Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >NCBI__GCF_001623255.1:WP_068005521.1 Length = 515 Score = 284 bits (726), Expect = 6e-81 Identities = 169/506 (33%), Positives = 293/506 (57%), Gaps = 25/506 (4%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +L + I K F +VA NV+ +++ EIV+L+GENGAGK+TL+ IL G D G ++V Sbjct: 10 LLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVMV 69 Query: 74 ---NGERVEFH--SPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRV 128 +G V+ +P A + GI ++HQ L +N+T ENI L E++ +K + S Sbjct: 70 RTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFARKFSRSKA- 128 Query: 129 DENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLT 188 + +EL+ G + D V L +RQ VEI KAL ++ RI+ +DEPT+ LT Sbjct: 129 -----RAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLT 183 Query: 189 VEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTI 248 +E++ LF +++L ++G++++F+SH++ EV+ SDR+ V+R G+ + +L + D + Sbjct: 184 PQESDSLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKL 243 Query: 249 IKMMVGREVEFFPHGIETRPGEIALEVRNLK------WKDKVKNVSFEVRKGEVLGFAGL 302 ++MVG V+ E PG E+ K ++ ++NV+ +RKGE++G AG+ Sbjct: 244 AELMVGHAVQM----AEREPGNPGEEILVFKGVSAGEGRELIENVNLSLRKGEIIGLAGV 299 Query: 303 VGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMT 362 G G++ ++ G+ + +G + + + ++ N AI+ G+ IPEDR G+V M+ Sbjct: 300 SGNGQSMLAKVLSGLEEPTAGAVTLGSQPLK-ANAAAAIQSGVARIPEDRHHDGIVGAMS 358 Query: 363 VKDNIVLPSLKK--ISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKV 420 V++N+VL ++K R+GL L + + +++ +K I+ ++ LSGGN QK+ Sbjct: 359 VEENLVLEEIRKPAYQRFGL-LRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKI 417 Query: 421 VLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDR 480 VLA+ L I++ +P+RG+DVGA A++HR ++E +G V++IS +L E+ LSDR Sbjct: 418 VLARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDR 477 Query: 481 IVVMWEGEITAVLDNREKRVTQEEIM 506 I V+ G ++ + + E Q +M Sbjct: 478 IAVIHRGHVSEPMASEELDKKQVGLM 503 Score = 90.1 bits (222), Expect = 2e-22 Identities = 68/250 (27%), Positives = 125/250 (50%), Gaps = 8/250 (3%) Query: 13 EILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEIL 72 EIL KG V G ++NV+ + + EI+ L G +G G+S L K+L+G+ +P AG + Sbjct: 265 EILVFKG-VSAGEGRELIENVNLSLRKGEIIGLAGVSGNGQSMLAKVLSGLEEPTAGAVT 323 Query: 73 VNGERVEFHSPVDAFKKGISVIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVD 129 + + ++ ++ A + G++ I ++ + + M+V EN+ L E +R + Sbjct: 324 LGSQPLKANAAA-AIQSGVARIPEDRHHDGIVGAMSVEENLVL--EEIRKPAYQRFGLLR 380 Query: 130 ENYMYTRSKELLDLIGAKFS-PDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLT 188 N + R++E + + S P A+ R L+ Q + + + L +EP I+ +P+ L Sbjct: 381 FNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIVLARTLDQEPAIVLAAQPSRGLD 440 Query: 189 VEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTI 248 V T + ++ + RG V+ +S LDE+ ++SDRI V+ G + E D + Sbjct: 441 VGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRIAVIHRGHVSEPMASEELDKKQV 500 Query: 249 IKMMVGREVE 258 MM G + Sbjct: 501 GLMMAGHSAK 510 Lambda K H 0.319 0.138 0.381 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 629 Number of extensions: 40 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 520 Length of database: 515 Length adjustment: 35 Effective length of query: 485 Effective length of database: 480 Effective search space: 232800 Effective search space used: 232800 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory