Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate H281DRAFT_04150 H281DRAFT_04150 monosaccharide ABC transporter substrate-binding protein, CUT2 family
Query= uniprot:D8IZC6 (316 letters) >FitnessBrowser__Burk376:H281DRAFT_04150 Length = 317 Score = 173 bits (438), Expect = 6e-48 Identities = 110/296 (37%), Positives = 169/296 (57%), Gaps = 9/296 (3%) Query: 15 LAAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINPDAKVTVVSSKYDLN 74 L+ A PA A PLK +G+T +L NP+FV + K A + A V V + +D++ Sbjct: 28 LSMIAVPAAQA-APLK-IGMTFQELNNPYFVTMQKALNDAA--ASTGATVIVTDAHHDVS 83 Query: 75 TQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDVAAAG-ADVTVMSDN 133 QV +E+ + K+D++++N DS G+ AV A+KAG+VVVAVD A G D V S N Sbjct: 84 KQVSDVEDMLQKKIDILLVNPTDSTGIQSAVTSAKKAGVVVVAVDANANGPVDSFVGSKN 143 Query: 134 TMAGAESCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKSPGIKILSDNQNAGG 193 AG +C++L++ + G G V I++G PV +++RV GCKA KSPG+K++ D QN Sbjct: 144 FDAGQMACEYLSKSIGGSGEVAILDGIPVVPILERVRGCKAALAKSPGVKLV-DTQNGKQ 202 Query: 194 SRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIKWISGVDGAPDAERA 253 R ++ N++ A P + VF++ND ++GA AI ++ DIK ++ VDGAP+A A Sbjct: 203 ERATALSVTENMIQAHPNLKGVFSVNDGGSMGALSAI-ESSGKDIK-LTSVDGAPEAIAA 260 Query: 254 LKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKVKLLPVKLITRDNVADY 309 ++ S F + AQ P ++ I YA G A K + VK+I + N + Sbjct: 261 IQKPNSKFVETSAQFPADQVRIALGIAYAKKWG-ANVPKAIPVDVKMIDKSNAKGF 315 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: 208 Number of extensions: 13 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: 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