Align Putative xylitol transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_106714416.1 CU102_RS28790 sugar ABC transporter substrate-binding protein
Query= uniprot:A0A1N7UEK0 (335 letters) >NCBI__GCF_003010955.1:WP_106714416.1 Length = 309 Score = 133 bits (334), Expect = 7e-36 Identities = 88/288 (30%), Positives = 147/288 (51%), Gaps = 15/288 (5%) Query: 7 LAATAALSLLACSIAMAADGKTYKVGAAVYGLKGQFMQNWVRELKEHPAVKDGTVQLTVF 66 L T A+S L S A AA+ +G ++ F+ ++++ DG V L V Sbjct: 4 LLMTVAVSALMSSSAFAAN-----IGVSMALFDDNFLTVLRNGMQDYAKTLDG-VTLQVE 57 Query: 67 DGNYDALTQNNQIENMVTQRYDAILFVPIDTKAGVGTVKAAMSNDVVVIASNTKVADASV 126 D D Q +QI+N + + DAI+ P+DT A K A + ++ N + + + Sbjct: 58 DAQNDVAKQQSQIQNFIASKVDAIIVNPVDTDATAAMSKIAAEAGIPLVYVNREPVNVNE 117 Query: 127 -----PYVGNDDVEGGRLQAQAMVDKLNGKGNVVIIQGPIGQSAQIDREKGELEVLGKHP 181 +V +++VE G L+ + + L GKG +V++ G + A R K +V+ Sbjct: 118 LPEKQAFVASNEVESGTLETKEVCRLLKGKGKIVVMMGELSNQAARQRTKDIHDVIATDE 177 Query: 182 --DIKIIEKKTANWDRAQALALTEDWLNAHPKGINGVIAQNDDMALGAVQALKSHGLTSK 239 ++I+E++TANW R Q L +WL+A + + V++ ND+MA+GA+QALK+ G + Sbjct: 178 CKGLEIVEEQTANWSRTQGADLMTNWLSAGLE-FDAVVSNNDEMAIGAIQALKAAGRSMD 236 Query: 240 DVPVTSIDGMPDAIQAAKKDEV-TTFLQDAQAQSQGALDVALRALAGK 286 V V +D DA+ A ++ T Q+A Q QGA+D AL+ G+ Sbjct: 237 SVVVGGVDATQDALAAMSAGDLDVTVFQNAAGQGQGAVDAALKLSKGE 284 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: 252 Number of extensions: 15 Number of successful extensions: 5 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: 309 Length adjustment: 28 Effective length of query: 307 Effective length of database: 281 Effective search space: 86267 Effective search space used: 86267 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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