RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780140|ref|YP_003064553.1| putative ABC transporter, substrate-binding protein [Candidatus Liberibacter asiaticus str. psy62] (452 letters) >gnl|CDD|31652 COG1463, Ttg2C, ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]. Length = 359 Score = 87.5 bits (216), Expect = 8e-18 Identities = 57/301 (18%), Positives = 101/301 (33%), Gaps = 21/301 (6%) Query: 1 MESKNYYTSVGLFVVSILFFSFFSIYWLSRSNQYDGPMAEVIIRIPG-SVDGLSTDSSVR 59 ME++ VGLF++ L + WL+ G + GL S VR Sbjct: 1 METRANRVLVGLFLLLGLLAVLLFVLWLATLPGLPGGTGTYTVTAYFDDAGGLYVGSPVR 60 Query: 60 FNGIPVGRIVGLFLDQEYPNHSLAKALIRPDTPLYPSTTATIRTQGLAGITYIELSTLRK 119 + G+ VG++ + LD + PN + I D P+ +TA+IRT GL G YIEL+ Sbjct: 61 YRGVKVGKVASISLDPK-PNGARVTLEIDSDYPIPADSTASIRTTGLLGEKYIELTPGDA 119 Query: 120 EKKTI---FQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENIEKPL 176 + I ER Q + G + + +++ + L Sbjct: 120 GGPKLRLGATIPLERTQVPIDLEDLLGDLLLLLGGLDP-DRLNAILNEAAAALAGTGPQL 178 Query: 177 TTTIANIETISTVLANNISHIDKMMH-----TTQVTPHSSDSKNTFNTITDLITSLDKMI 231 + N+ + L I ++ + S + + L +L Sbjct: 179 NALLDNLAQFTDALNARDGDIGALIANLNQLLDSLAAASDQLDRLLDNLATLTAALAARR 238 Query: 232 KAID---------LQKVNQILENIQVSSNNFVKSSDQVINTVHDVR-ETTQTFQEVGQKI 281 A+D VN +L + + N + + + + D Q + Sbjct: 239 DALDDALAALSALAATVNDLLAENRPNLNQALANLRPLATLLVDYLPGLEQLLHGLPTYA 298 Query: 282 D 282 Sbjct: 299 A 299 >gnl|CDD|111376 pfam02470, MCE, mce related protein. This family of proteins contains the mce (mammalian cell entry) proteins from Mycobacterium tuberculosis. The archetype (Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage. This family contains proteins of unknown function from other bacteria. Length = 80 Score = 57.2 bits (139), Expect = 8e-09 Identities = 23/69 (33%), Positives = 32/69 (46%), Gaps = 2/69 (2%) Query: 48 SVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPD-TPLYPSTTATIRTQGL 106 GL + VR+ G+PVGR+ + LD + I PD + + A IR+ GL Sbjct: 11 DAGGLEVGAPVRYRGVPVGRVTSIDLDPD-GGGVRVTLRIDPDVVVIPKDSRAGIRSLGL 69 Query: 107 AGITYIELS 115 G YI L Sbjct: 70 LGEKYIALD 78 >gnl|CDD|36151 KOG0933, KOG0933, KOG0933, Structural maintenance of chromosome protein 2 (chromosome condensation complex Condensin, subunit E) [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning]. Length = 1174 Score = 34.5 bits (79), Expect = 0.056 Identities = 37/252 (14%), Positives = 91/252 (36%), Gaps = 23/252 (9%) Query: 151 AENTSKKISDSSRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTPHS 210 EN +++ ++K I ++++ L I ++ + L N + +DK+ Sbjct: 813 RENEYERLQLEHEELEKEISSLKQQLEQLEKQISSLKSELGNLEAKVDKVEKDV------ 866 Query: 211 SDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRET 270 + + ID + ++ +L + + + + H+V + Sbjct: 867 -------KKAQAELKDQKAKQRDIDTE-ISGLLTSQEKCLSEKSDGELERKKLEHEVTKL 918 Query: 271 TQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIAD-STSNMRSSISAIREITDQRQKII 329 ++++ LL K D + + + ++++ ++++K+ Sbjct: 919 ESEKANARKEVEKLLKKHEWIGDEKRLFGKKGTDYDFESYDPHEAREELKKLQEKKEKLE 978 Query: 330 STINTIENITSNLNDSSQKFAELMSKINNI----SALKENNSLFKDAQRAMHTFRDTSEK 385 T+N L + +K A L +K I S +K+ + +R EK Sbjct: 979 KTVNP--KNMDMLERAEEKEAALKTKKEIIEKDKSKIKKTIEKLDEKKR--EELNKAWEK 1034 Query: 386 INRYIPSIGNNL 397 +N+ SI + L Sbjct: 1035 VNKDFGSIFSTL 1046 >gnl|CDD|37815 KOG2604, KOG2604, KOG2604, Subunit of cis-Golgi transport vesicle tethering complex - Sec34p [Intracellular trafficking, secretion, and vesicular transport]. Length = 733 Score = 33.8 bits (77), Expect = 0.091 Identities = 25/118 (21%), Positives = 46/118 (38%), Gaps = 10/118 (8%) Query: 269 ETTQTFQEVGQKIDHLLSDFSSKMK-SKETSAFLENIADSTSNMRSSISAIREITDQRQK 327 E + +D LLS S++TSA E + + S + E+ + +K Sbjct: 106 ECDAILDQTNNALDTLLSLQKKFEFVSQKTSALHE----ACEQLLEEQSKLSELAEGIRK 161 Query: 328 IISTINTIENITSNLND-----SSQKFAELMSKINNISALKENNSLFKDAQRAMHTFR 380 + +E + LN F E+++K++ E N FKDA + ++ Sbjct: 162 KLHYFAELEELNRRLNHPTLSVGKVSFKEMLAKLDECIMFLEENPDFKDAPAYLGKYK 219 >gnl|CDD|177098 CHL00207, rpoB, RNA polymerase beta subunit; Provisional. Length = 1077 Score = 33.5 bits (77), Expect = 0.12 Identities = 52/326 (15%), Positives = 110/326 (33%), Gaps = 57/326 (17%) Query: 111 YIELSTLRKEKKTIFQIATERNQRAMITATPSGINYFIS---NAENTSKKISDSSRHIQK 167 +EL K K + +++A NY I + + K + + I Sbjct: 42 NLELLLFGKNYKLKYPKYN------LLSAKSYDSNYSIQIYLPLKFINLKTNKI-KFINY 94 Query: 168 IIENIEKPLTTTIANI-------ETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTI 220 +I N+ P T +S ++ + + K + KN+ Sbjct: 95 LIGNL--PKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIK-----------KNSNKIY 141 Query: 221 TDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQK 280 + + +L K +I I++ N + ++ T Q++ + Sbjct: 142 SATLIPNRGSWIKFELDKNKEIW--IRIDKNR-------KKPLIIFLKALGLTDQDIYSR 192 Query: 281 IDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREIT--DQRQKIISTINTIEN- 337 + S+F K+K ++ + + ++S I T D Q + S +N Sbjct: 193 LTK--SEFLKKLKPILLNSNSYTNEEILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNY 250 Query: 338 ---------ITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINR 388 I + LN + + ++ + +S + + + F D NR Sbjct: 251 DLGKVGRYKINNKLNLNIPERVRNLTYEDILSII----DKLINLKINKGNFDDIDHLKNR 306 Query: 389 YIPSIGNNLQNFSQSGLNDIQNLVRK 414 + S+G LQN + GL ++ ++R Sbjct: 307 RVRSVGELLQNQFRIGLKRLERILRN 332 >gnl|CDD|112929 pfam04136, Sec34, Sec34-like family. Sec34 and Sec35 form a sub-complex, in a seven protein complex that includes Dor1 (pfam04124). This complex is thought to be important for tether vesicles to the Golgi. Length = 157 Score = 32.9 bits (75), Expect = 0.19 Identities = 25/124 (20%), Positives = 44/124 (35%), Gaps = 24/124 (19%) Query: 266 DVRETTQTFQEVGQKIDHLLSDFSSKMK------------SKETSAFLENIADSTSNMRS 313 QTF D +L ++ SK+TS E + + + Sbjct: 4 KKINYLQTFT---NICDQILGQTNNAESTLLSLKEKYEFVSKKTSELSE----ACEQLST 56 Query: 314 SISAIREITDQRQKIISTINTIENITSNLND-----SSQKFAELMSKINNISALKENNSL 368 + E+ D QK ++ +E + L +S F E ++K++ E N Sbjct: 57 EQMRLSELADGIQKGLTYFAPLEELNRVLRSPTLSVASVSFKEHLTKLDTCIMYIEENPD 116 Query: 369 FKDA 372 FKD+ Sbjct: 117 FKDS 120 >gnl|CDD|39589 KOG4388, KOG4388, KOG4388, Hormone-sensitive lipase HSL [Lipid transport and metabolism]. Length = 880 Score = 31.6 bits (71), Expect = 0.50 Identities = 29/140 (20%), Positives = 53/140 (37%), Gaps = 13/140 (9%) Query: 90 DTPL--YPSTTATIRTQGLAGITYIELSTLRKE-----KKTIFQIATERNQRA--MITAT 140 D P+ PS A + QG G I+ TLR +T + E + A + +T Sbjct: 635 DIPMRRSPSEAALAQPQGPLGTDSIKNLTLRDLSLTGNSETSSETHPEMSLSAETLSPST 694 Query: 141 PSGINYFISNAENTSKKISDSSRHIQKIIENIEKPLT--TTIANIETISTVLANNISHID 198 PS +N+ + A +T + D+ + + P+ + + ++ Sbjct: 695 PSDVNFLLPTAPSTPLQQEDAGEE-AEAKNELSPPMDRGLGVRAAFPEGFHARRSSQNLQ 753 Query: 199 KMMHTTQVTPHSSD-SKNTF 217 T + +SSD K+ F Sbjct: 754 DWFGRTPMELYSSDVPKDPF 773 >gnl|CDD|146867 pfam04437, RINT1_TIP1, RINT-1 / TIP-1 family. This family includes RINT-1, a Rad50 interacting protein which participates in radiation induced checkpoint control, as well as the TIP-1 protein from yeast that seems to be involved in a complex with Sec20p that is required for golgi transport. Length = 485 Score = 31.2 bits (71), Expect = 0.65 Identities = 6/46 (13%), Positives = 20/46 (43%), Gaps = 1/46 (2%) Query: 203 TTQVTPHSSDSKNTFNTITDLITSLDKMIKAIDLQKV-NQILENIQ 247 + SS+ + I+ L++++ +++ Q+L ++ Sbjct: 338 ALESLSPSSELVEALRYLRRRISFLERLLNPAIFRRIWRQLLLSLD 383 Score = 30.0 bits (68), Expect = 1.5 Identities = 23/173 (13%), Positives = 53/173 (30%), Gaps = 45/173 (26%) Query: 284 LLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKIISTINTIENITSNLN 343 L D +++ S + F E +I+++ + + I + Sbjct: 275 SLGDIANRTSSNYGALFDE-----------TINSLERLRLDSEGSIVH-----RLVKGFK 318 Query: 344 DSSQKFAELMSKIN-----NISALKENNSLFKDAQRAMHTFRDTSEKINRYIP------- 391 + + + KI+ + ++ E+ S + A+ R + R + Sbjct: 319 AALRNY----FKISTWSSLSSTSALESLSPSSELVEALRYLRRRISFLERLLNPAIFRRI 374 Query: 392 --SIGNNLQN-----------FSQSGLNDIQNLVRKLQETVNHFDDCLNNFER 431 + +L FS+ G +R L E + + NF + Sbjct: 375 WRQLLLSLDTYIISSILMLNKFSEGGAAQFHFDMRNLFEVFSLYCMRPENFFK 427 >gnl|CDD|143806 pfam00015, MCPsignal, Methyl-accepting chemotaxis protein (MCP) signaling domain. This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs. Length = 213 Score = 30.9 bits (70), Expect = 0.73 Identities = 22/165 (13%), Positives = 50/165 (30%), Gaps = 48/165 (29%) Query: 160 DSSRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNT 219 +++ I+ +IE I K + A+I+ T + + ++ + Sbjct: 93 QAAKEIEALIEEIVKQTNDSTASIQQTRTEVEVGSTIVE-------------STGEALKE 139 Query: 220 ITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQ 279 I D + + ++ + I +S+ DQV V + + TQ Sbjct: 140 IVDAVAEIADIV------------QEIAAASDEQSAGIDQVNQAVARIDQVTQ------- 180 Query: 280 KIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQ 324 + +A +E A + + + Q Sbjct: 181 ----------------QNAALVEESAAAAETLEEQAEELTASVAQ 209 >gnl|CDD|34155 COG4477, EzrA, Negative regulator of septation ring formation [Cell division and chromosome partitioning]. Length = 570 Score = 30.6 bits (69), Expect = 0.88 Identities = 30/216 (13%), Positives = 80/216 (37%), Gaps = 16/216 (7%) Query: 214 KNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQT 273 + + + + +++ ++L + + L IQ + ++ + + V E Sbjct: 254 DSRLERLKEQLVENSELLTQLELDEAEEELGLIQEKIESLYDLLEREVEAKNVVEENLPI 313 Query: 274 FQEVGQKI----DHLLSDFSSKMKS----KETSAFLENIADSTSNMRSSISAIREITDQR 325 + +K +HL + +S + + + S + I E + + Sbjct: 314 LPDYLEKAKENNEHLKEEIERVKESYRLAETELGSVRKFEKELKELESVLDEILENIEAQ 373 Query: 326 QKIIS----TINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRD 381 + S + IE +++ D +K E ++ + N + + +H + Sbjct: 374 EVAYSELQDNLEEIEKALTDIEDEQEKVQEHLTSLRKDELEAREN--LERLKSKLHEIKR 431 Query: 382 TSEKINRYIPSIGNNLQNFSQSGLNDIQNLVRKLQE 417 EK N +P + + + ++IQ+L+++L E Sbjct: 432 YMEKSN--LPGLPETFLSLFFTAGHEIQDLMKELSE 465 >gnl|CDD|58155 cd03680, MM_CoA_mutase_ICM_like, Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, isobutyryl-CoA mutase (ICM)-like subfamily; contains archaeal and bacterial proteins similar to the large subunit of Streptomyces cinnamonensis coenzyme B12-dependent ICM. ICM from S. cinnamonensis is comprised of a large and a small subunit. The holoenzyme appears to be an alpha2beta2 heterotetramer with up to 2 molecules of coenzyme B12 bound. The small subunit binds coenzyme B12. ICM catalyzes the reversible rearrangement of n-butyryl-CoA to isobutyryl-CoA, intermediates in fatty acid and valine catabolism, which in S. cinnamonensis can be converted to methylmalonyl-CoA and used in polyketide synthesis.. Length = 538 Score = 29.8 bits (67), Expect = 1.4 Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 11/101 (10%) Query: 106 LAGITYIELSTLRKEKKTIFQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHI 165 L G Y+E T E++ I MI A G YF ++I+D++ Sbjct: 391 LGGSYYVEALTDEIEEEAWKYIDKIDAMGGMIKAIEDG--YF-------QREIADAAYKY 441 Query: 166 QKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQV 206 QK IE+ E+ + N + + +D + Q+ Sbjct: 442 QKEIESGERIVVG--VNKFVVEEEPPIILLKVDDEVEERQI 480 >gnl|CDD|147584 pfam05478, Prominin, Prominin. The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration. Length = 809 Score = 28.8 bits (65), Expect = 2.8 Identities = 24/95 (25%), Positives = 44/95 (46%), Gaps = 6/95 (6%) Query: 166 QKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTT-QVTPHSSDSKNTFNTITDLI 224 +I+EN+E+ + ++I I K+ + T V P D K +++ I Sbjct: 320 TEILENLEEVVKADFSSIVQEGNSTFEEIP--SKVKNQTSSVVP---DVKAALDSLGTDI 374 Query: 225 TSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQ 259 S+ + + L ++QIL N Q SSN ++ +Q Sbjct: 375 KSVAEDLPLQVLSVLSQILNNTQSSSNPYLPYVEQ 409 Score = 28.1 bits (63), Expect = 5.7 Identities = 21/133 (15%), Positives = 45/133 (33%), Gaps = 39/133 (29%) Query: 326 QKIISTINTIENITSNLNDSSQ--KFAELMSKINNISALKENNSLFKDAQRAMHTFRDTS 383 ++ ++T N+ + S + ++ ++N L+ Q ++ D + Sbjct: 502 NELFQVLDTPGNLNPGYLNLSGTLELKINLTISEVYRDCEQNEPLYTVLQ--LNNSYDLN 559 Query: 384 EK--INRYIPSIGN---------------------NLQNFSQSGLNDIQNLVRKLQETVN 420 E I +Y P I NL++ + SGL+DI Sbjct: 560 ELLDIKQYTPEIDQELESLKVNLSTITLLTPEARRNLEDLASSGLDDI------------ 607 Query: 421 HFDDCLNNFERNP 433 +F + L ++ Sbjct: 608 NFSNFLKQIQKPL 620 >gnl|CDD|34381 COG4768, COG4768, Uncharacterized protein containing a divergent version of the methyl-accepting chemotaxis-like domain [General function prediction only]. Length = 139 Score = 28.8 bits (64), Expect = 3.1 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 4/70 (5%) Query: 236 LQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSK 295 L K N + E++Q V + D V + V D+ ++ + + + ++ K + K Sbjct: 58 LHKTNTLAEDVQGK----VATLDPVFDAVKDLGQSVSDLNQSVRHLATRATNAVEKNEKK 113 Query: 296 ETSAFLENIA 305 A + N+A Sbjct: 114 IAQAVVSNVA 123 >gnl|CDD|34711 COG5108, RPO41, Mitochondrial DNA-directed RNA polymerase [Transcription]. Length = 1117 Score = 28.9 bits (64), Expect = 3.4 Identities = 13/78 (16%), Positives = 35/78 (44%), Gaps = 3/78 (3%) Query: 343 NDSSQKFAELMSKINNISALKE---NNSLFKDAQRAMHTFRDTSEKINRYIPSIGNNLQN 399 + + F +S + ++L E N F +++ + +F D ++ +P I ++ Sbjct: 15 SKIGKDFIIDLSYKSGTASLFEACVYNGDFLRSKQLLKSFIDHNKGDKILLPMINLYIRE 74 Query: 400 FSQSGLNDIQNLVRKLQE 417 Q G ++ +++ +E Sbjct: 75 IIQRGSFELTDVLSNAKE 92 >gnl|CDD|113356 pfam04582, Reo_sigmaC, Reovirus sigma C capsid protein. Length = 326 Score = 28.7 bits (64), Expect = 3.7 Identities = 27/124 (21%), Positives = 57/124 (45%), Gaps = 5/124 (4%) Query: 301 LENIADSTSNMRSSISAI-REITDQRQKIISTINTIENITSNLNDSSQKFAELMSKINNI 359 L N+ +T+++ S+S I ++D + ++++ + LN L + ++++ Sbjct: 37 LTNLESATASLSESVSTISSRLSDLSADLQDMTTSLDDAKATLNGLITTVQALQTSVDSL 96 Query: 360 SALKENNSLFKDAQRAMHTFRDTSEKINRYIPSIGNNLQNFSQSGLN--DIQNLVRKLQE 417 S+ + SL A A + T+ N I N + S +GLN D++ V+ L+ Sbjct: 97 SSELADLSLTVSAHDAAISDLQTTVHANS--TDISNLKSSVSANGLNITDLEQRVKSLES 154 Query: 418 TVNH 421 +H Sbjct: 155 GSSH 158 >gnl|CDD|35552 KOG0331, KOG0331, KOG0331, ATP-dependent RNA helicase [RNA processing and modification]. Length = 519 Score = 28.4 bits (63), Expect = 3.8 Identities = 24/122 (19%), Positives = 44/122 (36%), Gaps = 20/122 (16%) Query: 165 IQKIIENIEKPLTTTIANIETIST---VLANNISHIDKMMHTTQVTPHSSDSKNTFNTIT 221 I+KI+ I +P T+ T LA + + Q+ + + I Sbjct: 260 IRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNP-----IQINVGNKKELKANHNIR 314 Query: 222 DLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVI---NTVHDVRETTQTFQEVG 278 ++ D+ K L+K+ ++LE+I S +VI T E + + G Sbjct: 315 QIVEVCDETAK---LRKLGKLLEDISSDSEG------KVIIFCETKRTCDELARNLRRKG 365 Query: 279 QK 280 Sbjct: 366 WP 367 >gnl|CDD|38731 KOG3522, KOG3522, KOG3522, Predicted guanine nucleotide exchange factor [Signal transduction mechanisms]. Length = 925 Score = 28.4 bits (63), Expect = 3.9 Identities = 41/227 (18%), Positives = 70/227 (30%), Gaps = 44/227 (19%) Query: 236 LQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDH-----------L 284 LQ +LE + N + +D++ E +E+ + + L Sbjct: 150 LQLALTLLETLAEKINEHKRFADEI-------NELQAALREIEVRSELMEDLGAGRRQLL 202 Query: 285 LSDFSSKMK----SKETSAFLENI-ADSTSNMRSSISAIREIT----------------- 322 L D S+ K+ AFL +T R+S S+ + T Sbjct: 203 LQDLVSETVYTGRKKDRKAFLFRDLIVNTDLKRASGSSRKPSTAASVVDTAKYKLLWKDP 262 Query: 323 -DQRQKIISTINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMH--TF 379 + S IE I + + A L K + L +D QR +H Sbjct: 263 LVFADVVKSRAGNIEEIPILIAHLVEDCAHLRQKTKENKVYVGPHQLLQDLQRLLHALDV 322 Query: 380 RDTSEK-INRYIPSIGNNLQNFSQSGLNDIQNLVRKLQETVNHFDDC 425 R SE+ R + N + N +Q L+ + + Sbjct: 323 RRLSERQARRLSLNYQNLNLELAADWPNGLQRLIFVFEAEIGSTPLE 369 >gnl|CDD|36214 KOG0996, KOG0996, KOG0996, Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning]. Length = 1293 Score = 28.4 bits (63), Expect = 4.5 Identities = 32/260 (12%), Positives = 88/260 (33%), Gaps = 27/260 (10%) Query: 113 ELSTLRKEKKTIFQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENI 172 + L+ + I + Q+ + ++ ++ + I S R+I K + + Sbjct: 886 RIKELQNKIDEIGGEKVQA-QKDKVEKINEQLDKLEADIAKLTVAIKTSDRNIAKAQKKL 944 Query: 173 EKPLTTTIANIETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTITDLITSLDKMIK 232 + L I + E L + +++ + K ++ ++ L + Sbjct: 945 SE-LEREIEDTEKELDDLTEELKGLEEKA-----AELEKEYKEAEESLKEIKKELRDLKS 998 Query: 233 AI-DLQKVNQILENIQVSSNNFVKSSDQVINTV----------------HDVRETTQTFQ 275 + +++K L+ ++ N +++ + +N + ++ ET + Sbjct: 999 ELENIKKSENELKAERIDIENKLEAINGELNEIESKIKQPEKELKKLSLCNMTETRPQIE 1058 Query: 276 EVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKIISTINTI 335 + L + E A LE + + + I E + + + + + Sbjct: 1059 L-DVESPEELEAEMLEDNINEKIALLEKRVEELREV--DLGVIAEYAKKVELYLKRVAEL 1115 Query: 336 ENITSNLNDSSQKFAELMSK 355 E T ++ +K EL + Sbjct: 1116 EKFTQKRDEHREKLEELRKR 1135 >gnl|CDD|38897 KOG3693, KOG3693, KOG3693, Uncharacterized conserved protein [Function unknown]. Length = 1117 Score = 28.2 bits (62), Expect = 5.0 Identities = 18/54 (33%), Positives = 23/54 (42%) Query: 47 GSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDTPLYPSTTAT 100 GS+DGLS +S + VGR + L + P SLA I P P Sbjct: 114 GSMDGLSMNSFSMPFSVSVGRQMSLTPPLDVPATSLAIHKIPSSAPTLPFKFMK 167 >gnl|CDD|39873 KOG4674, KOG4674, KOG4674, Uncharacterized conserved coiled-coil protein [Function unknown]. Length = 1822 Score = 28.0 bits (62), Expect = 5.7 Identities = 41/277 (14%), Positives = 101/277 (36%), Gaps = 19/277 (6%) Query: 153 NTSKKISD----SSRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTP 208 +T KK+++ + + +++ + +E S N + ++ + Sbjct: 280 STQKKLNELWKSKLEELSHEVAELQRAIEELEKLLEDASERNKENTDQLKELEQS----- 334 Query: 209 HSSDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVR 268 S ++ ++ L L+ ++ + ++ +++ ++ + Sbjct: 335 LSKLNEKLEKKVSRLEGELEDANDSLSATGESSMVSEKAALASSLIRPGSSLTKLYSKYS 394 Query: 269 ETTQTFQEVGQKIDHLLSDFSSKMK-SKETSAFLENIADSTSNMRSSISAI-REITDQRQ 326 + Q + + +++ L + SS + K+ + L+ M+ + + + E+ Q Sbjct: 395 KLQQQLESLKLELERLQNILSSFKEEVKQKAPILKEQRSELERMQETKAELSEELDFSNQ 454 Query: 327 KIISTINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKI 386 KI +E++ LND ++ L +I+++S L D R +S+ Sbjct: 455 KIQKLEKELESLKKQLNDLERENKLLEQQISDLSRQVNVLLLELDELRKGSKITVSSDST 514 Query: 387 NRYIPS---IGNNLQNFSQSGLNDIQNLVRKLQETVN 420 S I L FS +I L K E +N Sbjct: 515 ENESDSEEIISERLVEFS-----NINELQEKNVELLN 546 >gnl|CDD|37906 KOG2695, KOG2695, KOG2695, WD40 repeat protein [General function prediction only]. Length = 425 Score = 27.7 bits (61), Expect = 5.9 Identities = 15/92 (16%), Positives = 24/92 (26%), Gaps = 7/92 (7%) Query: 330 STINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRD-------T 382 S I T E + + K N + + + ++ RD Sbjct: 31 SNIYTKERLKPGKRFENISQKRTKGKGLNPVFNRSTYLFDRQFSQYPYSCRDDRDYCAKN 90 Query: 383 SEKINRYIPSIGNNLQNFSQSGLNDIQNLVRK 414 + IN +G LQ L K Sbjct: 91 LKVINLRQLPVGTELQKIGWLREVTTIILTSK 122 >gnl|CDD|111435 pfam02534, TraG, TraG/TraD family. These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems. Length = 468 Score = 27.8 bits (62), Expect = 6.6 Identities = 30/130 (23%), Positives = 47/130 (36%), Gaps = 24/130 (18%) Query: 32 NQYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDT 91 P+ V V L +G P V LD E+P+ L K Sbjct: 272 LTVVSPLLRVFF---QMVVELLYLKLPNGDGRPKE--VLFLLD-EFPS--LGK------L 317 Query: 92 PLYPSTTATIRTQGLAGITYI--ELSTLRKEKKTIFQIATERNQRAMITATPSGINYFIS 149 + ATIR G+ +T I +S L+ + +++++ I + S Sbjct: 318 EILEEALATIRGYGI-RLTTICQSISQLK-------ETYGGEGAKSILSNHAVVICFAAS 369 Query: 150 NAENTSKKIS 159 N E T+K IS Sbjct: 370 NDEETAKYIS 379 >gnl|CDD|29736 cd01017, AdcA, Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).. Length = 282 Score = 27.5 bits (61), Expect = 7.2 Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 2/36 (5%) Query: 329 ISTINTIENITSNLNDSSQKFAELMSKINNISALKE 364 + +N +E +T D + + LM + N+ LK Sbjct: 246 LLVLNPLETLTKEEIDDGKDYFSLMKE--NLETLKR 279 >gnl|CDD|153311 cd07627, BAR_Vps5p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps5p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Vsp5p is the yeast counterpart of human SNX1 and is part of the retromer complex, which functions in the endosome-to-Golgi retrieval of vacuolar protein sorting receptor Vps10p, the Golgi-resident membrane protein A-ALP, and endopeptidase Kex2. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. Length = 216 Score = 27.7 bits (62), Expect = 7.3 Identities = 37/210 (17%), Positives = 74/210 (35%), Gaps = 45/210 (21%) Query: 219 TITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQ--E 276 + L + L ++ K+++L ++ + + ET + E Sbjct: 12 YLDSLESQLKQLYKSLEL----------------VSSQRKELASATEEFAETLEALSSLE 55 Query: 277 VGQKIDHLLSDFSS-KMKSKETSAFLENIADSTSNMRS--------SISAIREITDQRQK 327 + + + LL+ + + + KE+ LE A SI ++R QRQK Sbjct: 56 LSKSLSDLLAALAEVQKRIKES---LERQALQDVLTLGVTLDEYIRSIGSVRAAFAQRQK 112 Query: 328 IISTINTIENITSNLNDSSQKFAELMSKINNISA-LKENNSLFKDAQRAMHT----FRDT 382 + + E+ L+ + +L + L S ++A+R F + Sbjct: 113 LWQYWQSAES---ELSKKKAQLEKLKRQGKTQQEKLNSLLSELEEAERRASELKKEFEEV 169 Query: 383 SEKINRYIPSIGNNLQNFSQSGLNDIQNLV 412 SE I L+ F + + D +N V Sbjct: 170 SELIKS-------ELERFERERVEDFRNSV 192 >gnl|CDD|37518 KOG2307, KOG2307, KOG2307, Low density lipoprotein receptor [Intracellular trafficking, secretion, and vesicular transport]. Length = 705 Score = 27.6 bits (61), Expect = 7.8 Identities = 26/146 (17%), Positives = 49/146 (33%), Gaps = 10/146 (6%) Query: 272 QTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKIIST 331 ++ Q ++ L + S S + S + + RE + +I Sbjct: 89 DALNKIEQPLNQLREEIKSTRGSVGEAERALR------QQCSELCSNREKKIELLDLIYV 142 Query: 332 INTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYIP 391 + IE ++ L K + + AL+ N F + F + E+I Sbjct: 143 LVAIEKLSKMLLSPPSKEQQDGATSLERIALELNQLKFHASHLKGSLFPHSEERIAAEKI 202 Query: 392 SIGNNLQNFSQSGLN----DIQNLVR 413 + +L GL D+QN +R Sbjct: 203 ILSQSLAVLFAEGLQSAAGDLQNCLR 228 >gnl|CDD|29484 cd00386, Heme_Cu_Oxidase_III_like, Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The heme-copper oxidase superfamily is diverse in terms of electron donors, subunit composition, and heme types. This superfamily includes cytochrome c and ubiquinol oxidases. Bacterial oxidases typically contain 3 or 4 subunits in contrast to the 13 subunit bovine cytochrome c oxidase (CcO). Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunits I, II and III of ubiquinol oxidase are homologous to the corresponding subunits in CcO. This group additionally contains proteins which are fusions between subunits I and III, such as Sulfolobus acidocaldarius SoxM, a subunit of the SoxM terminal oxidase complex. It also includes NorE which has been speculated to be a subunit of nitric oxide reductase. Some archaebacterial cytochrome oxidases lack subunit III. Although not required for catalytic activity, subunit III is believed to play a role in assembly of the multimer complex. Rhodobacter CcO subunit III stabilizes the integrity of the binuclear center in subunit I. It has been proposed that archaea acquired heme-copper oxidases through gene transfer from gram-positive bacteria.. Length = 183 Score = 27.5 bits (61), Expect = 8.0 Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 2/43 (4%) Query: 1 MESKNYYTSVGLFVVS--ILFFSFFSIYWLSRSNQYDGPMAEV 41 + LF++S +LF SFF Y+ SR + A + Sbjct: 4 SVRSGGRLGMWLFILSEVMLFGSFFWAYFHSRLSPPVEFGAGL 46 >gnl|CDD|32784 COG2964, COG2964, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 220 Score = 27.5 bits (61), Expect = 8.1 Identities = 23/149 (15%), Positives = 45/149 (30%), Gaps = 24/149 (16%) Query: 278 GQKIDHLLSDFSSKM------KSKETSAFLENIADSTSNMRSSISAIREITDQRQKIIST 331 G+++ ++D + + K A ++SS IR ++ +II Sbjct: 53 GRQVGSPITDLALDLLHNKEGSEKSVIGNYFTRAKDGRLIKSSSIFIR---NKEGRIIGM 109 Query: 332 INTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYI- 390 + I S L S M + N F + E + + Sbjct: 110 L-CINMDLSLLVPVSAFLQTFMPTDETPKRVSSVN------------FASSVEDLVAQLL 156 Query: 391 -PSIGNNLQNFSQSGLNDIQNLVRKLQET 418 +I + S + +V+ L E Sbjct: 157 EWTIQEVNADRLLSNNAKNREIVKALYEK 185 >gnl|CDD|153293 cd07609, BAR_SIP3_fungi, The Bin/Amphiphysin/Rvs (BAR) domain of fungal Snf1p-interacting protein 3. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This group is composed of mostly uncharacterized fungal proteins with similarity to Saccharomyces cerevisiae Snf1p-interacting protein 3 (SIP3). These proteins contain an N-terminal BAR domain followed by a Pleckstrin Homology (PH) domain. SIP3 interacts with SNF1 protein kinase and activates transcription when anchored to DNA. It may function in the SNF1 pathway. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. Length = 214 Score = 27.2 bits (61), Expect = 8.4 Identities = 10/61 (16%), Positives = 29/61 (47%), Gaps = 1/61 (1%) Query: 240 NQILENIQVSSNNFVKSSDQVINTVHDV-RETTQTFQEVGQKIDHLLSDFSSKMKSKETS 298 +L ++ + + + + + +E + F+ +K D +L+ + ++ K+KE S Sbjct: 77 GGVLSALKGNDSLILDPLRSFVKSDIRPYKELRKNFEYYQRKYDSMLARYVAQSKTKEPS 136 Query: 299 A 299 + Sbjct: 137 S 137 >gnl|CDD|35383 KOG0161, KOG0161, KOG0161, Myosin class II heavy chain [Cytoskeleton]. Length = 1930 Score = 27.1 bits (60), Expect = 9.2 Identities = 35/212 (16%), Positives = 82/212 (38%), Gaps = 26/212 (12%) Query: 228 DKMIKAID--LQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLL 285 ++ ++A + +QK+ + L+ + + +++ +D++E Q +E + + LL Sbjct: 837 EEEMRAKEEEIQKLKEELQKSESKRKELEEKLVKLLEEKNDLQEQLQAEKENLAEAEELL 896 Query: 286 SDFSSKMKS-----KETSAFLENI----ADSTSNMRSSISAIREITDQ-------RQKII 329 ++ + KE LE A+ R ++E+ +Q QK+ Sbjct: 897 ERLRAEKQELEKELKELKERLEEEEEKNAELERKKRKLEQEVQELKEQLEELELTLQKLE 956 Query: 330 STINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRY 389 N EN NL + E +SK++ E ++ Q + + ++ +N+ Sbjct: 957 LEKNAAENKLKNLEEEINSLDENISKLSKEKKELEERI--RELQDDLQAEEEKAKSLNKA 1014 Query: 390 IPSIGNNLQNF------SQSGLNDIQNLVRKL 415 + L + + +++ RKL Sbjct: 1015 KAKLEQQLDDLEVTLEREKRIRMELEKAKRKL 1046 >gnl|CDD|31758 COG1570, XseA, Exonuclease VII, large subunit [DNA replication, recombination, and repair]. Length = 440 Score = 27.2 bits (60), Expect = 9.7 Identities = 20/155 (12%), Positives = 62/155 (40%), Gaps = 5/155 (3%) Query: 277 VGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQ--RQKIISTINT 334 VG + D L+DF + +++ +A E + ++ + + ++ + R+ + Sbjct: 232 VGHETDFTLADFVADLRAPTPTAAAELVVPDSAELLQQLDQLQRRLHRALRRLLDQKKQR 291 Query: 335 IENITSNL--NDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYIPS 392 +E++ L + +E +++ + A++ +L ++++N I Sbjct: 292 LEHLARRLQFRSPERLLSEQQQRLDEL-AIRLRRALENQLALKKQRLERLTQRLNPQIQR 350 Query: 393 IGNNLQNFSQSGLNDIQNLVRKLQETVNHFDDCLN 427 LQ + ++ +++ +E + + L Sbjct: 351 QQQRLQQLERRLDKALRRQLKRKRERLEALVEQLE 385 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 0.314 0.129 0.350 Gapped Lambda K H 0.267 0.0723 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,847,080 Number of extensions: 243456 Number of successful extensions: 976 Number of sequences better than 10.0: 1 Number of HSP's gapped: 972 Number of HSP's successfully gapped: 98 Length of query: 452 Length of database: 6,263,737 Length adjustment: 97 Effective length of query: 355 Effective length of database: 4,167,664 Effective search space: 1479520720 Effective search space used: 1479520720 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 (21.6 bits) S2: 59 (26.5 bits)