Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate AZOBR_RS00685 AZOBR_RS00685 amino acid ABC transporter substrate-binding protein
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__azobra:AZOBR_RS00685 Length = 278 Score = 221 bits (564), Expect = 1e-62 Identities = 124/284 (43%), Positives = 164/284 (57%), Gaps = 9/284 (3%) Query: 3 VKRTTAAKTLIGAVLGAAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPEL 62 VK+ AA L GA++ A+ A+AKDWK + IA EG YAPWN T P GKL GFEP+L Sbjct: 1 VKKIVAALAL-GAIV---AVAGTAAEAKDWKKIRIATEGAYAPWNATDPSGKLIGFEPDL 56 Query: 63 VANLCERIKLQCNLVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPAT 122 LC+RIK +C +VAQDWDGMIP +Q GK+D +M A+SIT EREK+IAF+ PY P+ Sbjct: 57 ALELCKRIKAECEIVAQDWDGMIPAIQQGKYDAIMAAMSITDEREKVIAFAGPYGTEPSM 116 Query: 123 FAVADAKVLPKAA-PGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDG 181 F L KA PG DPKA + AL LKGKT+G+Q+ T+ F+ Sbjct: 117 FGTMKNSPLAKATFPGERYDLSKDDPKA---AIAALADALKGKTVGVQTSTIQANFMEKL 173 Query: 182 FKDIATIRVYKTSPERDLDLANGRIDASFDDVTYYAANIDKKETASIVMAGPKIGGPIWG 241 +A +R Y +D+A GR+DA F D + A + + + GP + G Sbjct: 174 LPQVA-VRTYDKLDNAGIDMAAGRVDAIFGDRSAVDAILKADAGNGMTLFGPAFARGVLG 232 Query: 242 PGEGLAFRKQDADLKAKFDTAISAALADGTVKKLSNKWFKTDVT 285 G G+ RK D DLK F+ AI+ A DGT+ KLS + F D++ Sbjct: 233 KGVGVGLRKADGDLKELFNKAIAEANQDGTITKLSTQHFGYDIS 276 Lambda K H 0.316 0.134 0.396 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: 213 Number of extensions: 10 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: 286 Length of database: 278 Length adjustment: 26 Effective length of query: 260 Effective length of database: 252 Effective search space: 65520 Effective search space used: 65520 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