Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate 6939496 Sama_3588 putative ABC-type multidrug transport system, ATPase component (RefSeq)
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__SB2B:6939496 Length = 322 Score = 112 bits (280), Expect = 9e-30 Identities = 68/234 (29%), Positives = 127/234 (54%), Gaps = 5/234 (2%) Query: 6 LKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHIE 65 ++ + ++ +G ++AV G+DL + G + +G NG GK+T+++ +TG L + G I Sbjct: 17 IETRGMTRQFGALKAVDGVDLAIPRGSIYGFLGPNGCGKSTSIRMLTGLLKPT--SGEIR 74 Query: 66 YLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWFA 125 LG+PLKG + E ++ ++ + + ++ +++ ENL A +G A D + Sbjct: 75 VLGEPLKGAE--EKLRRRIGYMTQKFSLYENLTVLENLRFVARIYGLQGNKAKDRIEQLL 132 Query: 126 VFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIRN 185 L+ R +QMAG++SGG++Q LA+A A + P+LL LDEP+ + P + +E + + Sbjct: 133 SLYSLEGRESQMAGSMSGGQKQRLALAAATIHEPELLFLDEPTSAVDPENRREFWERLFD 192 Query: 186 VSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYLG 239 +SA+G TI LV + E H ++E G+ G + ++ + +G Sbjct: 193 LSAKGCTI-LVSTHYMDEAERCHGLAILERGIKRADGSPKALMQAMGARVVEIG 245 Lambda K H 0.317 0.134 0.365 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: 161 Number of extensions: 7 Number of successful extensions: 3 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: 241 Length of database: 322 Length adjustment: 25 Effective length of query: 216 Effective length of database: 297 Effective search space: 64152 Effective search space used: 64152 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 (21.6 bits) S2: 47 (22.7 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