Align ABC transporter for L-Histidine, permease component 2 (characterized)
to candidate GFF225 PS417_01140 taurine ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_2561 (252 letters) >FitnessBrowser__WCS417:GFF225 Length = 278 Score = 151 bits (381), Expect = 2e-41 Identities = 80/252 (31%), Positives = 135/252 (53%), Gaps = 7/252 (2%) Query: 2 SARARWMLGLAFFVVFVAVWAFFTLGGFVSPTFLASPITMAKEGWLLFTEYGFI-----K 56 S RW + L V + +W T G + P FL P + ++GWLL T G++ + Sbjct: 24 SLSTRW-ISLLTLVALLIIWWAVTATGVIEPLFLPPPSAVLQKGWLLATT-GYMDSTLWQ 81 Query: 57 DIGMTIWRVVGGFVLAAVIAVPLGIAMGAYKGIEAFFEPFISFCRYLPASAFIPLLILWA 116 + ++ R+ G A + AVP+GIA+G+ + +P I F R +P A++PL+++W Sbjct: 82 HLSASLSRIGLGLGFAVLTAVPVGIAIGSNRIARGILDPLIEFYRPIPPLAYLPLIVIWC 141 Query: 117 GIGEAQKILVIFIGSVFQITLMVAVTVGGARRDLVEAAYTLGAGHKGIVTRVLIPGAAPE 176 GIGE K+L+I++ I + A V + AA +LGA ++ V++P A P+ Sbjct: 142 GIGELSKVLLIYLAIFAPIAIATATGVRTVDPAKLRAAQSLGATRAQLIRHVILPSALPD 201 Query: 177 IAETLRLVLGWAWTYVIVAELIGSSSGIGHMITDSQSLLNTGQIIFGIIIIGLIGLVSDF 236 I +R+ LG W+ ++ AELI ++SG+G M+ + L T ++ GI++I LI + Sbjct: 202 ILTGVRIGLGVGWSTLVAAELIAATSGLGFMVQSAAQFLVTDVVVLGILVIALIAFAMEM 261 Query: 237 AFKALNHRLFAW 248 +AL +L W Sbjct: 262 GLRALQRKLVPW 273 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: 178 Number of extensions: 11 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: 278 Length adjustment: 25 Effective length of query: 227 Effective length of database: 253 Effective search space: 57431 Effective search space used: 57431 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