Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate AO356_23200 AO356_23200 rhizopine-binding protein
Query= uniprot:D8IZC6 (316 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23200 Length = 308 Score = 127 bits (319), Expect = 3e-34 Identities = 101/315 (32%), Positives = 156/315 (49%), Gaps = 17/315 (5%) Query: 3 KNTIAIACSTLLLAAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINPDA 62 K IA +L+L + A A+A K +GV++ + + + + + A + Sbjct: 4 KTRIASLALSLMLTSGA--ALADLK----IGVSMSQFDDTWLTYLRESMDKKAKSLPDGV 57 Query: 63 KVTVVSSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAV---- 118 + ++ D+ Q+ Q+E+FI+ KVD +++N D+ K A AGI +V V Sbjct: 58 TLQFEDARSDVVKQLSQVESFISQKVDALIVNPVDTAATQRITKAAVAAGIPLVYVNRRP 117 Query: 119 -DVAAAGADVTVMSDNTMAGAESCKFLAEKLQGKGNVVIVNGPPV-SAVMDRVTGCKAEF 176 D VTV SD+ AG ++LAEK+ GKGN+VI+ G ++ +R G K Sbjct: 118 DDPKLPEGVVTVASDDLEAGRMQMQYLAEKMGGKGNIVILLGDLANNSTANRTKGVKDVL 177 Query: 177 KKSPGIKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQA-KR 235 K PGIKI Q RD GMT +++ L + AV A ND AIGA +A++QA Sbjct: 178 AKYPGIKI-EQEQTGIWLRDKGMTLVNDWLTQGREFQAVVANNDEMAIGAAMALKQAGTE 236 Query: 236 SDIKWISGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKVKL 295 I+GVDG PD A+K K A S QD G A S+ ++ + P ++ Sbjct: 237 KGSVLIAGVDGTPDGLNAIK--KGEMAVSVFQDAKGQADGSIDTAVKMVK-KQPVEQAVW 293 Query: 296 LPVKLITRDNVADYQ 310 +P +LIT +NV ++ Sbjct: 294 VPYRLITPENVDQFK 308 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: 202 Number of extensions: 10 Number of successful extensions: 6 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: 308 Length adjustment: 27 Effective length of query: 289 Effective length of database: 281 Effective search space: 81209 Effective search space used: 81209 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