Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate GFF2162 PS417_11030 L-arabinose transporter ATP-binding protein
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__WCS417:GFF2162 Length = 500 Score = 407 bits (1046), Expect = e-118 Identities = 219/492 (44%), Positives = 326/492 (66%), Gaps = 3/492 (0%) Query: 3 ALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLL 62 A L+ GI K FPGVKAL G + + +PG+V AL+GENGAGKST++K+L G Y ++GTL Sbjct: 4 AALRFDGIGKTFPGVKALDGISFSAHPGQVHALMGENGAGKSTLLKILGGAYIPNSGTLH 63 Query: 63 WLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEA 122 + F S +G+ +IHQEL+L+P++++AEN+FLG +RFG ++ + +A Sbjct: 64 IGEQVMAFKSAADSIASGVAVIHQELHLVPEMSVAENLFLGH-LPSRFGVVNRGLLRKQA 122 Query: 123 DKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFR 182 L L + +G LS+G +Q+VEIAK LS + VI DEPT +L+ E + L Sbjct: 123 LACLKGLADEIDPAEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMA 182 Query: 183 VIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAERE-VASLTEDSLIEMMVGRK 241 +I L+ +G+ ++Y+SHRM+E+F IC+ VTVF+DG+++ E +++LT D L+ MVGR Sbjct: 183 IIARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFEDMSALTHDQLVTCMVGRD 242 Query: 242 LEDQYPHLDKAPGDIRLKVDNLCGPGVND-VSFTLRKGEILGVSGLMGAGRTELMKVLYG 300 ++D Y + + G++ LKVD L GPG+ + VSF +RKGEILG+ GL+GAGRTEL ++L G Sbjct: 243 IQDIYDYRPREHGEVALKVDGLLGPGLREPVSFNVRKGEILGLFGLVGAGRTELFRLLSG 302 Query: 301 ALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS 360 ++G + L G + +SP+D +A G++ EDRK++G++ SV EN++++A S Sbjct: 303 LERASAGQLELCGEPLHLQSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAHS 362 Query: 361 RAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILD 420 G L+ E+ I VKTP+ Q I LSGGNQQK + R L KVL+LD Sbjct: 363 TFGWLLREGWEKGNADQQINAMKVKTPNAAQKIMYLSGGNQQKSILGRWLSMPMKVLLLD 422 Query: 421 EPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTRE 480 EPTRG+D+GAK EIYQ+I+ A G+++I+VSS++ EV+G++DRI+V+ EG L GE TRE Sbjct: 423 EPTRGIDIGAKAEIYQIIHNLAAQGIAVIVVSSDLMEVMGIADRILVLCEGALRGEQTRE 482 Query: 481 QATQEVLMAAAV 492 AT+ L+ A+ Sbjct: 483 HATESNLLQLAL 494 Score = 84.0 bits (206), Expect = 1e-20 Identities = 60/235 (25%), Positives = 117/235 (49%), Gaps = 10/235 (4%) Query: 15 PGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWLGKETTFTGPK 74 PG++ + NV G ++ L G GAG++ + ++L+G+ AG L G+ P+ Sbjct: 267 PGLR--EPVSFNVRKGEILGLFGLVGAGRTELFRLLSGLERASAGQLELCGEPLHLQSPR 324 Query: 75 SSQEAGIGIIHQELN---LIPQLTIAENIFLG-REFVNRFGKI---DWKTMYAEADKLLA 127 + AG+ + ++ +IP ++AENI + R + FG + W+ A+ Sbjct: 325 DAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAHSTFGWLLREGWEKGNADQQINAM 384 Query: 128 KLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIREL 187 K+ + K++ LS G+QQ + + LS KV+++DEPT + ++++I L Sbjct: 385 KVKTPNAAQKIMY-LSGGNQQKSILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNL 443 Query: 188 KSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKL 242 +QG ++ +S + E+ I D + V +G E+ TE +L+++ + R + Sbjct: 444 AAQGIAVIVVSSDLMEVMGIADRILVLCEGALRGEQTREHATESNLLQLALPRSV 498 Lambda K H 0.318 0.137 0.380 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: 640 Number of extensions: 28 Number of successful extensions: 8 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: 501 Length of database: 500 Length adjustment: 34 Effective length of query: 467 Effective length of database: 466 Effective search space: 217622 Effective search space used: 217622 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 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