Query 040959
Match_columns 391
No_of_seqs 120 out of 466
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 02:27:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040959.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040959hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2335 Secreted and surface p 99.9 9.7E-24 2.1E-28 194.0 10.4 134 28-174 42-184 (187)
2 PF02469 Fasciclin: Fasciclin 99.8 1.4E-21 3E-26 159.9 4.6 118 44-171 2-128 (128)
3 smart00554 FAS1 Four repeated 99.8 2.9E-20 6.3E-25 147.5 6.7 92 68-172 1-99 (99)
4 KOG1437 Fasciclin and related 98.6 9.9E-08 2.2E-12 102.4 6.8 138 33-181 373-517 (682)
5 KOG1437 Fasciclin and related 98.3 1.7E-06 3.6E-11 93.2 7.9 127 37-172 511-642 (682)
6 PF07172 GRP: Glycine rich pro 64.6 5.9 0.00013 33.7 2.6 16 1-16 1-16 (95)
7 PF11393 IcmL: Macrophage kill 28.9 43 0.00092 28.5 2.2 41 30-71 40-80 (108)
8 COG5233 GRH1 Peripheral Golgi 14.6 1.9E+02 0.0041 30.5 3.7 44 237-281 328-371 (417)
9 PF14810 TGT_C2: Patch-forming 14.4 1E+02 0.0022 25.1 1.5 16 374-389 32-47 (74)
10 COG4669 EscJ Type III secretor 13.8 2.4E+02 0.0052 28.3 4.1 55 26-100 26-80 (246)
No 1
>COG2335 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]
Probab=99.90 E-value=9.7e-24 Score=194.01 Aligned_cols=134 Identities=18% Similarity=0.257 Sum_probs=115.3
Q ss_pred CCchhHHHHHHHHH-hCChHHHHHHHHhcCchhhccCCCCeEEEccCChhhccCC------CC--CChhHHHhccccccc
Q 040959 28 IPTSDLDAVLLLLH-AGGHTLFANAIATSDLLFDLLSLPSLTLFAPTDPSLFAVD------MT--QTPPFYLSILRLHVL 98 (391)
Q Consensus 28 ~p~~ele~IietLr-s~GytsfA~AL~aAgLl~~Ll~~gpfTIFAPTDeAF~ald------L~--~n~~~L~sVLrYHVV 98 (391)
.......+|++... ...|+.|..++++++|.+.|.+.++||||||+|+||.++. +. +++..|+++|.|||+
T Consensus 42 ~~~~~~~~iV~~a~~~~~f~tl~~a~~aa~Lv~~L~~~gp~TVFaPtn~AFa~lp~~T~~~Ll~pen~~~L~~iLtYHVv 121 (187)
T COG2335 42 AVKGNRADIVESAANNPSFTTLVAALKAAGLVDTLNETGPFTVFAPTNEAFAKLPAGTLDALLKPENKPLLTKILTYHVV 121 (187)
T ss_pred hhccchhHHHHHHccCcchHHHHHHHHhhhhHHHhcCCCCeEEecCCHHHHHhCChhHHHHHhCccchhhhheeeEEEEE
Confidence 33556788888884 5569999999999999999999999999999999999852 23 489999999999999
Q ss_pred CCccCHHHHHhhcCCCCCCCCCCeeccccCCCeEEEEEcCCCcEEEccEEEeCCCccccCCEEEEEeCccccCCCC
Q 040959 99 PLRLSWTELLQLISPSNNNNNSSRLPTLLPSRDLHVTRGDSGALLVGGVQVVMPGLYYSSYVAVHGLAGILTFRSP 174 (391)
Q Consensus 99 PGrLs~sDL~~Li~~~~~~pnGTtLpTLL~G~~LtVT~~sgg~V~VNgVkVV~PDI~~ssNGVVHGIDgVLlP~SP 174 (391)
+|+++.+||... ..+.| ++|.+|.|... +++++||++.|+.+|+.. +|||||+||.||+|+.+
T Consensus 122 ~Gk~~~~~l~~~----------~~v~t-~~G~~~~i~~~-~~~~~Vn~a~v~~~di~a-~NgvIhvID~Vl~Pp~~ 184 (187)
T COG2335 122 EGKITAADLKSS----------GSVKT-VQGADLKIKVT-GGGVYVNDATVTIADINA-SNGVIHVIDKVLIPPMD 184 (187)
T ss_pred cCcccHHHhhcc----------cccee-ecCceEEEEEc-CCcEEEeeeEEEeccEec-cCcEEEEEeeeccCCCc
Confidence 999999999754 35677 58999999984 667999999999999976 58999999999999653
No 2
>PF02469 Fasciclin: Fasciclin domain; InterPro: IPR000782 The FAS1 (fasciclin-like) domain is an extracellular module of about 140 amino acid residues. It has been suggested that the FAS1 domain represents an ancient cell adhesion domain common to plants and animals []; related FAS1 domains are also found in bacteria []. The crystal structure of FAS1 domains 3 and 4 of fasciclin I from Drosophila melanogaster (Fruit fly) has been determined, revealing a novel domain fold consisting of a seven-stranded beta wedge and at least five alpha helices; two well-ordered N-acetylglucosamine groups attached to a conserved asparagine are located in the interface region between the two FAS1 domains []. Fasciclin I is an insect neural cell adhesion molecule involved in axonal guidance that is attached to the membrane by a GPI-anchored protein. FAS1 domains are present in many secreted and membrane-anchored proteins. These proteins are usually GPI anchored and consist of: (i) a single FAS1 domain, (ii) a tandem array of FAS1 domains, or (iii) FAS1 domain(s) interspersed with other domains. Proteins known to contain a FAS1 domain include: Fasciclin I (4 FAS1 domains). Human TGF-beta induced Ig-H3 (BIgH3) protein (4 FAS1 domains), where the FAS1 domains mediate cell adhesion through an interaction with alpha3/beta1 integrin; mutation in the FAS1 domains result in corneal dystrophy []. Volvox major cell adhesion protein (2 FAS1 domains) []. Arabidopsis fasciclin-like arabinogalactan proteins (2 FAS1 domains) []. Mammalian stabilin protein, a family of fasciclin-like hyaluronan receptor homologues (7 FAS1 domains)[]. Human extracellular matrix protein periostin (4 FAS1 domains). Bacterial immunogenic protein MPT70 (1 FAS1 domain) []. The FAS1 domains of both human periostin (Q15063 from SWISSPROT) and BIgH3 (Q15582 from SWISSPROT) proteins were found to contain vitamin K-dependent gamma-carboxyglutamate residues []. Gamma-carboxyglutamate residues are more commonly associated with GLA domains (IPR000294 from INTERPRO), where they occur through post-translational modification catalysed by the vitamin K-dependent enzyme gamma-glutamylcarboxylase.; PDB: 1O70_A 1W7D_A 1W7E_A 1NYO_A 1X3B_A 2VXP_A.
Probab=99.84 E-value=1.4e-21 Score=159.90 Aligned_cols=118 Identities=24% Similarity=0.338 Sum_probs=95.8
Q ss_pred ChHHHHHHHHhcCchhhc-cCCCCeEEEccCChhhccCC------CCCChhHHHhcccccccCCccCHHHHHhhcCCCCC
Q 040959 44 GHTLFANAIATSDLLFDL-LSLPSLTLFAPTDPSLFAVD------MTQTPPFYLSILRLHVLPLRLSWTELLQLISPSNN 116 (391)
Q Consensus 44 GytsfA~AL~aAgLl~~L-l~~gpfTIFAPTDeAF~ald------L~~n~~~L~sVLrYHVVPGrLs~sDL~~Li~~~~~ 116 (391)
+|+.|+.+|+++|+...| ...+.+|||||+|+||.+.. +..+.+.+.++|+||+++|++..++|...
T Consensus 2 ~~s~f~~~l~~~~l~~~l~~~~~~~TvfaP~d~a~~~~~~~~~~~~~~~~~~l~~~l~~hiv~~~~~~~~l~~~------ 75 (128)
T PF02469_consen 2 DLSTFSRLLEQAGLADLLNDSDGNYTVFAPTDDAFQKLSQETNSSLADSKEQLKSLLKYHIVPGSITSSDLRNG------ 75 (128)
T ss_dssp TTHHHHHHHHHTTCHHHHGCSSSSEEEEEE-HHHHHHSHHHHHHHHHTHHHHHHHHHHHTEEES---HCHHHCH------
T ss_pred CHHHHHHHHHHcCCHHHHhcCCCCEEEEEECHHHHHhccccccchhhhhhhhHhhhhhhEEEcCceehhhhccc------
Confidence 689999999999999988 66799999999999997641 11256789999999999999999988542
Q ss_pred CCCCCeeccccCCCeEEEEEc-CCCcEEEcc-EEEeCCCccccCCEEEEEeCccccC
Q 040959 117 NNNSSRLPTLLPSRDLHVTRG-DSGALLVGG-VQVVMPGLYYSSYVAVHGLAGILTF 171 (391)
Q Consensus 117 ~pnGTtLpTLL~G~~LtVT~~-sgg~V~VNg-VkVV~PDI~~ssNGVVHGIDgVLlP 171 (391)
++.++|++.|+.+.|+.. +++.++||+ ++|+..|+.. +||+||+||+||+|
T Consensus 76 ---~~~~~t~~~g~~~~v~~~~~~~~~~v~~~a~i~~~~~~~-~nG~ih~id~vL~P 128 (128)
T PF02469_consen 76 ---KQTLETLLNGQPLRVSSSPSNGTIYVNGKARIVKSDIEA-SNGVIHIIDDVLIP 128 (128)
T ss_dssp ---HEEEEBSSTTCEEEEEEEGGTTEEEECCEEEESEEEEEE-SSEEEEEESS-TSS
T ss_pred ---cccceeccCCCEEEEEEEecCCceEecCceEEEeCCEEe-CCEEEEEECceECc
Confidence 257888678999999985 368999999 9999999976 58999999999998
No 3
>smart00554 FAS1 Four repeated domains in the Fasciclin I family of proteins, present in many other contexts.
Probab=99.81 E-value=2.9e-20 Score=147.48 Aligned_cols=92 Identities=34% Similarity=0.496 Sum_probs=77.1
Q ss_pred EEEccCChhhccCC------CCCChhHHHhcccccccCCccCHHHHHhhcCCCCCCCCCCeeccccCCCeEEEEEcCC-C
Q 040959 68 TLFAPTDPSLFAVD------MTQTPPFYLSILRLHVLPLRLSWTELLQLISPSNNNNNSSRLPTLLPSRDLHVTRGDS-G 140 (391)
Q Consensus 68 TIFAPTDeAF~ald------L~~n~~~L~sVLrYHVVPGrLs~sDL~~Li~~~~~~pnGTtLpTLL~G~~LtVT~~sg-g 140 (391)
|||||+|+||.+.. +..+. .++++|+||++|+++..++|.. |..++|+ .|+.|.|+...+ +
T Consensus 1 TvfaP~d~Af~~~~~~~~~~l~~~~-~l~~ll~~Hiv~~~~~~~~l~~----------~~~~~Tl-~g~~l~v~~~~~~~ 68 (99)
T smart00554 1 TVFAPTDEAFQKLPPGTLNSLLADP-KLKNLLLYHVVPGRLSSADLLN----------GGTLPTL-AGSKLRVTRSGDSG 68 (99)
T ss_pred CEeCcCHHHHHhcCHHHHHHHhCCH-HHHHHHHhcEeCceEcHHHhcc----------CCccccC-CCCEEEEEEeCCCC
Confidence 89999999998852 11222 7899999999999999999843 4678886 589999999543 7
Q ss_pred cEEEccEEEeCCCccccCCEEEEEeCccccCC
Q 040959 141 ALLVGGVQVVMPGLYYSSYVAVHGLAGILTFR 172 (391)
Q Consensus 141 ~V~VNgVkVV~PDI~~ssNGVVHGIDgVLlP~ 172 (391)
.++||+++|+.+|+.. +|||||+||+||+|.
T Consensus 69 ~i~in~~~v~~~di~~-~nGvih~Id~vL~P~ 99 (99)
T smart00554 69 TVTVNGARIVEADIAA-TNGVVHVIDRVLLPP 99 (99)
T ss_pred eEEEcceEEEECCEec-CCeEEEEECceeCCC
Confidence 8999999999999987 489999999999984
No 4
>KOG1437 consensus Fasciclin and related adhesion glycoproteins [Cell wall/membrane/envelope biogenesis; Extracellular structures]
Probab=98.55 E-value=9.9e-08 Score=102.39 Aligned_cols=138 Identities=18% Similarity=0.193 Sum_probs=99.7
Q ss_pred HHHHHHHHHhCChHHHHHHHHhcCchhhccCCCCeEEEccCChhhccCCCCCChhHHHhcccccccCCccCHHHHHhhcC
Q 040959 33 LDAVLLLLHAGGHTLFANAIATSDLLFDLLSLPSLTLFAPTDPSLFAVDMTQTPPFYLSILRLHVLPLRLSWTELLQLIS 112 (391)
Q Consensus 33 le~IietLrs~GytsfA~AL~aAgLl~~Ll~~gpfTIFAPTDeAF~aldL~~n~~~L~sVLrYHVVPGrLs~sDL~~Li~ 112 (391)
.....+..++...+++...+...+++.-|...+.+|+|+|+|++|..++...-...+..+|.||++|-++..+++.+.
T Consensus 373 ~~~l~~La~e~~~st~~rlv~elgll~~L~~n~e~t~~lp~n~~fd~~~~~~~r~l~~qIL~~HII~~~~~~~~~y~~-- 450 (682)
T KOG1437|consen 373 LKNLMSLAREDEISTSMRLVAELGLLTALAPNDEATLLLPTNNLFDDLTPLESRRLAEQILYNHIIPEYLTSSSMYNG-- 450 (682)
T ss_pred HHHHHHHHhcccccHHHHHHHhccceEEEcCCCceEEeeehhhhccCCChhhhHHHHHHHHHHhCcchhhhhhhhhcc--
Confidence 556677788888889999998889888776555599999999999985432222336789999999999999876432
Q ss_pred CCCCCCCCCeeccccCCCeEEE--EEcCC----CcEEEcc-EEEeCCCccccCCEEEEEeCccccCCCCCCCCCCC
Q 040959 113 PSNNNNNSSRLPTLLPSRDLHV--TRGDS----GALLVGG-VQVVMPGLYYSSYVAVHGLAGILTFRSPIHNNHSN 181 (391)
Q Consensus 113 ~~~~~pnGTtLpTLL~G~~LtV--T~~sg----g~V~VNg-VkVV~PDI~~ssNGVVHGIDgVLlP~SP~~~~~~~ 181 (391)
++.++|+ .|..+.+ .+..+ ..+.++| +.|++.|+.. +||+||.||+||.|.++.+.+.+.
T Consensus 451 -------~~~v~t~-g~~~l~~fv~r~~~s~~~t~i~~~~~~~Ii~aDi~~-~nGvvH~id~vl~p~~l~~~l~~d 517 (682)
T KOG1437|consen 451 -------QTTVRTL-GKNKLLYFVYRHSVSANVTDILIGNEACIIEADISV-KNGVVHIIDRVLDPVSLMEDLKTD 517 (682)
T ss_pred -------cceeecc-CCeEEEEEEecccccccceeeeccceeeEEecccce-ecCceEEeeEEcCcccHHHHHhhc
Confidence 3377774 4543333 22111 2355555 5788999976 589999999999997776665554
No 5
>KOG1437 consensus Fasciclin and related adhesion glycoproteins [Cell wall/membrane/envelope biogenesis; Extracellular structures]
Probab=98.28 E-value=1.7e-06 Score=93.21 Aligned_cols=127 Identities=17% Similarity=0.051 Sum_probs=83.8
Q ss_pred HHHHHh-CChHHHHHHHHhcCchhhccCCCCeEEEccCChhhccCCCC----CChhHHHhcccccccCCccCHHHHHhhc
Q 040959 37 LLLLHA-GGHTLFANAIATSDLLFDLLSLPSLTLFAPTDPSLFAVDMT----QTPPFYLSILRLHVLPLRLSWTELLQLI 111 (391)
Q Consensus 37 ietLrs-~GytsfA~AL~aAgLl~~Ll~~gpfTIFAPTDeAF~aldL~----~n~~~L~sVLrYHVVPGrLs~sDL~~Li 111 (391)
.+.|++ ..++.+..+++.+++-+++...+.+|+|+|+|+|+.+.... .+...|..+|.||++++.... ++...
T Consensus 511 ~~~l~~d~r~s~~~~~le~~~l~e~l~~~~~~t~fvPt~ka~~~~~~~~~~~~~~~~l~~~l~yH~v~~~~~l-s~~~~- 588 (682)
T KOG1437|consen 511 MEDLKTDGRISGTVQGLEGVLLPEELTPEGNYTLFVPTNKAWQKSTKDEKSLFHKKALQDFLKYHLVPGQSRL-SLGSS- 588 (682)
T ss_pred HHHHhhccchhhhHHhhhhcCChhhhccCCceEEEeecccccccCCcchhhcchHHHHHHHHHhccccceeee-ecccc-
Confidence 344443 44666666777778877776779999999999999884322 367889999999999998861 11110
Q ss_pred CCCCCCCCCCeeccccCCCeEEEEEcCCCcEEEccEEEeCCCccccCCEEEEEeCccccCC
Q 040959 112 SPSNNNNNSSRLPTLLPSRDLHVTRGDSGALLVGGVQVVMPGLYYSSYVAVHGLAGILTFR 172 (391)
Q Consensus 112 ~~~~~~pnGTtLpTLL~G~~LtVT~~sgg~V~VNgVkVV~PDI~~ssNGVVHGIDgVLlP~ 172 (391)
+. ...+ ...+ ..|..+.+... .....+|-.+++..|++. .|||+|.||.||.|.
T Consensus 589 -~~--v~~~-~k~s-~~~~~~~~~~~-~~~~~vn~e~~~~~~i~~-~n~~~h~i~~vl~p~ 642 (682)
T KOG1437|consen 589 -PY--VMIQ-VKLS-LRGDHLFFSLV-NPRGDVNKERLVGIDIMG-TNGVVHVIDLVLKPP 642 (682)
T ss_pred -cc--eeee-eeEE-EecccEEeeee-ccccceeeeeeeccceee-ecceeEEEEEEcccC
Confidence 00 0000 1112 12333333331 345667888999999975 589999999999994
No 6
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=64.55 E-value=5.9 Score=33.67 Aligned_cols=16 Identities=25% Similarity=0.432 Sum_probs=11.2
Q ss_pred CchhhHHHHHHHHHHH
Q 040959 1 MATHKILMTTILFTLT 16 (391)
Q Consensus 1 MAt~~il~~~il~~ll 16 (391)
||||++||+.++|..+
T Consensus 1 MaSK~~llL~l~LA~l 16 (95)
T PF07172_consen 1 MASKAFLLLGLLLAAL 16 (95)
T ss_pred CchhHHHHHHHHHHHH
Confidence 9988877776655444
No 7
>PF11393 IcmL: Macrophage killing protein with similarity to conjugation protein; InterPro: IPR021055 IcmL contains two amphipathic beta-sheet regions, required for the pore-forming ability which may be related to the transfer of this protein into a host cell membrane []. The icmL gene shows significant similarity to plasmid genes involved in conjugation however IcmL is thought to be required for macrophage killing. It is unknown whether conjugation plays a role in macrophage killing [].
Probab=28.87 E-value=43 Score=28.54 Aligned_cols=41 Identities=22% Similarity=0.257 Sum_probs=32.8
Q ss_pred chhHHHHHHHHHhCChHHHHHHHHhcCchhhccCCCCeEEEc
Q 040959 30 TSDLDAVLLLLHAGGHTLFANAIATSDLLFDLLSLPSLTLFA 71 (391)
Q Consensus 30 ~~ele~IietLrs~GytsfA~AL~aAgLl~~Ll~~gpfTIFA 71 (391)
+++++++.......|+..|..+|+++|+++...+ +.+++=|
T Consensus 40 ~~ql~~~~~~fT~~g~~~f~~aL~~Sg~l~~ik~-~~l~~~a 80 (108)
T PF11393_consen 40 RQQLNDARKCFTDEGWNSFQKALQKSGILDAIKD-KRLNLSA 80 (108)
T ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHCCCHHHHHh-cceEEee
Confidence 5677888888888999999999999999887654 4556553
No 8
>COG5233 GRH1 Peripheral Golgi membrane protein [Intracellular trafficking and secretion]
Probab=14.56 E-value=1.9e+02 Score=30.51 Aligned_cols=44 Identities=23% Similarity=0.150 Sum_probs=35.4
Q ss_pred CCCCCcccccCCCcceeeecccccccccccccCcCCCCCCCCCcc
Q 040959 237 EGLHGYTPAESPEGHVVLTGKPIKHKKAKQDTDRTSSSNVNDTVP 281 (391)
Q Consensus 237 ~~~~~~~~~~~~~~~~vl~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 (391)
.+-..+++|++ .+-.+..||-.+||++-|+.--+|--+-|...|
T Consensus 328 ~se~a~~~~~~-s~p~~~~~kks~hk~gtq~~~~~sy~~e~~~~~ 371 (417)
T COG5233 328 RSEFAAKNFLS-SLPLSFYGKKSEHKSGTQRAVTTSYHEENGECP 371 (417)
T ss_pred cchhccCcccc-cCCcccccccccccccccchhhHhHhhcCCccc
Confidence 55678899999 677788999999999999887777777666554
No 9
>PF14810 TGT_C2: Patch-forming domain C2 of tRNA-guanine transglycosylase; PDB: 1J2B_A 1IT8_A 1IT7_B 1IQ8_A.
Probab=14.38 E-value=1e+02 Score=25.10 Aligned_cols=16 Identities=44% Similarity=0.706 Sum_probs=12.3
Q ss_pred hhhhceeeeecceeee
Q 040959 374 RSRKIREVFVGGEICA 389 (391)
Q Consensus 374 ~~~~~~~~~~~~~~~~ 389 (391)
+..|||.|+++||..|
T Consensus 32 ~t~riR~v~~~~~~la 47 (74)
T PF14810_consen 32 KTGRIRQVLVDGERLA 47 (74)
T ss_dssp SSS-EEEEEETTEEEE
T ss_pred cCCceEEEEeCCeEEE
Confidence 4589999999999654
No 10
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=13.81 E-value=2.4e+02 Score=28.27 Aligned_cols=55 Identities=22% Similarity=0.260 Sum_probs=34.2
Q ss_pred CCCCchhHHHHHHHHHhCChHHHHHHHHhcCchhhccCCCCeEEEccCChhhccCCCCCChhHHHhcccccccCC
Q 040959 26 AGIPTSDLDAVLLLLHAGGHTLFANAIATSDLLFDLLSLPSLTLFAPTDPSLFAVDMTQTPPFYLSILRLHVLPL 100 (391)
Q Consensus 26 as~p~~ele~IietLrs~GytsfA~AL~aAgLl~~Ll~~gpfTIFAPTDeAF~aldL~~n~~~L~sVLrYHVVPG 100 (391)
++++++|-++++.+|+..| +++.+ .-.+.|.++|-.+..+.-.+ .++|+-|-.|.
T Consensus 26 ~gL~e~eANemlAlL~~~g-------I~A~K---~~~~~g~~~l~Ve~~~fa~A----------v~iL~~~GlPr 80 (246)
T COG4669 26 TGLSEKEANEMLALLMSHG-------INAEK---KADKDGGTSLLVEESDFAEA----------VEILNQNGLPR 80 (246)
T ss_pred cCCCHhHHHHHHHHHHHcC-------Cccee---eccCCCceEEEEcHHHHHHH----------HHHHHhcCCCC
Confidence 7788888888888888877 22112 12345777777665544333 35666666664
Done!