Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF3356 HP15_3298 glycine betaine/L-proline ABC transporter, ATPase subunit
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Marino:GFF3356 Length = 352 Score = 293 bits (751), Expect = 3e-84 Identities = 145/261 (55%), Positives = 189/261 (72%) Query: 4 IEIRNVYKIFGHDAKKALTMVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGLSG 63 I IRN+YKIFG AL V G+ KAD+L + +GL D+++ I G+I VIMGLSG Sbjct: 7 ISIRNLYKIFGPTPDVALEYVRKGMGKADLLEQQRHVLGLRDINVDIHDGEITVIMGLSG 66 Query: 64 SGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHRTVL 123 SGKSTL+RH+NRLI+PT+GE+ DG++I+ + LR R R+SMVFQ FAL+PH+TVL Sbjct: 67 SGKSTLIRHLNRLIDPTAGEIRVDGEDIMSYSEEQLRKLRRERMSMVFQKFALLPHKTVL 126 Query: 124 QNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAADTD 183 +N + +RG + D KW+ VGL G + ++PHQLSGGM+QRVG+ARAL +D Sbjct: 127 ENAGMAKDIRGYTTSDFEADARKWLARVGLEGNEYQYPHQLSGGMQQRVGIARALVSDAP 186 Query: 184 VILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQVV 243 ++LMDEAFSALDPLIR DMQD LL+LQ L KTIVFITHDLDEAL++ + IL+DG+VV Sbjct: 187 IMLMDEAFSALDPLIRSDMQDLLLELQEELQKTIVFITHDLDEALKLADHLVILKDGEVV 246 Query: 244 QVGTPNDILDNPANDYVARFV 264 Q G P +IL NP + Y+ F+ Sbjct: 247 QQGDPQEILLNPGDPYIVDFI 267 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: 329 Number of extensions: 7 Number of successful extensions: 1 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: 352 Length adjustment: 27 Effective length of query: 248 Effective length of database: 325 Effective search space: 80600 Effective search space used: 80600 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: 48 (23.1 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