Align ABC transporter for L-Histidine, permease component 2 (characterized)
to candidate PP_0231 PP_0231 taurine ABC transporter permease subunit
Query= reanno::acidovorax_3H11:Ac3H11_2561 (252 letters) >FitnessBrowser__Putida:PP_0231 Length = 279 Score = 147 bits (370), Expect = 3e-40 Identities = 78/248 (31%), Positives = 134/248 (54%), Gaps = 7/248 (2%) Query: 6 RWMLGLAFFVVFVAVWAFFTLGGFVSPTFLASPITMAKEGWLLFTEYGFI-----KDIGM 60 RW+ L + + VW T G+V P FL SP + + W L T+ G++ + + Sbjct: 29 RWISTLTLASLLM-VWWLVTAAGWVEPLFLPSPGDILAKAWTLLTQ-GYMDASLWQHLSA 86 Query: 61 TIWRVVGGFVLAAVIAVPLGIAMGAYKGIEAFFEPFISFCRYLPASAFIPLLILWAGIGE 120 ++ R+ V A + A+P+GIA+G + +P I F R +P A++PL+++W GIGE Sbjct: 87 SLGRIGLALVAATLTAIPVGIAIGYNRVARGILDPLIEFYRPIPPLAYLPLIVIWCGIGE 146 Query: 121 AQKILVIFIGSVFQITLMVAVTVGGARRDLVEAAYTLGAGHKGIVTRVLIPGAAPEIAET 180 K+L+I++ I + A V + AA +LGA ++ V++P A P+I Sbjct: 147 LSKVLLIYLAIFAPIAIATATGVRTVDPAKLRAAQSLGATKAQLIRHVILPSALPDILTG 206 Query: 181 LRLVLGWAWTYVIVAELIGSSSGIGHMITDSQSLLNTGQIIFGIIIIGLIGLVSDFAFKA 240 +R+ LG W+ ++ AELI ++SG+G M+ + L T ++ GI++I LI + + +A Sbjct: 207 IRIGLGVGWSTLVAAELIAATSGLGFMVQSAAQFLVTDVVVLGILLIALIAFALEMSLRA 266 Query: 241 LNHRLFAW 248 L +L W Sbjct: 267 LQRKLVPW 274 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: 173 Number of extensions: 12 Number of successful extensions: 2 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: 279 Length adjustment: 25 Effective length of query: 227 Effective length of database: 254 Effective search space: 57658 Effective search space used: 57658 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