Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate BWI76_RS00275 BWI76_RS00275 ribose ABC transporter ATP-binding protein RbsA
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Koxy:BWI76_RS00275 Length = 501 Score = 401 bits (1031), Expect = e-116 Identities = 216/495 (43%), Positives = 315/495 (63%), Gaps = 4/495 (0%) Query: 1 MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 60 M A L+ I K FPGV+AL G S +V G+V L+GENGAGKST++K+L G Y D+G Sbjct: 1 MEALLQLKGIDKAFPGVKALSGASLNVYPGRVMALVGENGAGKSTMMKVLTGIYARDAGS 60 Query: 61 VMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLG-QLPNSLGWVNKREAKR 119 ++ G E F SS AGI +IHQEL +P LT+AEN+ LG + N G ++ + Sbjct: 61 LLWLGKETTFNGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120 Query: 120 FVRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVL 179 + L + + + + LSI +QMVEI K L ++VI +DEPT +L+ ETE L Sbjct: 121 EADKLLAKLNLRFNSQKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180 Query: 180 FKLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVG 239 F+++R+L++ R ++YISHRM EI+E+CD T+FRDG+ IA + + D ++ MVG Sbjct: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAERE-VASLDEDLLIEMMVG 239 Query: 240 REISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLV 299 R++ D Y + G VR + G + + SF +R+GEI+G GL+GAGR+ELM ++ Sbjct: 240 RKLEDQYPRLDKAPGAVRLKVDNLCGSGV-ENISFILRQGEILGVAGLMGAGRTELMKVL 298 Query: 300 YGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRH 359 YGA + G + LDG+ + RS + + +GIV EDRK +G+V +V EN++++ R+ Sbjct: 299 YGALPRSSGSVTLDGREVVARSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRY 358 Query: 360 YLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVV 419 + R G L K E + FI+L +KTPS Q I LSGGNQQK ++R L KV+ Sbjct: 359 FSRGGGSLKHKDEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRP-KVL 417 Query: 420 ILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGEL 479 ILDEPTRG+DVGAK EIY +I Q G +I+++SSE+PEVLG+SDRI+VM +G + GE Sbjct: 418 ILDEPTRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRIMVMHEGHLGGEF 477 Query: 480 TRKDATEQSVLSLAL 494 TR+ AT++ +++ A+ Sbjct: 478 TREQATQEVLMAAAV 492 Lambda K H 0.320 0.136 0.385 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: 644 Number of extensions: 36 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 512 Length of database: 501 Length adjustment: 34 Effective length of query: 478 Effective length of database: 467 Effective search space: 223226 Effective search space used: 223226 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 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