Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2332 (517 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 300 bits (768), Expect = 8e-86 Identities = 177/497 (35%), Positives = 285/497 (57%), Gaps = 12/497 (2%) Query: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 L+ I ++K F VVA D+ L + PG V AL+GENGAGKSTLM ++AG YQPDAG I L Sbjct: 24 LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83 Query: 83 RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142 GKP+ F + A +AGI M++Q L+ M++AEN+ +G+E +N +EM Sbjct: 84 DGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQE---GSFFLNPKEMRNRVQ 140 Query: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202 EL R +++DP +V +LS+ E+Q VEI K + DS +LI DEPT+ +T +E HLF Sbjct: 141 ELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEA 200 Query: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIG-LQRADSMNSDSLISMMVGREL 261 + + QGK IV+I+HK+ EV A+ADE+A+ R G G ++ + L MVG+E+ Sbjct: 201 LWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVGKEV 260 Query: 262 SQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGI 321 P GD +L VR+LT G+ +D++FDLH GE++ + G+ G+G+ + E I G+ Sbjct: 261 LLEVDREAMPHGDAVLQVRNLTGIGL-EDITFDLHQGEVVAVVGVAGNGQKALVEAICGL 319 Query: 322 TPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPC--LSVLENMEMAVLPHY 379 + + GK R + + A + EDR GL C L++++N+ + + Sbjct: 320 RKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDR--LGLATCRNLNLVDNLLLTTRQGF 377 Query: 380 TGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILD 439 ++ +K ++ KK ++ + LSGGN QK++LAR L PRL++ + Sbjct: 378 ARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAE 437 Query: 440 EPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRS 499 +PT+G+D+ A +++ + A E +++++ +L E L ++DRV V++ G M S Sbjct: 438 QPTQGLDIAATEQVWNHL-LAAREMAGILLVTGDLNEALQLADRVAVIYRGRFMDVFSVS 496 Query: 500 EATQEKVMQLASGMTAV 516 + ++KV ++ M V Sbjct: 497 D--KQKVNRIGLMMAGV 511 Lambda K H 0.320 0.136 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: 537 Number of extensions: 35 Number of successful extensions: 8 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: 517 Length of database: 514 Length adjustment: 35 Effective length of query: 482 Effective length of database: 479 Effective search space: 230878 Effective search space used: 230878 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