Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 6938983 Sama_3081 ABC transporter, ATP-binding protein, putative (RefSeq)
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__SB2B:6938983 Length = 270 Score = 135 bits (339), Expect = 1e-36 Identities = 78/205 (38%), Positives = 119/205 (58%), Gaps = 2/205 (0%) Query: 45 DVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRM 104 D+SL I GK+ IMG SG GK+TL++ I + P GEVLFDG NI D+ L R Sbjct: 26 DISLSIPKGKVTAIMGPSGIGKTTLLKLIAGQLVPDHGEVLFDGVNIHDISRSELFELR- 84 Query: 105 RRVSMVFQSFALMPHRTVLQNVVYGQRVR-GVSKDDAREIGMKWIDTVGLSGYDAKFPHQ 163 +R+SM+FQS AL V N+ + R G+ + R I + ++ VGL G P + Sbjct: 85 KRMSMLFQSGALFTDMNVFDNIAFALREHSGLDEAIIRRIVLMKLEAVGLRGAAMLMPSE 144 Query: 164 LSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHD 223 LSGGM++RV LARA+A + ++++ DE F+ DP+ G + + +L L T V ++HD Sbjct: 145 LSGGMQRRVALARAIALEPEMVMYDEPFAGQDPISMGVLVKLIRELSDALNLTSVVVSHD 204 Query: 224 LDEALRIGSEIAILRDGQVVQVGTP 248 + E L I + ++ + +++ GTP Sbjct: 205 VGEVLGIADYVYVIAEKRIIAQGTP 229 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: 195 Number of extensions: 15 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: 270 Length adjustment: 25 Effective length of query: 250 Effective length of database: 245 Effective search space: 61250 Effective search space used: 61250 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