RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2168
(516 letters)
>gnl|CDD|227116 COG4775, COG4775, Outer membrane protein/protective antigen OMA87
[Cell envelope biogenesis, outer membrane].
Length = 766
Score = 141 bits (358), Expect = 8e-36
Identities = 115/484 (23%), Positives = 177/484 (36%), Gaps = 67/484 (13%)
Query: 36 VDRVKVEGIGRTYDDIITDSIKQTEIFKSSTFGQLIFQCHEVRNQLERLQCFQQVQIEID 95
V R+++ G RT D +I ++ E F + + Q + +L RL F+ V I+
Sbjct: 346 VRRIRIRGNTRTKDYVIRREMRLKE---GDVFNRKLVQRGK--RRLRRLGYFESVNIDTA 400
Query: 96 ASKGPDATPEHGYEITFRVKELKRYRAGVTTSIGNNEG-SVVVWGKMPNLYGRGELAEMS 154
G D ++ VKE G++ G S N G G+ ++
Sbjct: 401 PGSGSD-----QVDVVVDVKERSTGSINFGLGYGSDSGLSGFASLSERNFLGTGQSLSLN 455
Query: 155 YVYGTKSLVYNLTLRKPFFGPIDSMLSGSLLRQVNEMPASSCKLLEQGLILDYAILFPTI 214
G K Y+L+ P+F L +L + + D A +
Sbjct: 456 ANLGDKQTSYSLSFTDPYFLDDRVSLGFNLFSNRYDTFDA-----------DTANDSYRV 504
Query: 215 KNSIEWNGLIREIQPASRGTPFAIRESAGYTLKSSLKFITSLDKRDDKILPRHGQFCQGS 274
K + G + T SL ++ +L + S
Sbjct: 505 K---------------TYG--GGVSLGRPITENLSLGLGYGYEQNSLSLLNKSPPDEYAS 547
Query: 275 VEFAGLGGDVGFQKYSSLHRVVHRYTLKSSLKFITSLDKRDDKILPRHGQFCQGSVEFAG 334
+ GG + SSL + D RD+ + P G + + E AG
Sbjct: 548 LGVKLQGGK----------------SDLSSLSLGWTYDTRDNALFPTKGSYLSLTQEVAG 591
Query: 335 LGGDVGFQKYSSLFQVNYPLGPYI-TAQASLDAGLLGSFSQDKTFTLCDRFFLGGPLGLR 393
LGGD+ + K YPL YI T + G + K + +RF+LGG +R
Sbjct: 592 LGGDIKYYKLELDGSKYYPLTDYIFTLSLRGEVGYGKGYG-TKLLPIYERFYLGGSNSVR 650
Query: 394 GFAHYGIGPKSG-GSSLGGTVYWQGAYHIYTPLPFTKPTKGSFSDNFRLNFFANAGSIQD 452
GF G+GPK G +LGGT Y+ + + PLP R F +AGS+ +
Sbjct: 651 GFESGGLGPKDGYTDALGGTSYFVASAELRFPLPKVIG------SGVRGALFFDAGSVWN 704
Query: 453 MSASEITSK-WRKLGEELRISYGIGLAIRFAGLARVEINYCFPYSYQRDDSVVPGMQFGF 511
T + + G ELR S G+GL + L + +Y FP + D QFG
Sbjct: 705 TGTDPSTVRNFYGSGSELRASAGVGLRWA-SPLGPLRFDYAFPIKKKEGD-DTQRFQFGL 762
Query: 512 GITF 515
G F
Sbjct: 763 GTRF 766
>gnl|CDD|216300 pfam01103, Bac_surface_Ag, Surface antigen. This entry includes
the following surface antigens; D15 antigen from
H.influenzae, OMA87 from P.multocida, OMP85 from
N.meningitidis and N.gonorrhoeae. The family also
includes a number of eukaryotic proteins that are
members of the UPF0140 family. There also appears to be
a relationship to pfam03865 (personal obs: C Yeats). In
eukaryotes, it appears that these proteins are not
surface antigens; S. cerevisiae YNL026W (SAM50) is an
essential component of the Sorting and Assembly
Machinery (SAM) of the mitochondrial outer membrane. The
protein was localised to the mitochondria.
Length = 317
Score = 112 bits (282), Expect = 1e-27
Identities = 62/221 (28%), Positives = 91/221 (41%), Gaps = 14/221 (6%)
Query: 300 TLKSSLKFITSLDKRDDKILPRHGQFCQGSVEFAGLGG--DVGFQKYSSLFQVNYPLGPY 357
+L SSL F S D RD+ + P G + + ++EFAG DV F K + YPLG
Sbjct: 106 SLLSSLSFGLSYDTRDNGLFPTRGYYLRFNLEFAGPILGGDVKFLKLTGDASWYYPLGED 165
Query: 358 --ITAQASLDAGLLGSFSQDKTFTLCDRFFLGGPLGLRGFAHYGIGPKS-GGSSLGGTVY 414
A + G L + +RFF GG +RG+ + IGP+ G +LGG Y
Sbjct: 166 HDFVLAARVGLGYLLGYGAKDKLPPSERFFAGGSNSVRGYGYGSIGPRDEDGDALGGRSY 225
Query: 415 WQGAYHIYTPLPFTKPTKGSFSDNFRLNFFANAGSIQDMSASEITSKWRKLGEELRISYG 474
+ + + PLP F N R F +AG++ + + +R S G
Sbjct: 226 FTASAELRYPLP--------FIPNLRGALFVDAGNVWNSGGDTPGGSDGVRSKNIRASVG 277
Query: 475 IGLAIRFAGLARVEINYCFPYSYQRDDSVVPGMQFGFGITF 515
+GL + + +Y P D FG G F
Sbjct: 278 VGLRWD-SPFGPLRFDYAIPLKKPDGDRTEFRFYFGIGTEF 317
>gnl|CDD|234165 TIGR03303, OM_YaeT, outer membrane protein assembly complex, YaeT
protein. Members of this protein family are the YaeT
protein of the YaeT/YfiO complex for assembling proteins
into the outer membrane of Gram-negative bacteria. This
protein is similar in sequence and function to a
non-essential paralog, YtfM, that is also in the Omp85
family. Members of this family typically have five
tandem copies of the surface antigen variable number
repeat (pfam07244), followed by an outer membrane
beta-barrel domain (pfam01103), while the YtfM family
typically has a single pfam07244 repeat [Protein fate,
Protein and peptide secretion and trafficking].
Length = 741
Score = 111 bits (280), Expect = 7e-26
Identities = 61/242 (25%), Positives = 89/242 (36%), Gaps = 29/242 (11%)
Query: 286 FQKYSSLHRVVHRYTLKSSLKFITSLDKRDDKILPRHGQFCQGSVEFAGLGGDVGFQKYS 345
S + + SSL + S D D P G + S EFAG GGD+ + K +
Sbjct: 517 DSSASYFIKEQGGKFIDSSLSYGWSYDTLDSGYFPTKGSIQRLSQEFAGPGGDLKYYKLT 576
Query: 346 SLFQVNYPLGPY--ITAQASLDAGLLGSFSQDKTFTLCDRFFLGGPLGLRGFAHYGIGPK 403
+ PL G + K +RF+ GG +RGF GIGP+
Sbjct: 577 YDSEYYIPLSKEDDWVLSLRGRLGYGNGYG-GKDLPFYERFYAGGIGSVRGFESNGIGPR 635
Query: 404 ---SGGSSLGGTVYWQGAYHIYTPLPFTKPTKGSFSDNFRLNFFANAGSIQDMSASEITS 460
G S+GG + PLPF + R + F +AG++ + +
Sbjct: 636 DINDSGDSIGGNAMATANVELIFPLPFLPE-----DNGLRGSVFFDAGNVWG-TDQKKEG 689
Query: 461 KWRKLGEELRISYGIGLA-------IRFAGLARVEINYCFPYSYQRDDSVVPGMQFGFGI 513
+ LR S G+GL +RF+ Y P ++ D QF G
Sbjct: 690 DYSDDS-SLRASVGVGLRWISPMGPLRFS--------YAKPLKKKKGD-KTQSFQFSIGT 739
Query: 514 TF 515
TF
Sbjct: 740 TF 741
>gnl|CDD|223801 COG0729, COG0729, Outer membrane protein [Cell envelope biogenesis,
outer membrane].
Length = 594
Score = 50.8 bits (122), Expect = 1e-06
Identities = 97/494 (19%), Positives = 153/494 (30%), Gaps = 115/494 (23%)
Query: 33 PARVDRVKVEGIGRTYDDIITDSIKQTEIFKSSTFGQ--LIFQCHEVRNQLERLQCFQQV 90
R V VEG R ++ + + + FK G E+ +L + F V
Sbjct: 199 RYRFGPVTVEGSQRIDEEYLQNLVP----FKY---GLPYDPEDLAELNQRLRQTGYFSSV 251
Query: 91 QI-EIDASKGPDATPEHGYEITFRVKELKRYRAGVTTSIGNNEGSVV--VWGKMPNLYGR 147
+ D GPD + V E K + + G+ + W K NL+GR
Sbjct: 252 VVQPADKQAGPDGL----LPVKVSVSERKENTFELGVGYSTDVGAGLEAGWEK-RNLFGR 306
Query: 148 GELAEM-SYVYGTKSLVYNLTLRKPFFGPIDSMLSGSLLRQVNEMPASSCKLLEQGLILD 206
G + S + T + P L Q N + A
Sbjct: 307 GHSLRIESEISAPL-QTLEATYKAPLLFN--------PLGQYNPVSAG------------ 345
Query: 207 YAILFPTIKNSIEWNGLIREIQPASRGTPFAIRESAGYTLKSSLKFITSLDKRDDKILPR 266
E S ++ S G+ SL + SL R
Sbjct: 346 ---FDRLDLYDTE-----------SDAYTESLSASRGWDA--SLGWQRSLALR-----FS 384
Query: 267 HGQFCQGSVEFAGLGGDVGFQKYSSLHRVVHRYTLKSSLKFITSLDKRDDKILPRHGQFC 326
+ F QG + L ++F + DD + P G
Sbjct: 385 YDNFRQGDISG-------------------KTSLLTPGVEF-SYTRDTDDGLFPTWGDRL 424
Query: 327 QGSVEFA--GLGGDVGFQKYSSLFQVNYPLGPYITAQASLDAG-LLGSFSQDKTFTLCDR 383
++ + LG DV F+ + G + G +L D +L R
Sbjct: 425 DLTIGPSYEALGSDVDFRLVQARSGYLRTGGADHRLAGRGELGAILTGDLDDVPPSL--R 482
Query: 384 FFLGGPLGLRGFAHYGIGPK-SGGSSLGGTVYWQGAYHIYTPLPFTKPTKGSFSDNFRLN 442
FF GG +RG+ + IGP+ + G LGG G+ +D + L
Sbjct: 483 FFAGGDRSVRGYGYQSIGPQDANGDLLGGRSLVTGSLEYQYL----------VTDPWGLA 532
Query: 443 FFANAGSIQDMSASEITSKWRKLGEELRISYGIGLAIRFA---GLARVEINYCFPYSYQR 499
F +AGS + + +L +L+ G G+ +R+ G R F +
Sbjct: 533 VFVDAGS--------AGNNFTRLFSDLK--KGAGIGVRWDSPVGPIR------FDIAVPL 576
Query: 500 DDSVVPGMQFGFGI 513
+D QF GI
Sbjct: 577 EDKDDKKFQFYIGI 590
>gnl|CDD|236834 PRK11067, PRK11067, outer membrane protein assembly factor YaeT;
Provisional.
Length = 803
Score = 31.9 bits (73), Expect = 0.93
Identities = 30/129 (23%), Positives = 51/129 (39%), Gaps = 31/129 (24%)
Query: 376 KTFTLCDRFFLGGPLGLRGFAHYGIGPK-----------SGGS---------SLGGTVYW 415
K + F+ GG +RGF IGPK + ++GG
Sbjct: 643 KEMPFYENFYAGGSSTVRGFQSNTIGPKAVYYPGQASNYTQDGAKDLCKSDDAVGGNAMA 702
Query: 416 QGAYHIYTPLPFTKPTKGSFSDNFRLNFFANAGSIQDMSASEITSKWRKLG-------EE 468
+ + TP PF ++++ R +FF + G++ D + + T+ R G
Sbjct: 703 VASLELITPTPF---ISDKYANSVRTSFFWDMGTVWDTNW-DNTAYTRAAGYPDYSDPSN 758
Query: 469 LRISYGIGL 477
+R+S GI L
Sbjct: 759 IRMSAGIAL 767
>gnl|CDD|132403 TIGR03360, VI_minor_1, type VI secretion-associated protein,
VC_A0118 family. Members of this protein family,
including VC_A0118 from Vibrio cholerae El Tor N16961,
are restricted to a subset of bacteria with the type VI
secretion system, and are encoded among the type
VI-associated pathogenicity islands. However, many
species with type VI secretion lack a member of this
family. This lack suggests that members of this family
may be targets rather than components of the type VI
secretion system.
Length = 185
Score = 30.2 bits (68), Expect = 1.9
Identities = 37/182 (20%), Positives = 61/182 (33%), Gaps = 30/182 (16%)
Query: 73 QCHEVRNQLERLQCF-------QQVQIEIDASKGPDATPEHGYEITFRVKELKRYRAGVT 125
C + + LERL C+ + V IE G + R ++ R +
Sbjct: 4 LCRQEPSALERLACYDRAGAPGEAVAIEKANPYGAEWQ---------RALAQEKGRQPES 54
Query: 126 TS--IGNNEGS-VVVWGKMPNLYGRGELAEMSYVYGTKSLVYNLT-LRKPFFGPIDSMLS 181
+ + EGS + + P GE + S V N+T L+ P+
Sbjct: 55 GAFLLTQEEGSGSMTLIRTP---AIGETPPPVLMI---SCVDNITRLQLALPKPVAGSRV 108
Query: 182 GSLLRQVNEMPASSCKLLEQGLILDYAILFPTIKNSIEWNG----LIREIQPASRGTPFA 237
L + S + E GL+L+ P I+ G +R A+ G F
Sbjct: 109 QVSLDGEGATVSQSWFVRENGLLLESGRGLPAIEEIKRLIGARRLTVRGDNGAADGLRFD 168
Query: 238 IR 239
+
Sbjct: 169 LS 170
>gnl|CDD|236929 PRK11553, PRK11553, alkanesulfonate transporter substrate-binding
subunit; Provisional.
Length = 314
Score = 30.5 bits (69), Expect = 2.3
Identities = 30/124 (24%), Positives = 42/124 (33%), Gaps = 29/124 (23%)
Query: 281 GGDVGFQKYSSLHRVVHRYTLKSSLKF-------ITSLDKRDDKILPRHGQFCQGSVE-- 331
G V FQK SS H ++ R K+ LKF +T D R F QG+V+
Sbjct: 129 GHKVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYLTPADAR--------AAFQQGNVDAW 180
Query: 332 --------FAGLGGDVGFQKYSSLFQVNYPL----GPYITAQASLDAGLLGSFSQDKTFT 379
A L G V K + PY + +L + ++ T
Sbjct: 181 AIWDPYYSAALLQGGVRVLKDGTDLNQTGSFYLAARPYAEKNGAFIQQVLATLTEADALT 240
Query: 380 LCDR 383
R
Sbjct: 241 RSQR 244
>gnl|CDD|225387 COG2831, FhaC, Hemolysin activation/secretion protein
[Intracellular trafficking and secretion].
Length = 554
Score = 30.4 bits (69), Expect = 2.4
Identities = 35/198 (17%), Positives = 57/198 (28%), Gaps = 38/198 (19%)
Query: 321 RHGQFCQGSVEFAGLGGDVGFQKYSSL---FQVNYPLGPYITAQASLDAGLLGSFSQDKT 377
R G G+ + ++ L + P G +S D
Sbjct: 384 RRGLGALGASKDDEETNGEPTSRFKKLNGNASLLQPFGL---GPFLYATQFNAQYSGD-P 439
Query: 378 FTLCDRFFLGGPLGLRGFAHYGIGPKSGGSSLG--GTVYWQGAYHIYTPLPFTKPTKGSF 435
++F +GG +RGF GGS G G Y + PLP
Sbjct: 440 LLSSEKFSIGGRYSVRGF--------DGGSLSGDRG-WYLSN--ELRWPLP--------P 480
Query: 436 SDNFRLNFFANAGSIQDMSASEITSKWRKLGEELRISYGIGLAIRFAGLARVEINYCFP- 494
+ F + G + + SA + L G+GL +++ P
Sbjct: 481 GGALQPYVFVDYGKVYNNSAEYL--SGETLA-----GAGLGLRGNLKDGFSYDLDLGRPL 533
Query: 495 --YSYQRDDSVVPGMQFG 510
+ + V G F
Sbjct: 534 SKPAGFDNRRTVVGFSFS 551
>gnl|CDD|241153 cd12709, RRM_RCAN2, RNA recognition motif in vertebrate regulator
of calcineurin 2 (RCAN2). This subgroup corresponds to
the RRM of RCAN2, also termed calcipressin-2, or Down
syndrome candidate region 1-like 1 (DSCR1L1), or
myocyte-enriched calcineurin-interacting protein 2
(MCIP2), or thyroid hormone-responsive protein ZAKI-4,
encoded by a novel thyroid hormone-responsive gene
ZAKI-4 that is abundantly expressed in human brain,
heart and muscles. RCAN2 binds to the catalytic subunit
of Ca2+/calmodulin-dependent phosphatase calcineurin
(also termed PP2B or PP3C), calcineurin A, and inhibits
its phosphatase activity through its C-terminal region.
RCAN2 consists of an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a highly conserved SP repeat
domain containing the phosphorylation site by GSK-3, a
well-known PxIxIT motif responsible for docking many
substrates to calcineurin, and an unrecognized
C-terminal TxxP motif of unknown function. .
Length = 77
Score = 28.0 bits (62), Expect = 2.6
Identities = 26/95 (27%), Positives = 37/95 (38%), Gaps = 27/95 (28%)
Query: 28 HVMVAPARVDRVKVEGIGRTYDDIITDSIKQTEIFKSSTFGQLIFQCHEVRNQLERLQCF 87
V V +R + K EG+ R YDD +T ++FKS F
Sbjct: 9 DVEVFTSREVKEKFEGLFRAYDDCVT-----FQLFKS----------------------F 41
Query: 88 QQVQIEIDASKGPDATPEHGYEITFRVKELKRYRA 122
++V+I K +E FR K+LK Y A
Sbjct: 42 RRVRINFSNPKAAARARIELHETQFRGKKLKLYFA 76
>gnl|CDD|179216 PRK01064, PRK01064, hypothetical protein; Provisional.
Length = 78
Score = 28.0 bits (62), Expect = 2.7
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 143 NLYGRGELAEMSYVYGTKSLVYNLTLRKPFFGPI 176
NL R E + V GT +++Y LT+ KP G I
Sbjct: 11 NLVDRPEEVHIKEVQGTHTIIYELTVAKPDIGKI 44
>gnl|CDD|227273 COG4937, COG4937, Predicted regulatory domain of prephenate
dehydrogenase [Translation, ribosomal structure and
biogenesis].
Length = 171
Score = 29.5 bits (66), Expect = 3.2
Identities = 10/39 (25%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 77 VRNQLERLQCFQQVQIEIDASKGPDATPEHGYEITFRVK 115
+ N ++ L+ ++I ID +G + ITFR+
Sbjct: 100 ILNAVKLLKKMVDIEI-IDVYEGEKIEEDEYKSITFRIY 137
>gnl|CDD|219018 pfam06419, COG6, Conserved oligomeric complex COG6. COG6 is a
component of the conserved oligomeric golgi complex,
which is composed of eight different subunits and is
required for normal golgi morphology and localisation.
Length = 615
Score = 29.2 bits (66), Expect = 6.2
Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 5/66 (7%)
Query: 7 KEIPSQPYDELDSDPNDAMLGHVMVAPARVDRVKVEGIGRTYDDIITD-SIKQTEIFKSS 65
+ S+P+ E ++ +L ++ +R R +VE + ++ +D IT I F S
Sbjct: 289 SGLESEPWSEALNE----LLDRILQGLSRPLRQRVEQVIQSEEDAITLYKIANLLEFYRS 344
Query: 66 TFGQLI 71
F +L+
Sbjct: 345 MFSKLL 350
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.139 0.419
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,616,136
Number of extensions: 2617998
Number of successful extensions: 1652
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1631
Number of HSP's successfully gapped: 18
Length of query: 516
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 415
Effective length of database: 6,457,848
Effective search space: 2680006920
Effective search space used: 2680006920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.2 bits)