Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate Ga0059261_1870 Ga0059261_1870 ABC-type transport system involved in resistance to organic solvents, ATPase component
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Korea:Ga0059261_1870 Length = 273 Score = 117 bits (293), Expect = 3e-31 Identities = 79/215 (36%), Positives = 118/215 (54%), Gaps = 6/215 (2%) Query: 46 VSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMR 105 + L + G+I ++G SG+GKS L+R I L EP +G + G+++ L + R + Sbjct: 34 LDLDVRQGEILGVVGGSGTGKSVLMRSIIGLQEPDAGSIEVFGEDVQHLNTEEAIELR-K 92 Query: 106 RVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAR--EIGMKWIDTVGL-SGYDAKFPH 162 R ++FQ AL TV +NV + + D A EI + GL S K+P Sbjct: 93 RWGVLFQGGALFSTLTVAENVQVPLKEFYPAFDQALLDEIAAYKVVMTGLPSDAGPKYPA 152 Query: 163 QLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITH 222 +LSGGMK+R GLAR+LA D +++ +DE + LDP+ + L LQR L T+ ITH Sbjct: 153 ELSGGMKKRAGLARSLALDPELLFLDEPTAGLDPIGAAAFDELTLALQRTLGLTVFLITH 212 Query: 223 DLDEALRIGSEIAILRDGQVVQVGTPNDI--LDNP 255 DLD I +A+L D V+ VGT +++ LD+P Sbjct: 213 DLDTLYAICDRVAVLADKHVIAVGTIDELLALDHP 247 Lambda K H 0.323 0.139 0.397 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: 187 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: 275 Length of database: 273 Length adjustment: 25 Effective length of query: 250 Effective length of database: 248 Effective search space: 62000 Effective search space used: 62000 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