Align Xylose ABC transporter, periplasmic xylose-binding protein XylF (characterized, see rationale)
to candidate H281DRAFT_02705 H281DRAFT_02705 monosaccharide ABC transporter substrate-binding protein, CUT2 family
Query= uniprot:A0A0C4Y591 (325 letters) >FitnessBrowser__Burk376:H281DRAFT_02705 Length = 365 Score = 113 bits (283), Expect = 6e-30 Identities = 97/314 (30%), Positives = 152/314 (48%), Gaps = 23/314 (7%) Query: 19 TGAAAQSAPDAAPASAAAQRPLKKVGVTLGSLGNPYFVALAHGAEAAAKKINPDAKVTVL 78 T A SAP +AP A A KVG ++ +L N +FV L G E AK+ D T Sbjct: 43 TSGQAASAPASAPV-ANASGGKTKVGFSVSTLNNAFFVGLKAGVEKGAKEQGFDLVQT-- 99 Query: 79 SADYDLNKQFSHIDSFIVSKVDLILINAADARAIEPAVRKARKAGIVVVAVDVAAAGADA 138 +A+ D +Q + + + V +++N D++AI PAV KA I V +D + G Sbjct: 100 NANGDAQQQVNDAINLLSQGVTALVLNPIDSKAIIPAVEKANSMNIPVFMLDRGSDGGKV 159 Query: 139 T--VQTDNTRAGELACAFLAGRL-----GGRGNLIIQNG-PPVSAVLDRVKGCKMVLGKH 190 T V +DN G+ A ++A +L +GN++ G +A DR KG + K+ Sbjct: 160 TSFVASDNVALGQTAAKWIADQLTKRYGSAKGNVVDLIGLVGTTAATDREKGFSDEIAKY 219 Query: 191 PGIHVLSDDQDGKGSREGGLNVMQLYLTRFPKIDAVFTINDPQAVGADLAARQLNR---- 246 P I V++ Q+G +E LN M L ++P+IDAVF ND VGA+ A R Sbjct: 220 PDIKVVAR-QEGAFDQEKSLNAMTNILQKYPQIDAVFGANDDNTVGAEKAIDNAGRYKPL 278 Query: 247 ---GGILIASVDGAPDIEAALKANTLVQASASQDPWAIARTAVE-IGVGLMHGQAPANRT 302 IL+ DG +A++A A+ SQ+P +A +++ + + PAN Sbjct: 279 GDKQHILVIGADGTAQALSAIRAGK-QDATISQNPIQMAAKSLQFVADYSAKKEVPAN-- 335 Query: 303 VLLPPTLVTRANVN 316 P L+ ++N++ Sbjct: 336 YAWPTLLIDKSNID 349 Lambda K H 0.318 0.132 0.377 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: 232 Number of extensions: 6 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 325 Length of database: 365 Length adjustment: 29 Effective length of query: 296 Effective length of database: 336 Effective search space: 99456 Effective search space used: 99456 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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