RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780954|ref|YP_003065367.1| hypothetical protein CLIBASIA_04265 [Candidatus Liberibacter asiaticus str. psy62] (380 letters) >gnl|CDD|147383 pfam05170, AsmA, AsmA family. The AsmA gene, whose product is involved in the assembly of outer membrane proteins in Escherichia coli. AsmA mutations were isolated as extragenic suppressors of an OmpF assembly mutant. AsmA may have a role in LPS biogenesis. Length = 537 Score = 65.5 bits (160), Expect = 2e-11 Identities = 37/225 (16%), Positives = 83/225 (36%), Gaps = 26/225 (11%) Query: 2 LRRVLIGLGFLFSVVLVGAFTVPLFIDWTDFREDFERQATLIVGKKIAVKGGIKIHILPF 61 +++ L L + V+L+ + D F+ +++ + G+ + + G I + P+ Sbjct: 1 MKKALKILLIILIVLLLLIIALIALFDPNYFKPTIQQKVSAASGRPLQIDGDIGRSLFPW 60 Query: 62 PSVFFKDIRIDQKEDGSFESKIEGLSMRAEFLPLLSGEIRVFDMYIDQPHLNFYLSSKGV 121 P + +++ + + +E + + LPLL+ ++++ + +D L ++G Sbjct: 61 PHLSLENVTLGSPGGPATLVSVEQVDIWLSPLPLLTKQLQIDSILLDGASLALTRLTEGN 120 Query: 122 SNWFQRKSTMDM-IHNVI----------------LEKIHVKGGRIKIIDQESDQVYFLSD 164 NW D + N + I V G + D+ S +V D Sbjct: 121 PNWDDLLQLRDNALPNAPTQQPQPTWDRPAWSIDISAIQVSNGVVTWDDEASKKVLNDID 180 Query: 165 LNLQISARFLNIISPLSIDSIKGSVIAEGTGNFDNKRSAFKITAN 209 L LQ+ + S+ +G D + + N Sbjct: 181 LQLQVDP-----LYGPSVPWRN----VLISGKGDQDQQGWGSLVN 216 >gnl|CDD|32801 COG2982, AsmA, Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]. Length = 648 Score = 60.0 bits (145), Expect = 9e-10 Identities = 62/326 (19%), Positives = 121/326 (37%), Gaps = 28/326 (8%) Query: 2 LRRVLIGLGFLFSVVLVGAFTVPLFIDWTDFREDFERQATLIVGKKIAVKGGIKIHILPF 61 +R+VL+ L + +V+ V D DF++ +Q + G+ +A+ G + + P+ Sbjct: 4 MRKVLVSLLGILILVIALLAAVLPLFDPNDFKDTIVQQVSAATGRPLAINGDLGWRLWPW 63 Query: 62 PSVFFKDIRI---DQKEDGSFESKIEGLSMRAEFLPLLSGEIRVFDMYIDQPHLNFYLSS 118 PSV +DI + E ++ G S+ LPLLS ++++ + +D P + + Sbjct: 64 PSVILEDITLSNPGAAEPHLVSAERVGASLAL--LPLLSKQLQISQIRLDGPVIRLERLA 121 Query: 119 KGVSNW-----FQRKSTMDMIH-----NVILEKIHVKGGRIKIIDQESDQVYFLSDLNLQ 168 +G +NW Q +T + + + V GR+ D+ S+QV L Sbjct: 122 EGRNNWDAPTAPQDPNTTPSSSSASAWSFDIGSLKVDDGRVIFQDKNSEQVLDLQIEIDP 181 Query: 169 ISARFLNIISPLSIDSIKGSVIAEGTGNFDNKRSAFKITANFPAKNKAISLKIQLFPLAY 228 ++ L + D ++ EGT + + TAN A + + L Sbjct: 182 ELSKPLPFSARTGRDQRDITISGEGTKADASALGDVQGTANIEALAGKLKI-GDAAGLQG 240 Query: 229 PIIIDLFGNLFWNEKQPIYSGVFSVAGDFSKLLNLELSAKKSRLSGNFKISDGNVRISRY 288 + S +A + A RLS + + + ++ Sbjct: 241 ASG----EGSLQADPD---SSSTRLAANILN-----DPANDGRLSLSAQSLSLLLDLTWL 288 Query: 289 KLQSILPNSSTDEDNKTKVSQDEENL 314 +L P + + V+ L Sbjct: 289 QLPLTPPALTDGLLLASLVTAGAAAL 314 >gnl|CDD|29313 cd00236, FinO_conjug_rep, FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which encodes the proteins responsible for conjugative transfer of this plasmid from host to recipient Escherichia coli cells; antisense RNA, FinP is thought to interact with traJ mRNA to occlude its ribosome binding site, blocking traJ translation and thereby inhibiting transcription of the tra operon; FinO protects FinP against degradation by binding to FinP and sterically blocking the cellular endonuclease RNase E; FinO also also binds to the complementary stem-loop structures in traJ mRNA and promotes duplex formation between FinP and traJ RNA in vitro; this domain contains two independent RNA binding regions. Length = 146 Score = 31.9 bits (72), Expect = 0.32 Identities = 19/84 (22%), Positives = 30/84 (35%), Gaps = 9/84 (10%) Query: 186 KGSVIAEGTGNFDNKRSAFKITANFPAKNKAISLKIQLFPLAYPIIIDLFGNLFWNEKQP 245 K AE R A I N P A+ + FP +P G+ K Sbjct: 9 KADREAELAAKKKPARQALSIYLNLPTVEYAVECLKKWFPGLFP------GDTPRLLKCG 62 Query: 246 IYSGVFSVAGDFSKLLNLELSAKK 269 I G+ D ++ N+ L+ ++ Sbjct: 63 IKDGILQ---DVAQHPNIPLTHEE 83 >gnl|CDD|39358 KOG4156, KOG4156, KOG4156, Claspin, protein mediating phosphorylation and activation of Chk1 protein kinase in the DNA replication checkpoint response [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. Length = 1329 Score = 30.7 bits (68), Expect = 0.62 Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 3/52 (5%) Query: 329 NETDFFEEEEKKNKNDDLKKDDIQYSVNK---KEEKDNSHDKENQENFSGDK 377 NE EEEE++ + D ++D + V K +EE + +KE +E G++ Sbjct: 624 NEDGKEEEEEEEEEMTDESEEDGEEKVEKEEKEEELEEEEEKEEEEEEEGNQ 675 >gnl|CDD|35203 COG5644, COG5644, Uncharacterized conserved protein [Function unknown]. Length = 869 Score = 30.9 bits (69), Expect = 0.66 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 7/86 (8%) Query: 296 NSSTDEDNKTKVSQDEENLLNFSENGAESMHDLNETDFFEEEE-------KKNKNDDLKK 348 +S EDN + N + E ++ D + F + K NK+ Sbjct: 32 DSEELEDNDEQGYSFGVNSEDDEEIDSDEAFDEEDEKRFADWSFNASKSGKSNKDHKNLN 91 Query: 349 DDIQYSVNKKEEKDNSHDKENQENFS 374 + + S+N ++ NS EN+ + S Sbjct: 92 NTKEISLNDSDDSVNSDKLENEGSVS 117 >gnl|CDD|37249 KOG2038, KOG2038, KOG2038, CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis, Transcription]. Length = 988 Score = 29.6 bits (66), Expect = 1.5 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 4/77 (5%) Query: 300 DEDNKTKVSQDEENLLNFSENGAESMHDLNET----DFFEEEEKKNKNDDLKKDDIQYSV 355 DED + S+++ + E+ +S D ++T D FE+E+ +D+ + + Sbjct: 885 DEDENSLGSEEDGGEEDDDEDIGDSDDDEDDTSDAEDDFEDEDDDEVDDEDGGEGGKDDA 944 Query: 356 NKKEEKDNSHDKENQEN 372 + ++ KE N Sbjct: 945 DISGDRSKKKKKEKGLN 961 Score = 27.3 bits (60), Expect = 7.4 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 2/76 (2%) Query: 296 NSSTDEDNKTKVSQDEENLLNFSENGAESMHDLNETDFFEEEEKKNKNDDLKKDDIQYSV 355 + D+ NK ++ D++ + E+ E + L + EE+ D D+ S Sbjct: 861 GAEKDDKNKKDMTSDDDV--DADEDDDEDENSLGSEEDGGEEDDDEDIGDSDDDEDDTSD 918 Query: 356 NKKEEKDNSHDKENQE 371 + + +D D+ + E Sbjct: 919 AEDDFEDEDDDEVDDE 934 >gnl|CDD|34868 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]. Length = 4600 Score = 29.7 bits (66), Expect = 1.6 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 6/83 (7%) Query: 300 DEDNKTKVSQDEENLLNFSENGAESMHDLNETDFFE------EEEKKNKNDDLKKDDIQY 353 +E+ V D+E + EN ++ + + D E +E +K+ DL+ D++ Sbjct: 3956 EEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDEKEGDVSKDSDLEDMDMEA 4015 Query: 354 SVNKKEEKDNSHDKENQENFSGD 376 + KEE D D+ Q+ + Sbjct: 4016 ADENKEEADAEKDEPMQDEDPLE 4038 >gnl|CDD|146370 pfam03699, UPF0182, Uncharacterized protein family (UPF0182). This family contains uncharacterized integral membrane proteins. Length = 771 Score = 29.1 bits (66), Expect = 1.9 Identities = 10/34 (29%), Positives = 18/34 (52%) Query: 1 MLRRVLIGLGFLFSVVLVGAFTVPLFIDWTDFRE 34 +VLI L + ++L+ + L+ DW F+E Sbjct: 1 RRSKVLIILAIVVLLLLLISLLADLYTDWLWFKE 34 >gnl|CDD|39860 KOG4661, KOG4661, KOG4661, Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]. Length = 940 Score = 28.6 bits (63), Expect = 3.0 Identities = 16/88 (18%), Positives = 32/88 (36%) Query: 289 KLQSILPNSSTDEDNKTKVSQDEENLLNFSENGAESMHDLNETDFFEEEEKKNKNDDLKK 348 K+ IL + E K + S+ E+ + + E D F+ + + DL Sbjct: 216 KILDILGETCKSEPVKEESSELEQPFAQDTSSVGPDRKLAEEEDLFDSAHPEEGDLDLAS 275 Query: 349 DDIQYSVNKKEEKDNSHDKENQENFSGD 376 + ++ + K + + K GD Sbjct: 276 ESTAHAQSSKADSLLAVVKREPAEQPGD 303 >gnl|CDD|37467 KOG2256, KOG2256, KOG2256, Predicted protein involved in nuclear export of pre-ribosomes [Translation, ribosomal structure and biogenesis]. Length = 661 Score = 28.4 bits (63), Expect = 3.1 Identities = 16/111 (14%), Positives = 40/111 (36%), Gaps = 13/111 (11%) Query: 264 ELSAKKSRLSGNFKISDGNVRISRYKLQSILPNSSTDEDNKTKVSQDEENLLNFSENGAE 323 + ++ G G + +L+ D + + ++++ LLNF E+ Sbjct: 46 TEREQDDKVDGKVTSKKGGASKHKKELEK---LKDKDPEFFKFLKEEDKELLNFKEDS-- 100 Query: 324 SMHDLNETDFFEEEEKKNKNDDLKKDDIQYSVNKKEEKDNSHDKENQENFS 374 + D EE ++ D +D+ + +K+ K + + + Sbjct: 101 ------DDDEDLEEPDEDLEDF-SEDEED-DEEDEIDKETDKKKNSGKVIT 143 >gnl|CDD|36161 KOG0943, KOG0943, KOG0943, Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]. Length = 3015 Score = 28.6 bits (63), Expect = 3.3 Identities = 24/112 (21%), Positives = 44/112 (39%), Gaps = 11/112 (9%) Query: 266 SAKKSRLSGNFKISDGNVRISRYKLQSILPNSSTDEDNKTKVSQDEENLLNFSENGAESM 325 + + G+ + D R +L S + T+ DN +E G E Sbjct: 1683 IQESLPIRGDDEAQDDIPTPRRRRLLSGNTTNDTNADN------EEREGQEGEFAGEEDH 1736 Query: 326 HD-LNETDFFEEEEKKNKNDDLKKDDIQYSVNKKE----EKDNSHDKENQEN 372 HD N+ D ++ E ++ +DD DD ++ + E+D D+ Q+ Sbjct: 1737 HDDDNDDDDDDDAEAEDDDDDDDDDDEDMDLDAEAAAEDEEDEEGDEHEQDE 1788 >gnl|CDD|31311 COG1114, BrnQ, Branched-chain amino acid permeases [Amino acid transport and metabolism]. Length = 431 Score = 28.2 bits (63), Expect = 3.8 Identities = 13/54 (24%), Positives = 19/54 (35%), Gaps = 4/54 (7%) Query: 214 NKAISLKIQLFPLAYPIIIDL----FGNLFWNEKQPIYSGVFSVAGDFSKLLNL 263 + I + + + YPI I L F W + +Y V S L L Sbjct: 333 EQIIKISVPVLTAIYPIAIALVLLSFARKLWKNSKRVYRLTLLVTLIISILDGL 386 >gnl|CDD|37623 KOG2412, KOG2412, KOG2412, Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]. Length = 591 Score = 28.1 bits (62), Expect = 4.2 Identities = 19/91 (20%), Positives = 31/91 (34%), Gaps = 4/91 (4%) Query: 281 GNVRISRYKLQSILPNSSTDEDNKTKVSQDEENLLNFSENGAESMHDLNETDFFEEEEKK 340 + LQS+ + K + Q E E E + +EE + Sbjct: 183 RLLEEQNQVLQSLDTELQAIQREKQRKEQIRERK----ERSEEKREEAERKRRAHQEELR 238 Query: 341 NKNDDLKKDDIQYSVNKKEEKDNSHDKENQE 371 K D+ + Q + +EEK KE +E Sbjct: 239 QKEDEEAELQEQEKIRAEEEKQEEERKEAEE 269 >gnl|CDD|114257 pfam05525, Branch_AA_trans, Branched-chain amino acid transport protein. This family consists of several bacterial branched-chain amino acid transport proteins which are responsible for the transport of leucine, isoleucine and valine via proton motive force. Length = 428 Score = 28.0 bits (63), Expect = 5.2 Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 4/49 (8%) Query: 214 NKAISLKIQLFPLAYPIIIDL----FGNLFWNEKQPIYSGVFSVAGDFS 258 K IS+ + + L YPI I L + + +Y V S Sbjct: 331 TKIISISVPVLVLIYPIAIVLIVLSLFRKLFPNSKVVYKLTILVTLIIS 379 >gnl|CDD|36356 KOG1141, KOG1141, KOG1141, Predicted histone methyl transferase [Chromatin structure and dynamics]. Length = 1262 Score = 27.4 bits (60), Expect = 6.1 Identities = 21/109 (19%), Positives = 40/109 (36%), Gaps = 4/109 (3%) Query: 265 LSAKKSRLSGNFKISDGNVRISRYK---LQSILPNSSTDEDNKTKVSQDEENLLNFSENG 321 L K+ SG D ++ S + + + + DE + Q +L Sbjct: 1015 LQIFKTAQSGWGVREDTDIPQSTFICTYVGAPPTDDLADELRNAQADQYSNDLDLKDTVE 1074 Query: 322 AESMHDLNETDFFEEEEKKNKNDDLKKDDIQYSVNKKEEKDNSHDKENQ 370 E + +ETDF + + + DD Q + K E+ +S + + Sbjct: 1075 LEESREDHETDFRGDTSDYDDEEGSDGDDGQ-DIMKMVERQDSSESGEE 1122 >gnl|CDD|143330 cd07706, IgV_TCR_delta, Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain. IgV_TCR_delta: immunoglobulin (Ig) variable (V) domain of the delta chain of gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Length = 116 Score = 27.5 bits (61), Expect = 7.4 Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 5/43 (11%) Query: 238 LFWNEKQPIYSGVFSVAGDFSKLLNLELSAKKSRLSGNFKISD 280 +FW ++ P F + ++ +A K R S NF+ + Sbjct: 32 IFWYKQLPSGEMTFLIRQK-----SIYGNATKGRYSVNFQKAQ 69 >gnl|CDD|34730 COG5129, MAK16, Nuclear protein with HMG-like acidic region [General function prediction only]. Length = 303 Score = 27.4 bits (60), Expect = 7.7 Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 5/64 (7%) Query: 308 SQDEENLLNFSENGAESMHDLNETDFFEEEEKKNKNDDLKKDDIQYSVNKKEEKDNSHDK 367 Q E + E +ES E+D E+E+ K K K DD + S + ++ Sbjct: 238 DQSMETSESEEEESSES-----ESDEDEDEDNKGKIRKRKTDDAKKSRKPHIHIEYEQER 292 Query: 368 ENQE 371 EN++ Sbjct: 293 ENEK 296 >gnl|CDD|35464 KOG0243, KOG0243, KOG0243, Kinesin-like protein [Cytoskeleton]. Length = 1041 Score = 27.3 bits (60), Expect = 7.7 Identities = 25/162 (15%), Positives = 51/162 (31%), Gaps = 29/162 (17%) Query: 244 QPIYSGVFSVAGDFSKLLNLELSAKKSRLSGNFKIS--------DGNVRISRYKLQSILP 295 + I S V ++L + + ++ + S + + LQ+I Sbjct: 627 RDILSEVLESLQQLQEVLKKDSESCLEVINSSITSSINELESMLETIANTADDLLQNISS 686 Query: 296 NSSTDEDNKTKVSQDEENLLNFSENGAESM-------------HDLNETDFFEEEEKKN- 341 S ++ + + E L S++ A+ + T+ F E Sbjct: 687 RLSNQQEILSLFANQELQELVLSQDSAQELSELTSTFFQTLDNQAEKLTNLFSEANISLS 746 Query: 342 -------KNDDLKKDDIQYSVNKKEEKDNSHDKENQENFSGD 376 K + +D + V +E +SHD+ N E Sbjct: 747 QKLSSFQKKFESIAEDEKQLVEDIKELLSSHDQRNNELLDIA 788 >gnl|CDD|153331 cd07647, F-BAR_PSTPIP, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Proline-Serine-Threonine Phosphatase-Interacting Proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Vetebrates contain two Proline-Serine-Threonine Phosphatase-Interacting Proteins (PSTPIPs), PSTPIP1 and PSTPIP2. PSTPIPs are mainly expressed in hematopoietic cells and are involved in the regulation of cell adhesion and motility. Mutations in PSTPIPs have been shown to cause autoinflammatory disorders. PSTPIP1 contains an N-terminal F-BAR domain, PEST motifs, and a C-terminal SH3 domain, while PSTPIP2 contains only the N-terminal F-BAR domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. Length = 239 Score = 27.1 bits (60), Expect = 7.9 Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 4/62 (6%) Query: 307 VSQDEENLLNFSENGAESMHDLNETDFFEEEEKKNKNDDLKKDDI--QYSVNKKEEKDNS 364 + ++ EN+ N A+S+ + E + EE +K K + K +DI + NKKE + Sbjct: 65 LRKETENVANAHIQLAQSLRE--EAEKLEEFREKQKEERKKTEDIMKRSQKNKKELYKKT 122 Query: 365 HD 366 Sbjct: 123 MK 124 >gnl|CDD|39635 KOG4434, KOG4434, KOG4434, Molecular chaperone SEC63, endoplasmic reticulum translocon component [Intracellular trafficking, secretion, and vesicular transport, Posttranslational modification, protein turnover, chaperones]. Length = 520 Score = 27.4 bits (60), Expect = 7.9 Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 1/60 (1%) Query: 300 DEDNKTKVSQDEENLLNFSENGAESMHDLNETDFFEEEEKKNKNDDLKKDDIQYSVNKKE 359 +E+ K K S EE N ES ++D E++EK++ +DD + +++Q S+ K+ Sbjct: 331 EEEAKDKGSDSEEEETNRDSQDEESDASDRDSDR-EQDEKQDDDDDAEWEELQASIQKRA 389 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.318 0.137 0.387 Gapped Lambda K H 0.267 0.0574 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,503,230 Number of extensions: 240966 Number of successful extensions: 744 Number of sequences better than 10.0: 1 Number of HSP's gapped: 739 Number of HSP's successfully gapped: 57 Length of query: 380 Length of database: 6,263,737 Length adjustment: 95 Effective length of query: 285 Effective length of database: 4,210,882 Effective search space: 1200101370 Effective search space used: 1200101370 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 58 (26.5 bits)