Align Putative amino-acid binding periplasmic protein (characterized, see rationale)
to candidate AZOBR_RS15685 AZOBR_RS15685 ABC transporter substrate-binding protein
Query= uniprot:Q92PA9 (260 letters) >FitnessBrowser__azobra:AZOBR_RS15685 Length = 266 Score = 105 bits (262), Expect = 1e-27 Identities = 82/266 (30%), Positives = 128/266 (48%), Gaps = 17/266 (6%) Query: 1 MRISRRLAATA---SAAVFVLMAGVAMAEGE-----KVVIGTEGAYPPFNNLESDGTLTG 52 + I+RRLA +AAV + + A E K+ IG +PPF +DG G Sbjct: 3 LSITRRLAVAGVMMAAAVALAVPAAAQTVDEIKSKGKLTIGMLVDFPPFGITTADGKPDG 62 Query: 53 FDIDIAKALCEEMKAECTFVTQDWDGIIPALIAKKFDAIVASMSITEERKQQVDFTNKYY 112 +D D+AK L + M V IP L+ K D +VAS+ IT R +QV F+ Y Sbjct: 63 YDADVAKLLGKHMGVPVEIVPVTGPNRIPYLLTNKVDLLVASLGITPARAEQVQFSEPYA 122 Query: 113 NTPPAIVVPKDSPITEATAAALSGKALGAQGSTTHSNYAEA-HMKESEVKLYPTADEYKL 171 +V P ++ I E AA LSGK +G ++T N A K++ + + Sbjct: 123 AIEIGLVAPANTKIKE--AAELSGKRIGVARASTQDNALTAVAPKDARIMRFDDDASAVQ 180 Query: 172 DLANGRIDAAIDDVVVLSEWLKTEDGACCKLLGTLPIDPVINGEGAGIAIRKGDDALREK 231 + +G++DA VV E K A + V+N + GIA+RKG DAL + Sbjct: 181 AMLSGQVDALGLSNVVTKEIKKLAPQA------NYEMKFVLNRQVQGIAMRKGQDALLKW 234 Query: 232 LNKAIEAIRANGKYKQINEKYFPFDV 257 +N+ IE ++NG+ ++++K+ D+ Sbjct: 235 VNEFIETAKSNGELNEVHKKWLGTDL 260 Lambda K H 0.315 0.132 0.377 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: 175 Number of extensions: 11 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: 260 Length of database: 266 Length adjustment: 25 Effective length of query: 235 Effective length of database: 241 Effective search space: 56635 Effective search space used: 56635 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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