Align Putative xylitol transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate SM_b20072 SM_b20072 rhizopine binding protein
Query= uniprot:A0A1N7UEK0 (335 letters) >FitnessBrowser__Smeli:SM_b20072 Length = 309 Score = 125 bits (315), Expect = 1e-33 Identities = 87/297 (29%), Positives = 145/297 (48%), Gaps = 18/297 (6%) Query: 7 LAATAALSLLACSIAMAADGKTYKVGAAVYGLKGQFMQNWVRELKEHPAVKDGTVQLTVF 66 L + A L+L A S VG + F+ +++ A DG V + V Sbjct: 4 LLSAAVLALFAGS------AHAENVGITIARSDSAFLTILRNGMQDQAAKLDG-VTVQVE 56 Query: 67 DGNYDALTQNNQIENMVTQRYDAILFVPIDTKAGVGTVKAAMSNDVVVIASNTKVADA-- 124 D D Q +Q++N V+ DAI+ V +D + K A + ++ +N AD Sbjct: 57 DAQNDTSRQLDQVQNFVSSGVDAIIVVAVDGDSTPALTKMATDAGIPIVYANHPPADVDK 116 Query: 125 ---SVPYVGNDDVEGGRLQAQAMVDKLNGKGNVVIIQGPIGQSAQIDREKGELEVLGKHP 181 + +VG+++++ G L+ + + L GKG ++ GP+ + + R K +V+ Sbjct: 117 LPETAAFVGSNEIDSGTLETKEVCRLLGGKGAAYVLMGPLNNHSSLTRTKDIHDVIATDE 176 Query: 182 --DIKIIEKKTANWDRAQALALTEDWLNAHPKGINGVIAQNDDMALGAVQALKSHGLTSK 239 + +IE+++ANWDR +A + +WL+ + N +IA ND+MA+GA+QA+K+ G+ Sbjct: 177 CKGMSVIEEQSANWDRLEAANIMTNWLSTG-REFNAIIANNDEMAIGAIQAMKAAGVDMS 235 Query: 240 DVPVTSIDGMPDAIQA-AKKDEVTTFLQDAQAQSQGALDVALRALAGKDYKPQSVIW 295 V V ID PD + A A D T Q+A AQ A+D A+ +D K IW Sbjct: 236 KVVVGGIDATPDGLAAMAAGDLDVTVFQNAIAQGAAAMDAAV--ALSRDQKTARQIW 290 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: 261 Number of extensions: 20 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 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