Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate AZOBR_RS27935 AZOBR_RS27935 ABC transporter substrate-binding protein
Query= uniprot:D8IZC6 (316 letters) >FitnessBrowser__azobra:AZOBR_RS27935 Length = 317 Score = 107 bits (266), Expect = 5e-28 Identities = 81/266 (30%), Positives = 132/266 (49%), Gaps = 8/266 (3%) Query: 48 AKGAESGAHKINPDAKVTVVSSKYDLNTQVGQIENFIA-NKVDLIVLNAADSKGVGPAVK 106 A+ AE K P+ V +V+++ D+ Q +E+ ++ ++D +V+ +S + V+ Sbjct: 49 AQQAEKRLEKQYPNLDVVIVTAR-DVGRQANDLEDLVSVQRIDALVILPFESAPMTDPVR 107 Query: 107 KAQKAGIVVVAVDVAAAGA---DVTVMSDNTMAGAESCKFLAEKLQGKGNVVIVNGPPVS 163 ++AG V VD D+ V +N G S +F+ EK+ GKG++V++ G P Sbjct: 108 AVKQAGKFVTVVDRGLTDPSIQDLYVAGNNPQMGEVSARFMKEKMGGKGDIVVLRGIPTV 167 Query: 164 AVMDRVTGCKAEFKKSPGIKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTA 223 RV E + + IK+L Q A +RD G M + L+ PKIDAV+A +D A Sbjct: 168 IDNQRVDAFMKEIEGTQ-IKVLG-MQYANWNRDDGFKVMQDFLSRFPKIDAVWAQDDDIA 225 Query: 224 IGAELAIRQAKRSDIKWISGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYAV 283 +G A++QA R +I G G D + + D L A P M AE++ I Sbjct: 226 LGVIEAVKQAGREKEMFILGGAGMKDMIKRVMDKDVLVPADVLYPP-AMIAEAMEITAKH 284 Query: 284 MNGRAPQQKVKLLPVKLITRDNVADY 309 + +AP QK ++ L+T +N A Y Sbjct: 285 LVEKAPIQKEYIIEATLVTPENAAKY 310 Lambda K H 0.314 0.129 0.360 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: 170 Number of extensions: 12 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: 316 Length of database: 317 Length adjustment: 27 Effective length of query: 289 Effective length of database: 290 Effective search space: 83810 Effective search space used: 83810 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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