Align ABC transporter for L-Histidine, permease component 2 (characterized)
to candidate RR42_RS33670 RR42_RS33670 taurine ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_2561 (252 letters) >FitnessBrowser__Cup4G11:RR42_RS33670 Length = 291 Score = 140 bits (352), Expect = 4e-38 Identities = 77/244 (31%), Positives = 127/244 (52%), Gaps = 15/244 (6%) Query: 15 VVFVAVWAFFTLGGFVSPTFLASPITMAK----------EGWLLFTEYGFIKDIGMTIWR 64 V +A+W + ++ P FL +P + +G L TE+ ++ R Sbjct: 49 VSLLALWWIGSHLRWLPPLFLPTPEAIINAFIDAWNGNVQGGLPLTEH-----FRASMVR 103 Query: 65 VVGGFVLAAVIAVPLGIAMGAYKGIEAFFEPFISFCRYLPASAFIPLLILWAGIGEAQKI 124 V G F LA V AVP+G+ MG + F+P I F R LP A++PL+++W GI E KI Sbjct: 104 VFGAFALATVTAVPIGVMMGVSRIARGVFDPPIEFYRPLPPLAYLPLIVIWFGIDETSKI 163 Query: 125 LVIFIGSVFQITLMVAVTVGGARRDLVEAAYTLGAGHKGIVTRVLIPGAAPEIAETLRLV 184 L+IF+ + + V + + AAY++GA ++ V+IP A P+I +R+ Sbjct: 164 LLIFLACFAPLAMSAQAGVRSVTIEQINAAYSMGANRWQVIRHVVIPAALPDILTGMRIA 223 Query: 185 LGWAWTYVIVAELIGSSSGIGHMITDSQSLLNTGQIIFGIIIIGLIGLVSDFAFKALNHR 244 +G+ WT ++ AE++ ++SG+G M+ ++ + L T +I GI +IGLI D + Sbjct: 224 IGFGWTTLVAAEMVAATSGLGQMVLNASNFLRTDVVIMGIGLIGLIAYTFDLLMRKTEKW 283 Query: 245 LFAW 248 L W Sbjct: 284 LVPW 287 Lambda K H 0.331 0.145 0.456 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: 184 Number of extensions: 8 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: 252 Length of database: 291 Length adjustment: 25 Effective length of query: 227 Effective length of database: 266 Effective search space: 60382 Effective search space used: 60382 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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