Align ABC transporter for L-Histidine, permease component (characterized)
to candidate 16238 b2130 predicted transporter subunit: membrane component of ABC superfamily (NCBI)
Query= reanno::pseudo5_N2C3_1:AO356_09615 (283 letters) >FitnessBrowser__Keio:16238 Length = 385 Score = 103 bits (256), Expect = 8e-27 Identities = 63/197 (31%), Positives = 102/197 (51%), Gaps = 16/197 (8%) Query: 90 DKLMQTLALMLVATLISVLIGIPLGILSARSNRLRSVLMPLLDIMQTMPSFVYL------ 143 D L Q L L+ A L +++IG+PLGI S + + LL+++QT+PS Sbjct: 175 DALAQHLTLLFGAVLPALVIGVPLGIWCYFSTARQGAIFSLLNVIQTVPSVALFGLLIAP 234 Query: 144 ----------IPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVMEAINAFGA 193 + L + G G PA+ A V+YA PL+R +G+ Q+ +V+E+ A G Sbjct: 235 LAALVTAFPWLGTLGIAGTGMTPALIALVLYALLPLVRGVVVGLNQIPRDVLESARAMGM 294 Query: 194 NRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGEDVLVGIQTLNVGRG 253 + Q+ VQLPLALP + + + + M VIA++IGA G G V G+ + + Sbjct: 295 SGAQRFLHVQLPLALPVFLRSLRVVMVQTVGMAVIAALIGAGGFGALVFQGLLSSAIDLV 354 Query: 254 LEAGLAIVILAVVIDRI 270 L + +++LAV+ D + Sbjct: 355 LLGVIPVIVLAVLTDAL 371 Lambda K H 0.328 0.142 0.429 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: 300 Number of extensions: 10 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: 283 Length of database: 385 Length adjustment: 28 Effective length of query: 255 Effective length of database: 357 Effective search space: 91035 Effective search space used: 91035 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 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