Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate 5210878 Shew_3304 ABC transporter-related protein (RefSeq)
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__PV4:5210878 Length = 292 Score = 133 bits (335), Expect = 4e-36 Identities = 83/261 (31%), Positives = 146/261 (55%), Gaps = 13/261 (4%) Query: 12 PVDEPVAQPVTAAIKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRC 71 P+++ + V +++ G + G H + VSL +G V +++G SG GK+T+L+ Sbjct: 18 PMEQAPMEHVQPLVEISHLGFSR--GTHVIYDDVSLTIPRGKVTAIMGPSGIGKTTLLKL 75 Query: 72 INFLEQPDAGVITLDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLE 131 I +PD+GVI +DG+ + ++ +L LR R++M+FQ L++ M V + Sbjct: 76 IGGQLRPDSGVIKVDGVDVHKC---------NRSELFALRKRMSMLFQSGALFTDMNVFD 126 Query: 132 NITMAPRRVLDVSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEP 191 N+ A R D+ A + M L+ VGL A P+ LSGG Q+R A+ARA+A+EP Sbjct: 127 NVAFALREHSDLPEAIIRRIVLMKLEAVGLRG-AAQMMPSELSGGMQRRAALARAIALEP 185 Query: 192 EIILFDEPTSALDPELVGEVLKVIQTLAEE-GRTMLMVTHEMGFARQVSSQVLFLHQGRV 250 E++L+DEP + DP +G ++K+I+ L++ T ++V+H++ ++ V L +V Sbjct: 186 ELVLYDEPFAGQDPISMGVLVKLIRELSDALSLTSVVVSHDVQEVLGIADYVYVLADKKV 245 Query: 251 EEHGDARILDQPNSERLQQFL 271 HG L ++ +L+QF+ Sbjct: 246 IAHGTPAELKAADNPKLKQFI 266 Lambda K H 0.319 0.133 0.372 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: 171 Number of extensions: 9 Number of successful extensions: 4 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: 276 Length of database: 292 Length adjustment: 26 Effective length of query: 250 Effective length of database: 266 Effective search space: 66500 Effective search space used: 66500 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 (21.8 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