RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780289|ref|YP_003064702.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter asiaticus str. psy62] (682 letters) >gnl|CDD|30914 COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]. Length = 342 Score = 324 bits (832), Expect = 4e-89 Identities = 156/354 (44%), Positives = 223/354 (62%), Gaps = 19/354 (5%) Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389 L+ + ++++ I + E EL + + + + +L + Sbjct: 6 LSADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVE---LGEDLTDLKLGREPSERA 62 Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449 ++ I++I ++ E + + +++GE AKK++V Sbjct: 63 -------------RRPAGRLSFYIRAIEAAPLLTPEEEKALARRLKRGE-RDLDAKKKLV 108 Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509 E+NLRLV+S+AKKYT RGL FLDLIQEGNIGLMKA EKFD G+KFSTYA WW++QAIT Sbjct: 109 ESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAIT 168 Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569 R+IADQ+ TIRIPVH + I+K+ R R + ++ REPTPEEIA++L + + VR++LK Sbjct: 169 RAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKR 228 Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVL 628 EPISL+TPIGD++ S LGDF+ED +VSP D+ + +L+E VLA LT RE RV+ Sbjct: 229 ASEPISLDTPIGDDEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVI 288 Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681 R+RFG+ TLEE+G++F ++RER+RQIEAKA+RKL+ HP RS LRS+LD Sbjct: 289 RLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKLRRHPERSALLRSYLD 342 >gnl|CDD|31384 COG1191, FliA, DNA-directed RNA polymerase specialized sigma subunit [Transcription]. Length = 247 Score = 117 bits (295), Expect = 9e-27 Identities = 67/231 (29%), Positives = 112/231 (48%), Gaps = 9/231 (3%) Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFST 498 E + ++E L LV S+A+K+ NRG DLIQ G IGL+KA E++D G KFST Sbjct: 20 EGDEEARRLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFST 79 Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558 YA+ ++ I + +++P +R+ ++ + ++ REPT EEIA++L + Sbjct: 80 YAVRRIRGEILDYLRKNDS-VKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGI 138 Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618 E + L + DED D D +P D + L E + Sbjct: 139 DKEEYIEALLAIN---GSQLLSLDEDVLKDDDDDVDDQIENPDDGVEKEELLEILKEAIE 195 Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 L RE+ VL +R+ + T +E+ + ++ R+ ++ KAI+KL+ Sbjct: 196 PLPEREKLVLVLRYKEEL----TQKEIAEVLGISESRVSRLHKKAIKKLRK 242 >gnl|CDD|146934 pfam04539, Sigma70_r3, Sigma-70 region 3. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme. Length = 78 Score = 88.0 bits (219), Expect = 7e-18 Identities = 34/78 (43%), Positives = 55/78 (70%) Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586 + ++K+ R R + ++ REPTPEEIA++L + E VR+VL+ +EP+SL+ P+G+E+ Sbjct: 1 ELLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDG 60 Query: 587 HLGDFIEDKNAVSPLDSA 604 LGD +ED +A SP D+ Sbjct: 61 ELGDLLEDDDAESPEDAV 78 >gnl|CDD|146937 pfam04542, Sigma70_r2, Sigma-70 region 2. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation. Length = 71 Score = 86.1 bits (214), Expect = 3e-17 Identities = 27/69 (39%), Positives = 41/69 (59%) Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 +VE L LV S+A++Y G DL+QEG +GL++A E+FD G FST+ ++ A Sbjct: 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60 Query: 508 ITRSIADQS 516 I ++ Q Sbjct: 61 IIDALRKQR 69 >gnl|CDD|112778 pfam03979, Sigma70_r1_1, Sigma-70 factor, region 1.1. Region 1.1 modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase. Region 1.1 is also involved in promoter binding. Length = 79 Score = 73.5 bits (181), Expect = 2e-13 Identities = 31/71 (43%), Positives = 50/71 (70%), Gaps = 3/71 (4%) Query: 25 DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV---DGD 81 D S KK+I+ ++RGY+T +E+N LPPD+V SEQ++D ++ML +MGI VV D + Sbjct: 3 DLSQAQVKKLIEQGKKRGYLTYDEINEALPPDDVDSEQIDDIISMLEDMGIEVVEEADSE 62 Query: 82 DLEDEEGSEDS 92 +L++E S++ Sbjct: 63 ELDEETSSDED 73 >gnl|CDD|146939 pfam04545, Sigma70_r4, Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives. Length = 50 Score = 67.4 bits (166), Expect = 1e-11 Identities = 28/54 (51%), Positives = 38/54 (70%), Gaps = 4/54 (7%) Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 LASL PRE VL +RFG TLEE+G++ ++RER+RQIE +A+RKL+ Sbjct: 1 ALASLPPREREVLVLRFG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50 >gnl|CDD|143911 pfam00140, Sigma70_r1_2, Sigma-70 factor, region 1.2. Length = 37 Score = 56.6 bits (138), Expect = 2e-08 Identities = 18/33 (54%), Positives = 25/33 (75%) Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150 D VR+YLRE+G + LL+ E E+ +A+RIEAG Sbjct: 1 SDSVRLYLREIGRVPLLTAEEEVELARRIEAGD 33 >gnl|CDD|100119 cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).. Length = 55 Score = 56.3 bits (137), Expect = 3e-08 Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 4/59 (6%) Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668 RE L L RE V+ +RFG G+ + EE+ + ++R +RQ +A++KL+ Sbjct: 1 RERLEEALDKLPEREREVILLRFGEGL----SYEEIAEILGISRSTVRQRLHRALKKLR 55 >gnl|CDD|146940 pfam04546, Sigma70_ner, Sigma-70, non-essential region. The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 210 Score = 43.7 bits (104), Expect = 2e-04 Identities = 34/149 (22%), Positives = 60/149 (40%), Gaps = 8/149 (5%) Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIA-EVYRELRSL 297 D + E+ ++E D+D+DD E L P E A E + ELR Sbjct: 35 DAAAATAPAIESELDEEDLEDDDDDDDEDDDEEEEADLGP-----DPEEARERFAELREQ 89 Query: 298 QDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356 + +K + S K + +E L + L + D LV+ L + R+ E ++ Sbjct: 90 YEKTRKAIEKHGRGSKKAQKAREALAEEFKQFRLVPKQFDRLVDNLRGMVDRVRAQERQI 149 Query: 357 LRLAQSY-GIKRDVFLERHQGRELDPHWV 384 ++L + R F++ G E + W+ Sbjct: 150 MKLCVERAKMPRKDFIKSFPGNETNLDWL 178 >gnl|CDD|37202 KOG1991, KOG1991, KOG1991, Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport]. Length = 1010 Score = 35.3 bits (81), Expect = 0.052 Identities = 26/92 (28%), Positives = 43/92 (46%) Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268 Q E+ S+E E +D E E I+ + +DD+ +D E A E +LD+D+D Sbjct: 883 QVEEEDSEEGEEEDDDEEEDFIDDEDDIDEDDQDYLDEYGELALEKEDSLDDDDDFDEDE 942 Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300 L ED+L + +D + +LQ + Sbjct: 943 LDLEEDELFETPLDQVDPFQLFKEAITNLQSS 974 >gnl|CDD|35483 KOG0262, KOG0262, KOG0262, RNA polymerase I, large subunit [Transcription]. Length = 1640 Score = 34.2 bits (78), Expect = 0.12 Identities = 18/105 (17%), Positives = 36/105 (34%), Gaps = 13/105 (12%) Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSK----VDSPPENAENDERNLDEDEDDS 265 ++ DD E + D + A+ +++ +S E+ +ER + DED+ Sbjct: 1327 DEVGGEDNEDSDDESEDDEDDDDASDAKLHKKTEEEADYESEDEDERVEEREDEGDEDEE 1386 Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310 + D E E + Q ++ E+S Sbjct: 1387 SDEDDEEVGL---------DGTPEPEEEDQEGQPEVNAVERREQS 1422 >gnl|CDD|113695 pfam04931, DNA_pol_phi, DNA polymerase phi. This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784 Score = 33.7 bits (77), Expect = 0.19 Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 8/94 (8%) Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275 +E++ DD++ET+ D E + +D S+ +S E+ E DE +++D A+ Sbjct: 648 EEEDEDDLEETDDD-EDECEAIEDSESESESDGEDGEEDE----QEDDAEANEGVV---P 699 Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309 + V AL ++ + L G DE+ Sbjct: 700 IDKAVRRALPKVLNLPDALDGGDSEDEEGMDDEQ 733 >gnl|CDD|37327 KOG2116, KOG2116, KOG2116, Protein involved in plasmid maintenance/nuclear protein involved in lipid metabolism [Cell motility, Lipid transport and metabolism]. Length = 738 Score = 33.1 bits (75), Expect = 0.26 Identities = 38/236 (16%), Positives = 71/236 (30%), Gaps = 14/236 (5%) Query: 79 DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138 D +E EDSLD+ + D + T++ V ++ EL Sbjct: 150 DKRGDANESEQEDSLDIGQRSDTLPGSSFPESDRDNSPTENTVLAFVTPRSDSELEKSGS 209 Query: 139 EIAIAKRIEAGRAMMMASLCE-SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197 + + + ++ L E S N L RE D+ I SK Sbjct: 210 KRTLKSELSFSHSLSQRKLSEGSHFQKS---------NKEDALRRETHDMTRRIFLSSKS 260 Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257 K+ Q K ++ K ++ D + E D +N Sbjct: 261 LETFNAATLPIDKK---LQGKSDSELASKVDSPSR-KKDKREANDGADDLRLDDEGDYKN 316 Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313 D + ++ + + + +D E L S+ + D + ++K Sbjct: 317 ADPENSVTSSKWGELSESRQSVKSKGVDSGVEKTMRLASILCSLCLSLGDGREALK 372 >gnl|CDD|31168 COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]. Length = 347 Score = 32.6 bits (74), Expect = 0.37 Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 8/58 (13%) Query: 24 FDFSDDSWKKMIKLARQRG---YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78 +FS + + ++LA G YV + N L DE+ E +E + L +G++ V Sbjct: 44 LNFSVEDLAEAVELAHSAGKKVYVAV---NTLLHNDEL--ETLERYLDRLVELGVDAV 96 >gnl|CDD|36189 KOG0971, KOG0971, KOG0971, Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]. Length = 1243 Score = 31.9 bits (72), Expect = 0.66 Identities = 43/196 (21%), Positives = 72/196 (36%), Gaps = 24/196 (12%) Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE--------KERDDVQ 224 E D EI+ E E KG G SYQ ++ Q + RD Sbjct: 339 ERVDELETDLEILKAEM----EEKGS--DGQAASSYQFKQLEQQNARLKDALVRLRDLSA 392 Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED---------DSAHTLSAMEDQ 275 + D + K + S+++ E R LD+ E D+A M +Q Sbjct: 393 SEKQDHQKLQKELEKKNSELEELRRQKERLSRELDQAESTIADLKEQVDAALGAEEMVEQ 452 Query: 276 LRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334 L K + +++ + + L+ +N Q E + L+E+L G+ Q R Sbjct: 453 LTDKNLNLEEKVKLLEETVGDLEALEEMNEQLQESNRELELDLREELDMAKGARKELQKR 512 Query: 335 IDLLVEQLYDISKRIM 350 ++ E +YD + I Sbjct: 513 VEAAQETVYDRDQTIK 528 >gnl|CDD|37532 KOG2321, KOG2321, KOG2321, WD40 repeat protein [General function prediction only]. Length = 703 Score = 31.5 bits (71), Expect = 0.82 Identities = 26/173 (15%), Positives = 56/173 (32%), Gaps = 4/173 (2%) Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266 S + R + + Q E A D+ + ++ +A E + +E DD A Sbjct: 500 SEEYRLLAPVASKMSKKQPKELRELLEA-EESDEEEESENGESDAG-KEESDEEASDDDA 557 Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326 S+ E+ + A V R + +++ +K + K + + + G Sbjct: 558 DEASSDEETRKLYERKMEKHAAAVKRRRKEQKEDERTIRKPQTERSKQI--ENRAGNIFG 615 Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379 + + L + +GE+ G ++ F R + Sbjct: 616 ETKDSLLGQGGSKKSLQARLRSTARGDGEVTFEDGQRGKRQMTFTLRLKKSND 668 >gnl|CDD|40022 KOG4825, KOG4825, KOG4825, Component of synaptic membrane glycine-, glutamate- and thienylcyclohexylpiperidine-binding glycoprotein (43kDa) [Signal transduction mechanisms]. Length = 666 Score = 30.5 bits (68), Expect = 1.7 Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 9/88 (10%) Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED-DSAHTLSAMED 274 E +++ V + + D+ AK++ D K E END+ DED D A + Sbjct: 177 DENKQEAVAKEDFDLAKKAKLAIADLKKSGEELEELENDKGCAVADEDFDLAKDKKDEIE 236 Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAV 302 LR +++ LD L L+D + Sbjct: 237 ALRAEILAQLD--------LHLLEDAEL 256 >gnl|CDD|34730 COG5129, MAK16, Nuclear protein with HMG-like acidic region [General function prediction only]. Length = 303 Score = 30.1 bits (67), Expect = 2.0 Identities = 16/56 (28%), Positives = 26/56 (46%) Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264 ++ D+ E DD ++ + + K D+S S E E+ E DEDED+ Sbjct: 207 EEESDTELEAVTDDSEKEKTKKKDLEKWLGSDQSMETSESEEEESSESESDEDEDE 262 >gnl|CDD|36161 KOG0943, KOG0943, KOG0943, Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]. Length = 3015 Score = 30.2 bits (67), Expect = 2.1 Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 4/69 (5%) Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266 S D++ + E + QE E E D D ++AE ++ + D+D+DD Sbjct: 1709 SGNTTNDTNADNEEREGQEGEFAGEE----DHHDDDNDDDDDDDAEAEDDDDDDDDDDED 1764 Query: 267 HTLSAMEDQ 275 L A Sbjct: 1765 MDLDAEAAA 1773 >gnl|CDD|37249 KOG2038, KOG2038, KOG2038, CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis, Transcription]. Length = 988 Score = 30.0 bits (67), Expect = 2.5 Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 10/63 (15%) Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271 ED S +E DD E E E KDD++K D +D+ + DED+D+ ++L + Sbjct: 844 EDGSLPEEEDDDYEFEFGAE------KDDKNKKD----MTSDDDVDADEDDDEDENSLGS 893 Query: 272 MED 274 ED Sbjct: 894 EED 896 >gnl|CDD|39545 KOG4344, KOG4344, KOG4344, Uncharacterized conserved protein [Function unknown]. Length = 1121 Score = 29.8 bits (66), Expect = 2.7 Identities = 26/103 (25%), Positives = 47/103 (45%), Gaps = 15/103 (14%) Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVD--------SPPENAENDERN--LDEDE 262 +S +E ER+ E + D ++A + +D+ + E+ END+ + L+E++ Sbjct: 142 NSMEEAERNAEIEEKADFDAAKNLMEDEEMDIAALLDEDFLDEEEDDENDQLSDPLEEED 201 Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRE--LRSLQDNAVN 303 D L E+ + + LDE A V E S+ + VN Sbjct: 202 CDIQTDLKPDEEIDQNR---KLDECARVKDEADDASVLEGHVN 241 >gnl|CDD|143182 cd04981, IgV_H, Immunoglobulin (Ig) heavy chain (H), variable (V) domain. IgV_H: Immunoglobulin (Ig) heavy chain (H), variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains. Length = 117 Score = 29.3 bits (66), Expect = 3.5 Identities = 7/15 (46%), Positives = 12/15 (80%) Query: 493 GYKFSTYAMWWVKQA 507 G+ F++Y + WV+QA Sbjct: 23 GFTFTSYGVNWVRQA 37 >gnl|CDD|34868 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]. Length = 4600 Score = 29.3 bits (65), Expect = 3.7 Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 16/87 (18%) Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN------------ 250 T+ + E+S E+E D+ E DI S +++ + E+ Sbjct: 3868 TKDSVVSENENSDSEEENQDLDEEVNDIPEDLSNSLNEKLWDEPNEEDLLETEQKSNEQS 3927 Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLR 277 A N+E +L EDD+ A+ED+ R Sbjct: 3928 AANNESDLVSKEDDN----KALEDKDR 3950 Score = 28.9 bits (64), Expect = 4.4 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 11/74 (14%) Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD-------SPPENAEND---ERNLDE 260 +ED ++ E D QE E + E + V DD + D PPEN + D + LDE Sbjct: 3938 KEDDNKALEDKDRQEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDE 3997 Query: 261 DEDDSAHTLSAMED 274 E D + S +ED Sbjct: 3998 KEGDVSKD-SDLED 4010 >gnl|CDD|31783 COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]. Length = 182 Score = 28.9 bits (64), Expect = 4.7 Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 4/76 (5%) Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652 E A + + E R LA L PR+ +R+ G+ + EE+ + ++ Sbjct: 101 EADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEGL----SYEEIAEILGIS 156 Query: 653 RERIRQIEAKAIRKLK 668 ++ +A +KL+ Sbjct: 157 VGTVKSRLHRARKKLR 172 >gnl|CDD|39027 KOG3823, KOG3823, KOG3823, Uncharacterized conserved protein [Function unknown]. Length = 630 Score = 28.9 bits (64), Expect = 5.1 Identities = 10/62 (16%), Positives = 21/62 (33%) Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264 + Q+ S E + + +G +E + D++ P+ A + D Sbjct: 555 HLAGQEEAHESHESQSVSCDKPQGIVEIGREAELLDKTAQSEEPKIAAASQAGRPGCGGD 614 Query: 265 SA 266 A Sbjct: 615 VA 616 >gnl|CDD|37043 KOG1832, KOG1832, KOG1832, HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]. Length = 1516 Score = 28.9 bits (64), Expect = 5.3 Identities = 11/53 (20%), Positives = 26/53 (49%) Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264 E+ + ++ D+ + E D++ + D+ D + +N++ DED D+ Sbjct: 1410 EEDDETEDEDEDDDEEDDLDRDDGLEGDNSDSGDDDLSSEDNEDEVSDEDGDE 1462 Score = 28.1 bits (62), Expect = 8.8 Identities = 11/56 (19%), Positives = 22/56 (39%) Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265 +R + + + ++ ETE + E + DR + D+ ED +D Sbjct: 1399 RRRPTDDDSDEEEDDETEDEDEDDDEEDDLDRDDGLEGDNSDSGDDDLSSEDNEDE 1454 >gnl|CDD|32632 COG2771, CsgD, DNA-binding HTH domain-containing proteins [Transcription]. Length = 65 Score = 28.4 bits (63), Expect = 6.2 Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 5/58 (8%) Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673 A LTPRE +LR+ + + +E+ + ++ E ++ RKL +R Sbjct: 1 RTADLTPREREILRL-----VAQGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRV 53 >gnl|CDD|37045 KOG1834, KOG1834, KOG1834, Calsyntenin [Extracellular structures]. Length = 952 Score = 28.5 bits (63), Expect = 7.0 Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 6/64 (9%) Query: 207 SYQKREDSSQEKERDDVQETEGD-----IESAAKVSKDDRSKVDSPPENAENDERNLDED 261 Y+K +E E ++ +ETE + +SA S+D+ + P + +N++R + + Sbjct: 886 DYEKGGSIEEESEEEEEEETEDEEESSDSDSADSESEDEEEGTEVGP-HLQNNQRQVQLE 944 Query: 262 EDDS 265 DDS Sbjct: 945 WDDS 948 >gnl|CDD|146113 pfam03313, SDH_alpha, Serine dehydratase alpha chain. L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyses the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway. Length = 269 Score = 28.2 bits (64), Expect = 7.7 Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 6/67 (8%) Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478 E G+SISE + K E + V + + +GL+ L+ I G+ Sbjct: 2 EKGLSISE------NILKNEMSVGVPGTGEVGLKMAAALGAMGGDVEKGLEVLEGITPGD 55 Query: 479 IGLMKAA 485 + + A Sbjct: 56 LKKARRA 62 >gnl|CDD|35277 KOG0054, KOG0054, KOG0054, Multidrug resistance-associated protein/mitoxantrone resistance protein, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]. Length = 1381 Score = 28.3 bits (63), Expect = 7.8 Identities = 10/25 (40%), Positives = 13/25 (52%) Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671 K F E +RQ E K +RK + S Sbjct: 400 KPFLKKIEDLRQKELKLLRKSAYLS 424 >gnl|CDD|173900 cd00674, LysRS_core_class_I, catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity. Length = 353 Score = 28.1 bits (63), Expect = 8.1 Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 11/51 (21%) Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHI--------VSMVRKG 437 W + +A + I++ R + V +GIS S HI +V + Sbjct: 3 WADVIA---EKIIEERKGKEKYVVASGISPSGHIHIGNFREVITADLVARA 50 >gnl|CDD|30988 COG0643, CheA, Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]. Length = 716 Score = 28.0 bits (62), Expect = 9.2 Identities = 32/152 (21%), Positives = 59/152 (38%), Gaps = 2/152 (1%) Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271 E + +E + V TE D E V + + + A + L E + Sbjct: 229 EAEAAFEESEVVLATEQDEELIRDVL-ELVVEAEELEIAAVELDAELLELAESEQAADDV 287 Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK-EKLVKLVGSLSL 330 + Q P + E A++ + A SS++ V K ++L+ LVG L + Sbjct: 288 LAAQAEPLAEKSAAEAAKLSALEAAPAAKAAAAAAGASSSIRVDVEKLDRLMNLVGELVI 347 Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362 +SR+ L +L ++ + + +L RL Sbjct: 348 TRSRLSQLASELDEVREELDEALRQLSRLTTD 379 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 0.315 0.131 0.366 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: 7,835,413 Number of extensions: 413758 Number of successful extensions: 1259 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1225 Number of HSP's successfully gapped: 98 Length of query: 682 Length of database: 6,263,737 Length adjustment: 100 Effective length of query: 582 Effective length of database: 4,102,837 Effective search space: 2387851134 Effective search space used: 2387851134 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: 42 (22.0 bits) S2: 61 (27.6 bits)