Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 300 bits (768), Expect = 8e-86 Identities = 182/511 (35%), Positives = 291/511 (56%), Gaps = 13/511 (2%) Query: 1 MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 60 MS + +I K FPG+ A D V+ V G++H L+GENGAGKSTL+ +L G YQP+ G Sbjct: 1 MSYVIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGE 60 Query: 61 VMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRF 120 +++ G V+ T + GI ++HQ V TV EN++LG+ P + G +N ++A + Sbjct: 61 ILVKGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKA 120 Query: 121 VRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLF 180 V + G+A+DP AK++ +S+ +Q VEI K L R A ++ DEPT++L+ +E L Sbjct: 121 VETISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELI 180 Query: 181 KLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGR 240 ++++ L ++ +++I I+H++ EI E+CD CT+ R GR I + E T D++ + MVGR Sbjct: 181 QIMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISES-TPDSLAAMMVGR 239 Query: 241 EIS-DIYNYSARPLGEV----RFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSEL 295 E++ + A+P V K EV GEI+G G+ G G++EL Sbjct: 240 EVNFSVEKDPAQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTEL 299 Query: 296 MHLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINIS 355 + + G GG + L+G+ I + + G+ P+DR + G+V TV ENI + Sbjct: 300 IEAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQ 359 Query: 356 C--RRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWL-A 412 ++ Y G+ L+ + + A+ I+ ++TPS R LSGGNQQKAI++R + Sbjct: 360 TYYQKPYSTSGV-LNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDR 418 Query: 413 EPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQ 472 PDL +I +PTRG+DVGA I++ + + ++G A+++IS EL EVL VSDRI V+ + Sbjct: 419 SPDL--LIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYE 476 Query: 473 GRISGELTRKDATEQSVLSLALPQSSTALPG 503 G+I + D T ++ L L + S G Sbjct: 477 GKIVA-IVDADKTNENELGLLMAGGSAKKEG 506 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: 608 Number of extensions: 35 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: 509 Length adjustment: 35 Effective length of query: 477 Effective length of database: 474 Effective search space: 226098 Effective search space used: 226098 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 Apr 09 2024. 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