Align Putative xylitol transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate HSERO_RS05170 HSERO_RS05170 LacI family transcription regulator
Query= uniprot:A0A1N7UEK0 (335 letters) >FitnessBrowser__HerbieS:HSERO_RS05170 Length = 324 Score = 113 bits (283), Expect = 6e-30 Identities = 86/292 (29%), Positives = 143/292 (48%), Gaps = 13/292 (4%) Query: 7 LAATAALSL--LACSIAMAADGKTYKVGAAVYGLKGQFMQNWVRELKEHPAVKDGTVQLT 64 L A LSL A S+ A K +G + G + ++ +K+ A K V L Sbjct: 9 LGAAICLSLGSSAMSLPAFAADKPLTMGFSQVGAESEWRTANTVSIKD--AAKQAGVNLK 66 Query: 65 VFDGNYDALTQNNQIENMVTQRYDAILFVPIDTKAGVGTVKAAMSNDVVVIASN--TKVA 122 D Q I + + Q+ D I F P+ ++ A + + VI ++ V+ Sbjct: 67 FADAQQKQENQVKAIRSFIAQKVDVIAFSPVVESGWETVLREAKAAKIPVILTDRAVNVS 126 Query: 123 DAS--VPYVGNDDVEGGRLQAQAMVDKLN----GKGNVVIIQGPIGQSAQIDREKGELEV 176 D S V ++G+D VE GR + +++K G N+V +QG +G + IDR+ G EV Sbjct: 127 DKSLYVTFIGSDFVEEGRRAGRWLLEKAKSMPAGDINIVELQGTVGSAPAIDRKAGFEEV 186 Query: 177 LGKHPDIKIIEKKTANWDRAQALALTEDWLNAHPKGINGVIAQNDDMALGAVQALKSHGL 236 + P +KII +T ++ RA+ + E +L A K IN + A NDDMA+GA+QA++ G+ Sbjct: 187 IKGEPRLKIIRSQTGDFTRAKGKEVMEAFLKAEGKKINVLYAHNDDMAIGAIQAIEEAGM 246 Query: 237 -TSKDVPVTSIDGMPDAIQAAKKDEVTTFLQDAQAQSQGALDVALRALAGKD 287 KD+ + SIDG+ A +A ++ ++ + + +A AGK+ Sbjct: 247 KPGKDIIIISIDGVKGAFEAMMAGKLNVTVECSPLLGPQLMQIAKDIKAGKE 298 Lambda K H 0.314 0.130 0.373 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: 235 Number of extensions: 15 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: 335 Length of database: 324 Length adjustment: 28 Effective length of query: 307 Effective length of database: 296 Effective search space: 90872 Effective search space used: 90872 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 (21.9 bits) S2: 49 (23.5 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