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 WP_091519694.1 BM253_RS04260 phosphate ABC transporter ATP-binding protein
Query= uniprot:A0A1N7U8S3 (276 letters) >NCBI__GCF_900115115.1:WP_091519694.1 Length = 248 Score = 115 bits (289), Expect = 7e-31 Identities = 86/257 (33%), Positives = 142/257 (55%), Gaps = 26/257 (10%) Query: 26 KLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQ--PDA--- 80 KL E ++ +GE VLK +S++ + ++ +LIG SG GKST+LR N + PDA Sbjct: 4 KLSAENLNISFGEKHVLKNISVSFAEHEITALIGPSGCGKSTLLRSFNRMHDLFPDAKIN 63 Query: 81 GVITLDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRV 140 G + L+ + + R + +R R+ MVFQ N + ++ ENI Sbjct: 64 GSLHLEELDLYDRHV----------PVTEIRKRIGMVFQKANPFPK-SIYENIAYG---- 108 Query: 141 LDVSAAEAEKRA-RMYLDKVGLPSRVAD--QYPAF-LSGGQQQRVAIARALAMEPEIILF 196 L ++ K + L++ L V + + PA LSGGQQQR+ IARA+A+ PE+IL Sbjct: 109 LKINNLPCNKEVVQKALEEAYLWDEVKNDLKMPATRLSGGQQQRLCIARAVALRPEVILM 168 Query: 197 DEPTSALDPELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGDA 256 DEP SALDP ++ ++I+ L ++ T+++VTH M A++++ + +F++ G V+E G Sbjct: 169 DEPCSALDPVSTLKIEELIKHLKKK-YTIVIVTHNMQQAQRIADKTVFMYLGEVKEEGTT 227 Query: 257 -RILDQPNSERLQQFLS 272 I + P +E ++S Sbjct: 228 DEIFNHPKNEMTANYIS 244 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: 148 Number of extensions: 4 Number of successful extensions: 3 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: 248 Length adjustment: 25 Effective length of query: 251 Effective length of database: 223 Effective search space: 55973 Effective search space used: 55973 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 24 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