Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >NCBI__GCF_001623255.1:WP_068005521.1 Length = 515 Score = 276 bits (705), Expect = 2e-78 Identities = 166/505 (32%), Positives = 292/505 (57%), Gaps = 23/505 (4%) Query: 2 TQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQG 61 T PLL ++ I K FG +A +++L + GEI AL+GENGAGK+TLM +L G + D+G Sbjct: 6 TVHPLLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEG 65 Query: 62 EILLDGRPVALRD--PGASRAA---GINLIYQELAVAPNISVAANVFMGSELRTRLGLID 116 +++ L D PGA +AA GI +++Q +A N++ N+ +G+E L Sbjct: 66 RVMVRTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTE-----SLFA 120 Query: 117 HAAMRSRTDAVLRQLGAGFGAS---DL-AGRLSIAEQQQVEIARALVHRSRIVIMDEPTA 172 RS+ A L++L G DL +L++ E+Q+VEI +AL +RI+++DEPTA Sbjct: 121 RKFSRSKARAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTA 180 Query: 173 ALSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDS 232 L+ +E++ LFN ++ L +G+AII+ISH+MAEV +DRV VLR G V +L + D Sbjct: 181 VLTPQESDSLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDR 240 Query: 233 ERIVQMMVGRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGK--IRPASFDVRAGEVLGF 290 ++ ++MVG ++ Q P + + V + + G+ I + +R GE++G Sbjct: 241 HKLAELMVGHAV----QMAEREPGNPGEEILVFKGVSAGEGRELIENVNLSLRKGEIIGL 296 Query: 291 AGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFL 350 AG+ G G++ LA++L G + + G + L +P+ + AA+++G+A +PEDR G+ Sbjct: 297 AGVSGNGQSMLAKVLSGLEEPTAGAVTLGSQPLKAN-AAAAIQSGVARIPEDRHHDGIVG 355 Query: 351 QMAVAANATMNVASR--HTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQ 408 M+V N + + + R GL+R + A+ AI+ +++ + P LSGGN Q Sbjct: 356 AMSVEENLVLEEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQ 415 Query: 409 KVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGIC 468 K++LAR L+ P +++ +P+RG+D+ A +++++ + +G V++IS +L E+ + Sbjct: 416 KIVLARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLS 475 Query: 469 DRVLVMREGMITGELAGAAITQENI 493 DR+ V+ G ++ +A + ++ + Sbjct: 476 DRIAVIHRGHVSEPMASEELDKKQV 500 Score = 88.2 bits (217), Expect = 7e-22 Identities = 66/246 (26%), Positives = 119/246 (48%), Gaps = 11/246 (4%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 +L +G+ G L + +++L++R GEI L G +G G+S L KVLSG+ P G + L Sbjct: 266 ILVFKGVSAGEGREL-IENVNLSLRKGEIIGLAGVSGNGQSMLAKVLSGLEEPTAGAVTL 324 Query: 66 DGRPVALRDPGASRAAGINLIYQEL---AVAPNISVAANVFMGSELRT----RLGLIDHA 118 +P+ + A+ +G+ I ++ + +SV N+ + E+R R GL+ Sbjct: 325 GSQPLKA-NAAAAIQSGVARIPEDRHHDGIVGAMSVEENLVL-EEIRKPAYQRFGLLRFN 382 Query: 119 AMRSRTDAVLRQLGAGFGASDLAGRL-SIAEQQQVEIARALVHRSRIVIMDEPTAALSER 177 +R R ++ RL S Q++ +AR L IV+ +P+ L Sbjct: 383 EIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIVLARTLDQEPAIVLAAQPSRGLDVG 442 Query: 178 ETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQ 237 T + ++ RD G ++ IS + E++ L+DR+ V+ G + +E+D +++ Sbjct: 443 ATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRIAVIHRGHVSEPMASEELDKKQVGL 502 Query: 238 MMVGRS 243 MM G S Sbjct: 503 MMAGHS 508 Score = 79.3 bits (194), Expect = 3e-19 Identities = 65/226 (28%), Positives = 109/226 (48%), Gaps = 17/226 (7%) Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLE---GRPVHIDQ--PRAAMR 333 + D+ AGE++ G GAG+T L +LFG G +++ G V ++ P+AA+ Sbjct: 30 NLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVMVRTSSGTLVDLEPGAPQAALE 89 Query: 334 AGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVA 393 AGI V + L + N + S R RS+ ARA +Q L Sbjct: 90 AGIGMVHQHFT---LAENLTGLENIVLGTESLFARK-FSRSK-----ARAKLQELMQSSG 140 Query: 394 HP---ETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQ 450 + V KL+ G +Q+V + + L ++L+LDEPT + ++ + LA++ Sbjct: 141 LEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQESDSLFNTLKLLAAK 200 Query: 451 GVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRL 496 G+A++ IS ++ EV+G DRV V+R G I +L + + + L Sbjct: 201 GMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAEL 246 Lambda K H 0.320 0.135 0.378 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: 634 Number of extensions: 35 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 521 Length of database: 515 Length adjustment: 35 Effective length of query: 486 Effective length of database: 480 Effective search space: 233280 Effective search space used: 233280 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: 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