGW~vLs~S~Hv-----------G~GpvE~lG--nassillASP~gdr~ 68 (204)
|..++.|.-+|+++|+--||.|+.-|.-= ..|-.+-+| .-++++|..|++...
T Consensus 155 Cp~C~~~aPil~~fa~~yg~~v~~VS~DG~~~p~fp~~~~d~gqa~~l~v~~~PAl~Lv~~~t~~~ 220 (248)
T PRK13703 155 DPIDGQLAQVINDFRDTYGLSVIPVSVDGVINPLLPDSRTDQGQAQRLGVKYFPALMLVDPKSGSV 220 (248)
T ss_pred CchhHHHHHHHHHHHHHhCCeEEEEecCCCCCCCCCCCccChhHHHhcCCcccceEEEEECCCCcE
Confidence 77888999999999999999999887511 111111122 456677777776444
No 12
>PF12308 Noelin-1: Neurogenesis glycoprotein; InterPro: IPR022082 This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with PF02191 from PFAM. There are two conserved sequence motifs: SAQ and VQN. Noelin-1 is a glycoprotein which is secreted mainly by postmitotic neurogenic tissues in the developing central and peripheral nervous systems, first appearing after neural tube closure. It is likely that it forms large multimeric complexes.It has a divergent function in neurogenesis. In animal caps neuralized by expression of noggin, co-expression of Noelin-1 causes expression of neuronal differentiation markers several stages before neurogenesis normally occurs in this tissue. Finally, only secreted forms of the protein can activate sensory marker expression, while all forms of the protein can induce early neurogenesis.
Probab=28.05 E-value=51 Score=26.54 Aligned_cols=30 Identities=30% Similarity=0.352 Sum_probs=21.2
Q ss_pred hhHHHHHHHHHHhhhhhhhHHHHHHHhhcc
Q psy5788 121 NFLNKMELLMASLTSLIEGITVIAKLLSSR 150 (204)
Q Consensus 121 NFV~KMELLMa~Lt~~~~~~~~~~~~~~~~ 150 (204)
.||.|||-+|-.|.+-+.-+..=.+.|+.|
T Consensus 68 qyv~~~E~~mk~l~~k~~~~e~~~~~l~~k 97 (101)
T PF12308_consen 68 QYVRKMETQMKGLESKFRQVEDDRKSLSAK 97 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCHHHhhhh
Confidence 579999999999987766555444444433
No 13
>KOG4312|consensus
Probab=26.76 E-value=71 Score=31.12 Aligned_cols=41 Identities=32% Similarity=0.427 Sum_probs=28.3
Q ss_pred HHHHHHHhhhhhhhHHHHHHHhhcchhhhhhhhcccchhhhhhhcCCCCCCC
Q psy5788 126 MELLMASLTSLIEGITVIAKLLSSRDRREKEDRIGESNESILDKICPGRESN 177 (204)
Q Consensus 126 MELLMa~Lt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 (204)
|.+.+-+|+-.-+|-||.-|-|++| -|.-+..|.||||++-
T Consensus 335 ~~~vLlsLaFiay~E~vlRkrLa~~-----------lsaCv~ak~CP~~~~C 375 (449)
T KOG4312|consen 335 MTIVLLSLAFIAYSETVLRKRLAAR-----------LSACVAAKACPVRLSC 375 (449)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHhccCCCCccc
Confidence 4455555666667777777766654 3567899999999764
No 14
>COG4967 PilV Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=25.16 E-value=2.1e+02 Score=24.37 Aligned_cols=59 Identities=19% Similarity=0.025 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhceeecccCCccccCCCCccCCcceeEeecCCCCeeeEE
Q psy5788 11 RDLIFCQIYQHQISAMEKLAKCMGWQFLSSSAHLGLGGVEPLGNASSCLLSSPMGDRMISV 71 (204)
Q Consensus 11 rDlil~Qi~QHQV~~vq~LAK~MGW~vLs~S~HvG~GpvE~lGnassillASP~gdr~IaV 71 (204)
|-+-+.|=++||..+++...-.+-|....-+.=...+++-..||+ .+..+|+|+..+.|
T Consensus 37 ~s~~~t~~a~~r~~~~~l~~~~~e~m~an~~~~a~~a~~~~~~n~--~~~~~~~~~~~~dv 95 (162)
T COG4967 37 RTLRNTQEARQRSIAAQLWQNLLERMRANRSSAADGAKPFYTGNG--VTDTTAGGDVSIDV 95 (162)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccccccccceeccc--eeeeecCCceeeeh
Confidence 455678888888887776665554444333332223333367887 88889999999877
No 15
>PRK05406 LamB/YcsF family protein; Provisional
Probab=23.75 E-value=1.3e+02 Score=27.12 Aligned_cols=42 Identities=26% Similarity=0.420 Sum_probs=35.0
Q ss_pred cccCchHhHHHHHHHHHHHHHHHHHHHHHHHhceeecccCCccccCC
Q psy5788 2 KLSYEPQELRDLIFCQIYQHQISAMEKLAKCMGWQFLSSSAHLGLGG 48 (204)
Q Consensus 2 tLS~e~QELrDlil~Qi~QHQV~~vq~LAK~MGW~vLs~S~HvG~Gp 48 (204)
.+...++||++.+.- |+-+++.+|+..|-.+=+--+|=++.+
T Consensus 76 ~m~~s~~el~~~v~y-----QigAL~~~a~~~g~~l~hVKPHGALYN 117 (246)
T PRK05406 76 NMDLSPEELYALVLY-----QIGALQAIARAAGGRVSHVKPHGALYN 117 (246)
T ss_pred CCCCCHHHHHHHHHH-----HHHHHHHHHHHcCCeeEEeCccHHHHH
Confidence 456788999987764 677999999999999999999977764
No 16
>PF03746 LamB_YcsF: LamB/YcsF family; InterPro: IPR005501 This entry represents the uncharacterised protein family UPF0271, including LamB. The lam locus of Emericella nidulans (Aspergillus nidulans) consists of two divergently transcribed genes, lamA and lamB, involved in the utilization of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression []. The exact molecular function of the proteins in this family is unknown.; PDB: 1V6T_A 1XW8_A 2XU2_A 2DFA_A.
Probab=23.68 E-value=96 Score=27.75 Aligned_cols=41 Identities=29% Similarity=0.441 Sum_probs=26.8
Q ss_pred ccCchHhHHHHHHHHHHHHHHHHHHHHHHHhceeecccCCccccCC
Q psy5788 3 LSYEPQELRDLIFCQIYQHQISAMEKLAKCMGWQFLSSSAHLGLGG 48 (204)
Q Consensus 3 LS~e~QELrDlil~Qi~QHQV~~vq~LAK~MGW~vLs~S~HvG~Gp 48 (204)
+...++||++.++- |+.+++.+|+..|-.+=|--+|=++.+
T Consensus 75 m~~s~~el~~~v~y-----QigaL~~~a~~~g~~l~hVKPHGALYn 115 (242)
T PF03746_consen 75 MDISPEELRDSVLY-----QIGALQAIAAAEGVPLHHVKPHGALYN 115 (242)
T ss_dssp ----HHHHHHHHHH-----HHHHHHHHHHHTT--EEEE---HHHHH
T ss_pred CCCCHHHHHHHHHH-----HHHHHHHHHHHcCCeeEEecccHHHHH
Confidence 55678999988875 567899999999999999999977654
No 17
>KOG3725|consensus
Probab=23.61 E-value=97 Score=29.38 Aligned_cols=60 Identities=18% Similarity=0.141 Sum_probs=34.7
Q ss_pred CchHhHHHHHHHHHHH------HHHHHHHHHHHHhceeecccCCccccCCCCccCC--cceeEeecCCC
Q psy5788 5 YEPQELRDLIFCQIYQ------HQISAMEKLAKCMGWQFLSSSAHLGLGGVEPLGN--ASSCLLSSPMG 65 (204)
Q Consensus 5 ~e~QELrDlil~Qi~Q------HQV~~vq~LAK~MGW~vLs~S~HvG~GpvE~lGn--assillASP~g 65 (204)
+|+-=|+||...||.+ |-...-.+|...|+. ++++.+-+..-|+-|.|- |++++.|+|+|
T Consensus 232 nhLrCL~dFVeaQmtyYAQcyq~MlDLQkqLg~fps~-~~s~~~~~s~sp~ps~~pt~aaa~a~a~pSg 299 (375)
T KOG3725|consen 232 NHLRCLRDFVEAQMTYYAQCYQLMLDLQKQLGGFPSF-RGSSAILVSNSPDPSNGPTMAAAIAAAKPSG 299 (375)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccc-ccccccccCCCCCCCCCchHHHHHhccCCcc
Confidence 3556688999988853 222222345555553 456666666666666654 34556666665
No 18
>TIGR00828 EIID-AGA PTS system, mannose/fructose/sorbose family, IID component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Man family is unique in several respects among PTS permease families.It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine,N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IID subunits of this family of PTS transporters.
Probab=23.54 E-value=50 Score=29.73 Aligned_cols=57 Identities=25% Similarity=0.375 Sum_probs=34.2
Q ss_pred CCChhHHHHH-HHHHHhhh--hhhhHHHHHHHhhcchhhhhhhh-------ccc----chhhhhhhcCCCC
Q psy5788 118 EGKNFLNKME-LLMASLTS--LIEGITVIAKLLSSRDRREKEDR-------IGE----SNESILDKICPGR 174 (204)
Q Consensus 118 eGrNFV~KME-LLMa~Lt~--~~~~~~~~~~~~~~~~~~~~~~~-------~~~----~~~~~~~~~~~~~ 174 (204)
.|++|+.++. =.|..+|. .+=|.+|+.-+..+--.-.---. .|+ +-.++||+|+||-
T Consensus 162 ~G~~~i~~l~~~~~~~it~~a~ilGl~vvGal~as~V~v~~~l~~~~~~~~~g~~~~~~~Q~ilD~I~P~l 232 (271)
T TIGR00828 162 KGVKIVDDMGGNNLQKLTEGASILGLFVMGALVAKWTHINVPLVVSRINDHSGKVDVATVQNILDQLMPGL 232 (271)
T ss_pred hHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHhheeEEEEEeEEEEecccCCCceeeeeHHHHHHHHhhhh
Confidence 5788877665 24444443 46699999888776522110000 122 4558999999973
No 19
>PF02566 OsmC: OsmC-like protein; InterPro: IPR003718 Osmotically inducible protein C (OsmC) is a stress-induced protein found in Escherichia coli. The transcription of the osmC gene of E. coli is regulated as a function of the phase of growth and is induced during the late exponential phase when the growth rate slows before entry into stationary phase. The transcription is initiated by two overlapping promoters, osmCp1 and osmCp2 []. An organic hydroperoxide detoxification protein (OHR) from Xanthomonas campestris pv. phaseoli is highly induced by organic hydroperoxides, weakly induced by H2O2, and not induced at all by a superoxide generator. Ohr may be a new type of organic hydroperoxide detoxification protein [, ].; GO: 0006950 response to stress; PDB: 2D7V_A 2BJO_A 1USP_A 2PN2_A 2QL8_A 1N2F_A 1UKK_A 1VLA_D 3CJE_A 2ONF_B ....
Probab=22.54 E-value=55 Score=22.90 Aligned_cols=15 Identities=47% Similarity=0.565 Sum_probs=12.1
Q ss_pred HHHHHHHHHhhhhhh
Q psy5788 124 NKMELLMASLTSLIE 138 (204)
Q Consensus 124 ~KMELLMa~Lt~~~~ 138 (204)
+=+|||+++|.+|+-
T Consensus 7 ~P~elllaala~C~~ 21 (100)
T PF02566_consen 7 NPEELLLAALASCFA 21 (100)
T ss_dssp -HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHH
Confidence 447999999999974
No 20
>PRK07027 cobalamin biosynthesis protein CbiG; Provisional
Probab=22.47 E-value=74 Score=24.95 Aligned_cols=75 Identities=24% Similarity=0.429 Sum_probs=45.0
Q ss_pred CchHhHHHHHHHHHHHHHH-----------------HHHHHHHHHhceeeccc---------------C----CccccCC
Q psy5788 5 YEPQELRDLIFCQIYQHQI-----------------SAMEKLAKCMGWQFLSS---------------S----AHLGLGG 48 (204)
Q Consensus 5 ~e~QELrDlil~Qi~QHQV-----------------~~vq~LAK~MGW~vLs~---------------S----~HvG~Gp 48 (204)
.+.+++.+.|..-+.+|.+ ..+..+|+.+||-+.-+ | .|+|++.
T Consensus 14 ~~~e~i~~ai~~~L~~~~l~~~si~~lasi~~K~~E~~L~~~A~~lg~pl~~~~~~eL~~~~~~~~~~S~~v~~~~Gv~s 93 (126)
T PRK07027 14 VPAEQIEAAIRAALAQRPLASADVRVVATLDLKADEAGLLALCARHGWPLRAFSAAQLAASEGALSGPSDAVRARVGVDG 93 (126)
T ss_pred CCHHHHHHHHHHHHHHcCCCHHHhheeEehhhhcCCHHHHHHHHHhCCCeEEeCHHHHHhccCCCCCcCHHHHHHhCCCh
Confidence 3566777777766666543 46788999999977654 1 2345554
Q ss_pred CCccCCcceeEeecCCCCeeeEEeeCCCCceEEEEcC
Q psy5788 49 VEPLGNASSCLLSSPMGDRMISVRCEPQAGIQVAIAH 85 (204)
Q Consensus 49 vE~lGnassillASP~gdr~IaVR~~p~~gI~V~I~r 85 (204)
|.. ++.++++|+|... .=|.- ..|++|.|++
T Consensus 94 VaE----aaAl~a~~~~~Li-~~K~~-~~~vTvAiA~ 124 (126)
T PRK07027 94 VAE----PCALLAAPRGRLI-LPKTA-LDGVTVALAG 124 (126)
T ss_pred HHH----HHHHHhCCCCeEE-EEEEe-eCCeEEEEEe
Confidence 421 2226677766433 22322 3578888876
No 21
>PF15337 Vasculin: Vascular protein family Vasculin-like 1
Probab=22.07 E-value=59 Score=26.06 Aligned_cols=22 Identities=32% Similarity=0.616 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHhceeecc
Q psy5788 18 IYQHQISAMEKLAKCMGWQFLS 39 (204)
Q Consensus 18 i~QHQV~~vq~LAK~MGW~vLs 39 (204)
+.+|-..+=+.|-|-||||=-+
T Consensus 4 ~lS~SLEaEhRLLk~MGWqEy~ 25 (97)
T PF15337_consen 4 VLSSSLEAEHRLLKAMGWQEYP 25 (97)
T ss_pred chhhHHHHHHHHHHHhcccccC
Confidence 4566777888899999999765
No 22
>PF07539 DRIM: Down-regulated in metastasis; InterPro: IPR011430 These eukaryotic proteins include DRIM (Down-Regulated In Metastasis) (O75691 from SWISSPROT), which is differentially expressed in metastatic and non-metastatic human breast carcinoma cells []. It is believed to be involved in processing of non-coding RNA [].
Probab=20.37 E-value=71 Score=25.82 Aligned_cols=31 Identities=29% Similarity=0.734 Sum_probs=23.0
Q ss_pred CchHhHHHHHHHHHHHHHHHHHHHHH-HH-hcee
Q psy5788 5 YEPQELRDLIFCQIYQHQISAMEKLA-KC-MGWQ 36 (204)
Q Consensus 5 ~e~QELrDlil~Qi~QHQV~~vq~LA-K~-MGW~ 36 (204)
|..+||+++++ ++..|.-.-||++| +| +.|-
T Consensus 13 ~~~~~l~~~~~-~LL~~~d~~vQklAL~cll~~k 45 (141)
T PF07539_consen 13 YRSDELYDALL-RLLSSRDPEVQKLALDCLLTWK 45 (141)
T ss_pred hhHHHHHHHHH-HHHcCCCHHHHHHHHHHHHHhC
Confidence 66789999987 77777777788888 44 4564
No 23
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=20.20 E-value=6e+02 Score=22.73 Aligned_cols=107 Identities=15% Similarity=0.304 Sum_probs=61.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhceeecccCCccccCCCCccCCccee----EeecC------CCCeeeEEeeCCCCc
Q psy5788 9 ELRDLIFCQIYQHQISAMEKLAKCMGWQFLSSSAHLGLGGVEPLGNASSC----LLSSP------MGDRMISVRCEPQAG 78 (204)
Q Consensus 9 ELrDlil~Qi~QHQV~~vq~LAK~MGW~vLs~S~HvG~GpvE~lGnassi----llASP------~gdr~IaVR~~p~~g 78 (204)
+-.+=|..|+.+|=-.-++++|+..+|+=.....++-+-.. ...-+.| -+..| -|.-.+.|||+...+
T Consensus 46 ~~~~~l~~~v~~~~~~~i~~~a~~~~~~~y~~~~~i~ip~~--~~~lp~C~~pl~~~~~~~~~~~~gr~~~~V~C~~~~~ 123 (261)
T PRK06804 46 NTRKQVYTQVLHAATQDIAQTAKNKNWQGYQVKMNIFIPAE--ISRYKPCQKALQVALPTAETQHLSRLRYEVSCPDGQG 123 (261)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHhccccccccceeEecCCh--hhcCCCCCCCceEEcCCCCccccceeEEEEEeCCCCC
Confidence 34445666666666678999999999987665554443321 1111112 22222 355567899986556
Q ss_pred eEEEEcC---------CCCCCCCCcccccccccccCCCCceeeecccCCCChh
Q psy5788 79 IQVAIAH---------SPRKDFFCGQLVKERKWENLGGPFKEVRWDKMEGKNF 122 (204)
Q Consensus 79 I~V~I~r---------s~~~Df~~sdlv~D~KWe~Lgg~FKEV~w~kMeGrNF 122 (204)
-+++++= ....++.+++.++..- | .+++++.+++.|.-|
T Consensus 124 W~v~v~v~v~v~~~VvVA~r~L~rG~~I~~~D---l--~~~~~~~~~l~~~~~ 171 (261)
T PRK06804 124 WEVVVTVKPDIYLPVWVAKQTLERGRKVQADD---I--ELKKKNISGVQGGYI 171 (261)
T ss_pred EEEEEEEEEEEEEEEEEEccCcCCCCCcCHHH---e--EEEEEehhcCCcccc
Confidence 5555511 1235677777777543 2 256667777765444
Done!