RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781102|ref|YP_003065515.1| UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase [Candidatus Liberibacter asiaticus str. psy62] (497 letters) >gnl|CDD|31112 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]. Length = 475 Score = 379 bits (974), Expect = e-105 Identities = 188/472 (39%), Positives = 253/472 (53%), Gaps = 19/472 (4%) Query: 32 EVSSDSRHIQAGWIFVAIVGNKEDGHLFIPQAIAQGAEAIVVSSAYSLQDFSATIRSNTP 91 ++ DSR ++ G +FVA G K DGH FI AIA GA A+VV L + + P Sbjct: 12 GLTLDSRKVKEGDLFVAKPGTKVDGHDFIAGAIAPGAVAVVVEKDIKLAE------AGVP 65 Query: 92 ILVVDNTRKFLSLFASRLYGK--HPENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGP 149 ++VV T L+ A YG ++ VTGT+GK++ S + QI ++ G + IG Sbjct: 66 VIVVTGTNGKLTTLALAFYGLPSGKLKVIGVTGTNGKTTTTSLLAQILKKLGKKTALIGT 125 Query: 150 TSTISSFAQDN--RLTTPSPIYLAKALSYLSSQGVTHVSVEASSHGLDQHRLDGIKLIAG 207 S LTTP + L L L +G +E SSHGL Q R++G+ G Sbjct: 126 EGDELSPGILEPTGLTTPEALDLQNLLRDLLDRGAEIAVMEVSSHGLVQGRVEGVTFDVG 185 Query: 208 SFTNLGRDHIDYHQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKRAHNAGCRV 267 FTNL RDH+DYH T + Y AK LFE LP A+I DD + + +R NA Sbjct: 186 VFTNLSRDHLDYHGTMEYYGAAKAVLFE-SLPHSGEAVINPDDGHGLDYKERLKNALGDY 244 Query: 268 LSVGYQGKFIHLKK--VCAIHNKQQVTISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAI 325 ++ G K L + + G ++ PLPG F VYNAL A +A+ Sbjct: 245 ITYGCDFKRPDLDYRGIEESSSGSDFVFEPSGGIGEYELPLPGLFNVYNALAAVAAALAL 304 Query: 326 GIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYAHTSNSLEMILKNIRTITSGRII 385 G+D +L LE L VPGR E V N G + VDYAH + LE L+ +R +GR+I Sbjct: 305 GVDLEDILAGLETLKPVPGRMELV--NIGGKLVIVDYAHNPDGLEKALRAVRLHAAGRLI 362 Query: 386 VVFGCGGDRDQGKRPIMGKIALDLADIAIVTDDNPRSEDPEKIRAEIIHGIPG---FIEK 442 VVFGCGGDRD+ KRP MG IA LADI IVT DNPRSEDP I A+I+ GI + Sbjct: 363 VVFGCGGDRDKSKRPDMGAIAEQLADIVIVTSDNPRSEDPAVILADILAGIEAPEKYEII 422 Query: 443 GNRIEAIRTAIEMLNKQDVLVVAGKGHETVHIVTNGEKKMSVDCDIIREILG 494 +R EAIR A+++ + DV+++AGKGHET I+ K+ D +++RE L Sbjct: 423 EDREEAIRKALDLAKEGDVVLIAGKGHETYQIML-ELKRPFDDREVVREALL 473 >gnl|CDD|31113 COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]. Length = 451 Score = 140 bits (354), Expect = 8e-34 Identities = 92/366 (25%), Positives = 157/366 (42%), Gaps = 27/366 (7%) Query: 27 ERKINEVSSDSRHIQAGWIFVAIVGNKEDGHLFIPQAIAQGAEAIVVSSAYSLQDFSATI 86 ++ VS DSR ++ G +FVA+ G + DGH FI QA+A GA A++V+ Sbjct: 21 PVVVSGVSIDSRKVKPGDLFVALKGERFDGHDFIEQALAAGAAAVLVARPV------LPP 74 Query: 87 RSNTPILVVDNTRKFLSLFASRLYGKHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQ 146 +L+V +T + L A K ++A+TG++GK++ + I G Sbjct: 75 AIPLVVLLVLDTLEALGKLAKAYRQKFNAKVIAITGSNGKTTTKEMLAAILSTKGKVH-- 132 Query: 147 IGPTSTISSFAQDNRLTTPSPIYLAKALSYLSSQGVTHVSVEASSHGLDQHRLDGIKLIA 206 +T +F N + P + L + + + + G + + Sbjct: 133 ----ATPGNFN--NEIGLPLTL-----LRLPADTEYAVLEMGMNHPGEIAELSEIARPDI 181 Query: 207 GSFTNLGRDHIDYHQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKRAHNAGCR 266 TN+G H++ +++ AK + L E AI+ AD+ K + NA + Sbjct: 182 AVITNIGEAHLEGFGSREGIAEAKAEILAG-LRPEGIAILNADNPLLKNWAAKIGNA--K 238 Query: 267 VLSVG-YQGKFIHLKKVCAIHNKQQVTISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAI 325 VLS G G + T+ +EG + +F PLPG V NAL AA L + + Sbjct: 239 VLSFGLNNGGDFRATNIHLDEEGSSFTLDIEGGEAEFELPLPGRHNVTNALAAAALALEL 298 Query: 326 GIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYAHTSN--SLEMILKNIRTITSGR 383 G+D + L++L V GR E + G+ +D ++ +N S+ L + + + Sbjct: 299 GLDLEEIAAGLKELKPVKGRLEVILL--ANGKTLIDDSYNANPDSMRAALDLLAALPGRK 356 Query: 384 IIVVFG 389 I V G Sbjct: 357 GIAVLG 362 >gnl|CDD|31114 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]. Length = 448 Score = 117 bits (294), Expect = 9e-27 Identities = 90/367 (24%), Positives = 148/367 (40%), Gaps = 49/367 (13%) Query: 102 LSLFASRLYGKHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNR 161 + LF RL G+ P I+A+TGT+GK++ S + + + +GL + G Sbjct: 100 IELFY-RLSGEAP--IVAITGTNGKTTTTSLIAHLLKAAGLDALLGG------------N 144 Query: 162 LTTPSPIYLAKALSYLSSQ-GVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYH 220 + TP AL L +E SS L ++ N+ DH+D H Sbjct: 145 IGTP-------ALELLEQAEPADVYVLELSSFQL--ETTSSLRPEIAVILNISEDHLDRH 195 Query: 221 QTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLK 280 + + Y AK+R+ E + A+I ADDAY K + A A S G Sbjct: 196 GSMENYAAAKLRILEG---QTEVAVINADDAYLKTLADEATKARVIWFSFGEPLADGDYI 252 Query: 281 KVCAIHNKQQVTISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLH 340 + K + + + LPG + NAL A L A+G+ +LE L Sbjct: 253 YDGKLVFKGEKLLPAD------ELKLPGAHNLENALAALALARALGVPPEAILEALSSFT 306 Query: 341 VVPGRFEFVGTNSRGGRIYVDYAHTSN--SLEMILKNIRTITSGRIIVVFGCGGDRDQGK 398 +P R EFVG G ++++ + +N + L G +I++ GGD Sbjct: 307 GLPHRLEFVGEK--DGVLFINDSKATNVDATLAALSGFD----GPVILI--AGGDDKGAD 358 Query: 399 RPIMGKIALDLADIAIVTDDNPRSEDPEKIRAEIIHGIPGFIEKGNRIEAIRTAIEMLNK 458 + +I + ++ ED EKI A + P + EA++ A E+ Sbjct: 359 FSPLAEILAKVIKKLVL-----IGEDAEKIAAALKEAGPSLVICETLEEAVQLARELAQP 413 Query: 459 QDVLVVA 465 DV++++ Sbjct: 414 GDVVLLS 420 >gnl|CDD|31116 COG0773, MurC, UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]. Length = 459 Score = 106 bits (265), Expect = 2e-23 Identities = 93/421 (22%), Positives = 161/421 (38%), Gaps = 61/421 (14%) Query: 67 GAEAIVVSSAYS--LQDFSATIRSNTPILVVDNTRKFLSLFASRLYGKHPENILAVTGTS 124 A+ +VVS+A + A + P++ + A + + +AV GT Sbjct: 66 DADVVVVSNAIKEDNPEIVAALERGIPVI------SRAEMLAELMRFRT---SIAVAGTH 116 Query: 125 GKSSVASFVQQICQRSGLS-SFQIGPTSTISSFAQDNRLTTPSPIYLAKALSYLSSQGVT 183 GK++ S + + + +GL +F IG + +F + RL + ++A+A Sbjct: 117 GKTTTTSMLAWVLEAAGLDPTFLIG--GILKNFGTNARLGS-GDYFVAEA---------- 163 Query: 184 HVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEELLPKESP 243 E+ S L + I TN+ DH+DY+ +A A F +P Sbjct: 164 ---DESDSSFLHYNPRVAI------VTNIEFDHLDYYGDLEAIKQA-FHHFVRNVPFYGR 213 Query: 244 AIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKF-IHLKKVCAIHNKQQVTISVEGKD-FD 301 A++ DD +E++ R V++ G+ + + + + + G++ + Sbjct: 214 AVVCGDDPNLRELLSRGCW--SPVVTYGFDDEADWRAENIRQDGSGTTFDVLFRGEELGE 271 Query: 302 FLFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVD 361 PLPG V NAL A + +GID + E L V RFE G G + D Sbjct: 272 VKLPLPGRHNVLNALAAIAVARELGIDPEAIAEALASFQGVKRRFELKGE-VNGVTVIDD 330 Query: 362 YAHTSNSLEMILKNIRTIT--SGRIIVVFGCGGDRDQGKRPIMGK-------IALDLADI 412 YAH ++ L R RI+ VF Q R + AL AD Sbjct: 331 YAHHPTEIKATLAAARQKVPGGKRIVAVF-------QPHRYSRTRDLLDDFAKALSDADE 383 Query: 413 AIVTDDNPRSEDPEKIRAEIIH-----GIPGFIEKGNRIEAIRTAIEMLNKQDVLVVAGK 467 I+ D E+P + PG ++ + + + ++ DV++ G Sbjct: 384 VILLDVYAAGEEPIEGDVSSEDLAEKIRQPGHVDVPDLDDLVELLAKVAQPGDVILFMGA 443 Query: 468 G 468 G Sbjct: 444 G 444 >gnl|CDD|145824 pfam02875, Mur_ligase_C, Mur ligase family, glutamate ligase domain. This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC, MurD, MurE, MurF, Mpl and FolC. MurC, MurD, Mure and MurF catalyse consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesized by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate. Length = 87 Score = 93.2 bits (232), Expect = 1e-19 Identities = 39/88 (44%), Positives = 55/88 (62%), Gaps = 1/88 (1%) Query: 342 VPGRFEFVGTNSRGGRIYVDYAHTSNSLEMILKNIRTITSGRIIVVFGCGGDRDQGKRPI 401 VPGR E VG N G + DYAH ++LE L+ ++ + GR+I+VFG GGDRD + Sbjct: 1 VPGRLEVVGEN-NGVLVIDDYAHNPDALEAALQALKELFDGRLILVFGAGGDRDAEFHAL 59 Query: 402 MGKIALDLADIAIVTDDNPRSEDPEKIR 429 +G +A LAD+ I+T D PR+E+P Sbjct: 60 LGALAAALADVVILTGDYPRAEEPGAAI 87 >gnl|CDD|30633 COG0285, FolC, Folylpolyglutamate synthase [Coenzyme metabolism]. Length = 427 Score = 88.4 bits (219), Expect = 4e-18 Identities = 87/403 (21%), Positives = 149/403 (36%), Gaps = 67/403 (16%) Query: 105 FASRLYGKHPE-NILAVTGTSGKSSVASFVQQICQRSG----------LSSF-------- 145 RL ++ V GT+GK S +F++ I + +G L SF Sbjct: 33 LLERLGNPQKSPPVIHVAGTNGKGSTCAFLESILREAGYKVGVYTSPHLLSFNERIRING 92 Query: 146 -QIGPTSTISSFAQ----DNRLTTPSPIYL----AKALSYLSSQGVTHVSVEASSHGLDQ 196 I ++F + L S Y A A Y + V +E G Sbjct: 93 EPISDEELAAAFERVEEAAGSLDLISLTYFEVLTAMAFLYFAEAKVDVAILEVGLGG--- 149 Query: 197 HRLDGIKLIAGS---FTNLGRDHIDY---HQTQQAYFNAKMRLFEELLPKESPAIIYA-- 248 RLD +I T++G DH + A A ++ PA+I Sbjct: 150 -RLDATNVIEPDVSVITSIGLDHTAFLGDTLESIAREKAG------IIKAGKPAVIGEQQ 202 Query: 249 DDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIHNKQQVTISVEGKDFDFLFPLPG 308 + +RA G + +G + + + G D PL G Sbjct: 203 PPEALNVIAERAEELGAPLFVLGPDFQ--------VLEEGNGFSFQGGGGLLDLPLPLLG 254 Query: 309 E-FQVYNALVAAGLCIAIG--IDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYAHT 365 Q+ NA +A A+G I + + L + PGR E + S I +D AH Sbjct: 255 GHHQIENAALAIAALEALGKEISEEAIRKGLANVD-WPGRLERL---SENPLILLDGAHN 310 Query: 366 SNSLEMILKNIRTI--TSGRIIVVFGCGGDRDQGKRPIMGKIALDLADIAIVTDDNPRSE 423 ++ + + ++T+ R+ +VFG D+D ++ + + +I PR+ Sbjct: 311 PHAARALAETLKTLFNDRPRLTLVFGMLKDKDIA--GMLAALLPIVDEIYTTPLPWPRAL 368 Query: 424 DPEKIRAEIIHGIPGFIEKGNRIEAIRTAIEMLNKQDVLVVAG 466 D E++ A G G +E + EA+ A+E ++ D+++V G Sbjct: 369 DAEELLA--FAGERGGVELDDVAEALELALEKADEDDLVLVTG 409 >gnl|CDD|144716 pfam01225, Mur_ligase, Mur ligase family, catalytic domain. This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC, MurD, MurE, MurF, Mpl and FolC. MurC, MurD, Mure and MurF catalyse consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesized by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate. Length = 76 Score = 67.2 bits (165), Expect = 9e-12 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 6/82 (7%) Query: 29 KINEVSSDSRHIQAGWIFVAIVGNKEDGHLFIPQAIAQGAEAIVVSSAYSLQDFSATIRS 88 +I+ + DSR + G +F+A+ G + DG F AIA GA A+V S+ Sbjct: 1 EIHFIGIDSRGMSPGALFLALKGYRVDGSDFAESAIALGAVAVVSSA------IPRDPNP 54 Query: 89 NTPILVVDNTRKFLSLFASRLY 110 P + V + R+ L+ A+R Y Sbjct: 55 EVPGIPVIDRREALAELAARFY 76 >gnl|CDD|37736 KOG2525, KOG2525, KOG2525, Folylpolyglutamate synthase [Coenzyme transport and metabolism]. Length = 496 Score = 41.8 bits (98), Expect = 4e-04 Identities = 81/369 (21%), Positives = 120/369 (32%), Gaps = 69/369 (18%) Query: 78 SLQDFSATIRSNTPILVVDNTRKFLSLFASRLYGKH---PE-----NILAVTGTSGKSSV 129 SLQ +A I + D+ + L+L R + PE NI+ V GT GK S Sbjct: 30 SLQSNAALI---EKLRRQDDNPQGLTLPRMRKLLERLGNPEDQNSLNIIHVAGTKGKGST 86 Query: 130 ASFVQQICQRSGL------SSFQIGPTSTIS-----------------SFAQDNRLTT-- 164 +F + I ++ GL S + I + + Sbjct: 87 CAFTESILRQQGLRTGFYTSPHLLSVRERIRINGQPISEEKFTKYFWEVYERLKSTKLKE 146 Query: 165 -PSPIYL----AKALSYLSSQGVTHVSVEASSHGLDQHRLDGI----KLIAGSFTNLGRD 215 P Y A + V +E G LD K + T+LG D Sbjct: 147 VSMPTYFEFLTLLAFHVFVKENVDVAVIEVGLGG----ELDATNVIEKPVVCGITSLGLD 202 Query: 216 HIDY-HQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMK-RAHNAGCRVLSVGYQ 273 H + T K +F+E PA + V+K RA G + V Sbjct: 203 HTSFLGNTLSEIAWEKAGIFKE----GVPAFTVPQPPEALNVLKERASELGVPLFVVPPL 258 Query: 274 GKFIHLKKVCAIHNKQQVTISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVL 333 + + Q + + L E+ + N VA G+ A+ + Sbjct: 259 EAYELSGVNLGLIGTHQWSNAS------LAVQLASEWLIQNGRVAEGVLDALQTSGLIPP 312 Query: 334 EHLEKLHVV--PGRFEFVGTNSRGGRIYVDYAHTSNSLEMILKNIRTITSGR-----IIV 386 L L PGR + + RG +D AHT S E K R G +I+ Sbjct: 313 AFLSGLASTDWPGRLQILEYG-RGVTWLLDGAHTKESAEACAKWFRKAVRGLKKLTSLIL 371 Query: 387 VFGCGGDRD 395 +F C DRD Sbjct: 372 LFNCTSDRD 380 >gnl|CDD|177020 CHL00081, chlI, Mg-protoporyphyrin IX chelatase. Length = 350 Score = 31.5 bits (72), Expect = 0.49 Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 6/66 (9%) Query: 392 GDRDQGKRPIMGKIALDLADIAIVTDD--NPRSEDPEKIRAEIIHGIPGFIEKGNRIEAI 449 GDR GK + + L +I +V DD N DPE + E+ I+ G IE Sbjct: 45 GDRGTGKSTTIRALVDLLPEIEVVKDDPFNSHPSDPELMSDEVREA----IQNGETIETE 100 Query: 450 RTAIEM 455 + I M Sbjct: 101 KIKIPM 106 >gnl|CDD|31262 COG1062, AdhC, Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]. Length = 366 Score = 31.3 bits (71), Expect = 0.56 Identities = 28/118 (23%), Positives = 39/118 (33%), Gaps = 21/118 (17%) Query: 379 ITSGRIIVVFGCGGDRDQGKRPIMG-KIALDLADIAIVTDD---------------NPRS 422 + G + VFG GG G I G K A IA+ + NP+ Sbjct: 183 VEPGDTVAVFGLGG---VGLAAIQGAKAAGAGRIIAVDINPEKLELAKKFGATHFVNPKE 239 Query: 423 EDP--EKIRAEIIHGIPGFIEKGNRIEAIRTAIEMLNKQDVLVVAGKGHETVHIVTNG 478 D E I G E +E +R A+E ++ V+ G I T Sbjct: 240 VDDVVEAIVELTDGGADYAFECVGNVEVMRQALEATHRGGTSVIIGVAGAGQEISTRP 297 >gnl|CDD|35667 KOG0446, KOG0446, KOG0446, Vacuolar sorting protein VPS1, dynamin, and related proteins [Intracellular trafficking, secretion, and vesicular transport, General function prediction only]. Length = 657 Score = 30.7 bits (69), Expect = 0.87 Identities = 28/97 (28%), Positives = 44/97 (45%), Gaps = 10/97 (10%) Query: 390 CGGDRDQGKRPIMGKI-ALDLADIAIVTD----DNPRSEDPEKIRAEIIHGIPGFIEKGN 444 G ++ PI KI + +A++ +V P ++ P+ I EI I +IEK N Sbjct: 111 TGSNKGISPVPITLKIFSALVANLTLVDLPGLTKVPVADQPDDIEEEIKSMIEEYIEKPN 170 Query: 445 R-IEAIRTAIEMLNKQDVLVVAG----KGHETVHIVT 476 R I A+ A + LVVA G T+ ++T Sbjct: 171 RIILAVTPANSDIATSPALVVAREVDPGGSRTLEVIT 207 >gnl|CDD|32991 COG3178, COG3178, Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]. Length = 351 Score = 30.7 bits (69), Expect = 0.92 Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 15/71 (21%) Query: 113 HPENILAVTGTSGKSSVASFVQQICQRSGLSSFQ---IGPTS-TISSFAQDNRLTTPSPI 168 H N++ +G R G+ FQ IGP + ++S +D R+T Sbjct: 208 HSRNLMWTADRAGAD-----------RVGVLDFQDALIGPIAYDVASLLRDARVTWSPER 256 Query: 169 YLAKALSYLSS 179 LA Y ++ Sbjct: 257 ELALLDRYWAA 267 >gnl|CDD|33790 COG4031, COG4031, Predicted metal-binding protein [General function prediction only]. Length = 227 Score = 30.4 bits (68), Expect = 1.2 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 4/70 (5%) Query: 331 LVLEHLEKLHVVPGRFEFVGTNSRGG-RIYVDYAHTSNSLEMILKNIRTITSGRIIVVFG 389 LV +H V+PG G+ GG R+ V A +L ++L ++ R++ Sbjct: 148 LVAQHPYVKKVIPGVISAKGSAGGGGVRLKVTRADARGNLRLLLSEGSSVQEIRVVTT-- 205 Query: 390 CGGDRDQGKR 399 G R++G+R Sbjct: 206 -AGSREEGER 214 >gnl|CDD|133175 cd05043, PTK_Ryk, Pseudokinase domain of Ryk (Receptor related to tyrosine kinase). Protein Tyrosine Kinase (PTK) family; Receptor related to tyrosine kinase (Ryk); pseudokinase domain. The PTKc (catalytic domain) family to which this subfamily belongs, is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Ryk is a receptor tyr kinase (RTK) containing an extracellular region with two leucine-rich motifs, a transmembrane segment, and an intracellular inactive pseudokinase domain. The extracellular region of Ryk shows homology to the N-terminal domain of Wnt inhibitory factor-1 (WIF) and serves as the ligand (Wnt) binding domain of Ryk. Ryk is expressed in many different tissues both during development and in adults, suggesting a widespread function. It acts as a chemorepulsive axon guidance receptor of Wnt glycoproteins and is responsible for the establishment of axon tracts during the development of the central nervous system. In addition, studies in mice reveal that Ryk is essential in skeletal, craniofacial, and cardiac development. Thus, it appears Ryk is involved in signal transduction despite its lack of kinase activity. Ryk may function as an accessory protein that modulates the signals coming from catalytically active partner RTKs such as the Eph receptors. Length = 280 Score = 29.7 bits (67), Expect = 2.0 Identities = 21/93 (22%), Positives = 34/93 (36%), Gaps = 25/93 (26%) Query: 106 ASRLYGKHPENILAVTGTS--------------GKSSVASFVQQICQRSGLSSFQIGPTS 151 + LYG +NIL + ++ F+QQ C+ ++ Q T Sbjct: 59 SCLLYGLSHQNILPILHVCIEDGEPPFVLYPYMNWGNLKLFLQQ-CRLGEANNPQALSTQ 117 Query: 152 TISSFAQDNRLTTPSPIYLAKALSYLSSQGVTH 184 + A I +A +SYL +GV H Sbjct: 118 QLVHMA----------IQIACGMSYLHKRGVIH 140 >gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase. Glutathione-dependent formaldehyde dehydrogenases (FDHs, Class III ADH) are members of the zinc-dependent/medium chain alcohol dehydrogenase family. FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. Class III ADH are also known as glutathione-dependent formaldehyde dehydrogenase (FDH), which convert aldehydes to corresponding carboxylic acid and alcohol. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of an beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. Length = 363 Score = 29.0 bits (66), Expect = 2.7 Identities = 31/113 (27%), Positives = 41/113 (36%), Gaps = 19/113 (16%) Query: 379 ITSGRIIVVFGCGGDRD---QGKRPIMGK---IALDLAD----IAIV---TDD-NPRSED 424 + G + V GCGG QG R I G IA+D +A T N +D Sbjct: 180 VRPGDTVAVIGCGGVGLNAIQGAR-IAGASRIIAVDPVPEKLELARRFGATHTVNASEDD 238 Query: 425 PEKIRAEIIHGIPGF---IEKGNRIEAIRTAIEMLNKQDVLVVAGKGHETVHI 474 + ++ G G E R IR A+ M K VV G G + Sbjct: 239 AVEAVRDLTDGR-GADYAFEAVGRAATIRQALAMTRKGGTAVVVGMGPPGETV 290 >gnl|CDD|176133 cd08442, PBP2_YofA_SoxR_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 193 Score = 29.1 bits (66), Expect = 3.0 Identities = 37/169 (21%), Positives = 61/169 (36%), Gaps = 52/169 (30%) Query: 181 GVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEE---- 236 G T ++ + + RLDG +AG +H Q +F+E Sbjct: 36 GTTGALIQ----AVLEGRLDGA-FVAGPV-----EHPRLEQEP---------VFQEELVL 76 Query: 237 LLPKESPAIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIHNKQQVTISVE 296 + PK P + A+D ++ A AGC Y+ + + + + Sbjct: 77 VSPKGHPPVSRAEDLAGSTLL--AFRAGC-----SYRRRLEDWLAEEGVSPGKIM----- 124 Query: 297 GKDFDFLFPLPGEFQVYNAL---VAAGLCIAIGIDSALVLEHLEKLHVV 342 EF Y+A+ VAAG+ IA+ S VL+ L+ V Sbjct: 125 ------------EFGSYHAILGCVAAGMGIALLPRS--VLDSLQGRGSV 159 >gnl|CDD|31522 COG1331, COG1331, Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]. Length = 667 Score = 28.7 bits (64), Expect = 3.2 Identities = 14/60 (23%), Positives = 21/60 (35%), Gaps = 5/60 (8%) Query: 314 NALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYAHTSNSLEMIL 373 N L+ A L A VL E L +F+ N R+ Y ++ +L Sbjct: 413 NGLMIAALAEA-----GRVLGDPEYLEAAERAADFILDNLYVDRLLRRYRGGEAAVAGLL 467 >gnl|CDD|37624 KOG2413, KOG2413, KOG2413, Xaa-Pro aminopeptidase [Amino acid transport and metabolism]. Length = 606 Score = 28.3 bits (63), Expect = 4.8 Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 3/51 (5%) Query: 127 SSVASFVQQICQRSGLSSFQIGPTSTI---SSFAQDNRLTTPSPIYLAKAL 174 + S ++ I P + +D+ + PSPI AKA+ Sbjct: 257 DQIWSDIKNWASAFADKKIWISPETNYGIGELIGEDHSMIDPSPISRAKAI 307 >gnl|CDD|33514 COG3719, Rna, Ribonuclease I [Translation, ribosomal structure and biogenesis]. Length = 249 Score = 28.4 bits (63), Expect = 4.9 Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 2/32 (6%) Query: 222 TQQAYFNAKMRLFEELLPKESPAIIYADDAYS 253 +Q+AYF RLFEEL K P D + Sbjct: 150 SQEAYFATTRRLFEEL--KLPPVRKLLADGKT 179 >gnl|CDD|39608 KOG4407, KOG4407, KOG4407, Predicted Rho GTPase-activating protein [General function prediction only]. Length = 1973 Score = 28.2 bits (62), Expect = 5.4 Identities = 19/83 (22%), Positives = 27/83 (32%), Gaps = 3/83 (3%) Query: 62 QAIAQGAEAIVVSSAYSLQDFSATIRSNTPILVVDNTRKFLSLFASRLYGKHPENILAVT 121 Q ++ A + + LQ F A S+ P + R P + AV Sbjct: 758 QQTSRSLPAPHPPATHRLQRFIALFNSSKPSDGSGEHKPSRM---KRSRTSLPASRAAVP 814 Query: 122 GTSGKSSVASFVQQICQRSGLSS 144 GT +S V Q LS Sbjct: 815 GTILQSGVFRQTPVKHQEIALSK 837 >gnl|CDD|107248 cd01391, Periplasmic_Binding_Protein_Type_1, Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold. Length = 269 Score = 27.9 bits (62), Expect = 6.3 Identities = 29/155 (18%), Positives = 51/155 (32%), Gaps = 11/155 (7%) Query: 115 ENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRL--TTPSPIYLAK 172 + + + G SS A V ++ +G+ + +T + P + Sbjct: 57 QGVDGIIGPPS-SSSALAVVELAAAAGIP--VVSLDATAPDLTGYPYVFRVGPDNEQAGE 113 Query: 173 AL-SYLSSQGVTHVSV-EASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAK 230 A YL+ +G V++ + RL+G K + F A Sbjct: 114 AAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALKKAGIEVVAIEYGDLDTEKGFQA- 172 Query: 231 MRLFEELLPKESP-AIIYADDAYSKEVMKRAHNAG 264 L + L P AI +D + +K A AG Sbjct: 173 --LLQLLKAAPKPDAIFACNDEMAAGALKAAREAG 205 >gnl|CDD|176187 cd05284, arabinose_DH_like, D-arabinose dehydrogenase. This group contains arabinose dehydrogenase (AraDH) and related alcohol dehydrogenases. AraDH is a member of the medium chain dehydrogenase/reductase family and catalyzes the NAD(P)-dependent oxidation of D-arabinose and other pentoses, the initial step in the metabolism of d-arabinose into 2-oxoglutarate. Like the alcohol dehydrogenases, AraDH binds a zinc in the catalytic cleft as well as a distal structural zinc. AraDH forms homotetramers as a dimer of dimers. AraDH replaces a conserved catalytic His with replace with Arg, compared to the canonical ADH site. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. Length = 340 Score = 27.9 bits (63), Expect = 6.4 Identities = 28/142 (19%), Positives = 44/142 (30%), Gaps = 47/142 (33%) Query: 374 KNIRTITSGRIIVVFGCGG--------------------DRDQGKRPIMGKIALDL-ADI 412 K + + G +VV G GG DR + K+A L AD Sbjct: 160 KALPYLDPGSTVVVIGVGGLGHIAVQILRALTPATVIAVDRSEEAL----KLAERLGADH 215 Query: 413 AIVTDDNPRSEDPEKIRAEIIHGIPGFIEKGNRI--------EAIRTAIEMLNKQDVLVV 464 + D+ E +R E+ G +G E + A ++L K V+ Sbjct: 216 VLNASDDVVEE----VR-ELTGG------RGADAVIDFVGSDETLALAAKLLAKGGRYVI 264 Query: 465 ---AGKGHETVHIVTNGEKKMS 483 G G + E + Sbjct: 265 VGYGGHGRLPTSDLVPTEISVI 286 >gnl|CDD|32226 COG2043, COG2043, Uncharacterized protein conserved in archaea [Function unknown]. Length = 237 Score = 27.9 bits (62), Expect = 7.1 Identities = 19/81 (23%), Positives = 25/81 (30%), Gaps = 14/81 (17%) Query: 330 ALVLEHLEKLHVVPGRFEFVG------------TNSRGGRIYVDYAHTSNSLEMILKNIR 377 ALV LEK P + GGRI D+A + + Sbjct: 123 ALVYAPLEKAEFEPDVVVIICKPAQAMRLIQAYLYFMGGRINGDFAGIQSLCADAV--AL 180 Query: 378 TITSGRIIVVFGCGGDRDQGK 398 +G I + GC G R Sbjct: 181 PYLTGEINITLGCSGSRKYAG 201 >gnl|CDD|29513 cd01192, INT_P22_C, P22-like integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial and phage integrases, including those similar to phage P22-like integrases, DLP12 and APSE-1.. Length = 177 Score = 27.6 bits (61), Expect = 7.6 Identities = 11/46 (23%), Positives = 20/46 (43%) Query: 102 LSLFASRLYGKHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQI 147 L + + G H + A G + + +Q QR+G+S F+ Sbjct: 77 LQVLKRQKAGAHKPWVFAGAGGDPRIDSKTAWRQALQRAGISDFRW 122 >gnl|CDD|107389 cd06394, PBP1_iGluR_Kainate_KA1_2, N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMPA receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined. Length = 333 Score = 27.5 bits (61), Expect = 7.7 Identities = 12/39 (30%), Positives = 21/39 (53%) Query: 114 PENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTST 152 P+ +++V G S + +S V IC + F++GP T Sbjct: 63 PKGVVSVLGPSSSPASSSIVSHICGEKEIPHFKVGPEET 101 >gnl|CDD|35838 KOG0618, KOG0618, KOG0618, Serine/threonine phosphatase 2C containing leucine-rich repeats, similar to SCN circadian oscillatory protein (SCOP) [Signal transduction mechanisms]. Length = 1081 Score = 27.7 bits (61), Expect = 7.7 Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 1/52 (1%) Query: 128 SVASFVQQI-CQRSGLSSFQIGPTSTISSFAQDNRLTTPSPIYLAKALSYLS 178 S + ++ + C+R+ LS +I S + +A N LTT + L YL Sbjct: 196 SNLANLEVLHCERNQLSELEISGPSLTALYADHNPLTTLDVHPVPLNLQYLD 247 >gnl|CDD|145988 pfam03136, Pup_ligase, Pup-ligase protein. Pupylation is a novel protein modification system found in some bacteria. This family of proteins are the enzyme that can conjugate proteins of the Pup family to lysine residues in target proteins marking them for degradation. The archetypal protein in this family is PafA (proteasome accessory factor) from Mycobacterium tuberculosis. It has been suggested that these proteins are related to gamma-glutamyl-cysteine synthetases. Length = 444 Score = 27.6 bits (62), Expect = 8.3 Identities = 7/10 (70%), Positives = 9/10 (90%) Query: 355 GGRIYVDYAH 364 G R+YVD+AH Sbjct: 75 GARLYVDHAH 84 >gnl|CDD|38868 KOG3664, KOG3664, KOG3664, Predicted patched transmembrane receptor [Signal transduction mechanisms]. Length = 999 Score = 27.7 bits (61), Expect = 8.5 Identities = 17/71 (23%), Positives = 25/71 (35%), Gaps = 6/71 (8%) Query: 291 VTISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVL------EHLEKLHVVPG 344 + +S+ F + L +F Y LVA + I IG D + +L LH Sbjct: 359 ICLSLGVALFFYAVVLGIDFFPYLNLVAVVVIIGIGADDVFLFLKIYERSNLRMLHTQSQ 418 Query: 345 RFEFVGTNSRG 355 F S Sbjct: 419 SASFFLELSDH 429 >gnl|CDD|176239 cd08278, benzyl_alcohol_DH, Benzyl alcohol dehydrogenase. Benzyl alcohol dehydrogenase is similar to liver alcohol dehydrogenase, but has some amino acid substitutions near the active site, which may determine the enzyme's specificity of oxidizing aromatic substrates. Also known as aryl-alcohol dehydrogenases, they catalyze the conversion of an aromatic alcohol + NAD+ to an aromatic aldehyde + NADH + H+. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. Length = 365 Score = 27.5 bits (62), Expect = 9.9 Identities = 25/108 (23%), Positives = 36/108 (33%), Gaps = 28/108 (25%) Query: 380 TSGRIIVVFGCGG--------DRDQGKRPIMGKIALDL------------ADIAIVTDDN 419 G I VFG G + G I IA+D+ A I N Sbjct: 185 RPGSSIAVFGAGAVGLAAVMAAKIAGCTTI---IAVDIVDSRLELAKELGATHVI----N 237 Query: 420 PRSEDP-EKIRAEIIHGIPGFIEKGNRIEAIRTAIEMLNKQDVLVVAG 466 P+ ED IR G+ ++ I A++ L + L + G Sbjct: 238 PKEEDLVAAIREITGGGVDYALDTTGVPAVIEQAVDALAPRGTLALVG 285 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 0.321 0.137 0.394 Gapped Lambda K H 0.267 0.0739 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,870,572 Number of extensions: 315438 Number of successful extensions: 1057 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1037 Number of HSP's successfully gapped: 46 Length of query: 497 Length of database: 6,263,737 Length adjustment: 98 Effective length of query: 399 Effective length of database: 4,146,055 Effective search space: 1654275945 Effective search space used: 1654275945 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: 59 (26.5 bits)