Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate BPHYT_RS21720 BPHYT_RS21720 nitrate ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__BFirm:BPHYT_RS21720 Length = 271 Score = 222 bits (566), Expect = 6e-63 Identities = 116/251 (46%), Positives = 162/251 (64%), Gaps = 6/251 (2%) Query: 1 MSSVSIQAVSRVFETAK-GQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDH 59 M +++++ VS VF + GQ QAL ++ +R DFV LG SGCGK+TLL ++AG Sbjct: 1 MENMTVRNVSVVFPGRRPGQTVQALDDINLTIRSGDFVVALGASGCGKTTLLSLMAGFIA 60 Query: 60 ATSGRVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYF 119 + G +LL G P+ GPGA+RG+VFQ + L PWL + N FGL+ +G+P AQ++E A Sbjct: 61 PSRGELLLGGEPIAGPGADRGVVFQKHALLPWLNVIDNAEFGLKLQGVPRAQRREIAVRN 120 Query: 120 IAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLL 179 +A VGL+ F +H QLSGGMQQR IARAL DP +LLMDEP ALD TR +QELLL Sbjct: 121 LALVGLQDFHKHMIYQLSGGMQQRVGIARALTCDPAMLLMDEPMAALDALTRETIQELLL 180 Query: 180 GIWEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTELAVD-----LPHPRHYTIKT 234 +W+ K F+TH ++EA+F+A+R+ V S RPGRI +D L IK+ Sbjct: 181 DVWKKTNKMFFFITHSVEEALFLASRLIVMSPRPGRITHTYELDFNRRFLESRDARAIKS 240 Query: 235 SPEFMDLKARL 245 SP+F+ ++ ++ Sbjct: 241 SPDFIAMREQV 251 Lambda K H 0.322 0.136 0.394 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: 193 Number of extensions: 5 Number of successful extensions: 1 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: 259 Length of database: 271 Length adjustment: 25 Effective length of query: 234 Effective length of database: 246 Effective search space: 57564 Effective search space used: 57564 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 (21.9 bits) S2: 47 (22.7 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