Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate WP_008990494.1 I215_RS03100 D-xylose transporter XylE
Query= TCDB::P15729 (468 letters) >NCBI__GCF_000300875.1:WP_008990494.1 Length = 543 Score = 292 bits (747), Expect = 2e-83 Identities = 182/432 (42%), Positives = 261/432 (60%), Gaps = 38/432 (8%) Query: 51 TDSLLTGLSVSLALLGSALGAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLP-----F 105 T+S+L G VS AL+G +GA +A+ GR +++AA LF +S+ GSG P F Sbjct: 121 TNSIL-GFMVSSALVGCIIGASLGDRVANSVGRRNGLLIAAFLFFISAAGSGYPELLNPF 179 Query: 106 TIWD---FIFWRVLGGIGVGAASVIAPAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLS 162 + D FI +R++GGIGVG AS++AP YIAE++PA++RG+L S QLAIV G+ I Sbjct: 180 SSGDLSTFIVYRIIGGIGVGLASMLAPLYIAEMAPANIRGKLVSCNQLAIVGGMLIVYFV 239 Query: 163 NWFIALMAGGSAQNPWLFGAAAWRWMFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKA 222 N+FI + G S Q W+ WR+MF +E IPA+L+ + F +P++PR+ V +G E A Sbjct: 240 NYFI--VKGQSDQ--WI-NTIGWRYMFLSECIPAVLFLISLFFVPKTPRFQVLKGNDEAA 294 Query: 223 AAILWKVEGGDVPSRIEEIQATVSLDHKPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGI 282 L K G PS+ I + K + + LS G I+ IG+ LS QQFVGI Sbjct: 295 IETLTKYNG---PSKASLILTEIKRSFKIKKAPWLSYGWG---IIIIGLLLSVFQQFVGI 348 Query: 283 NVIFYYSSVLWRSVGFTEEKSLLITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMT 342 NV+ YY+ +++ +G + S+L T+I G IN++ T++AI VDKFGRK L+ +GS+ M Sbjct: 349 NVVLYYAPEIFKGMGMKTDASMLQTIIVGIINLIFTVIAIFTVDKFGRKKLMFIGSVIMA 408 Query: 343 ITLGILSVVFGGATVVNGQPTLTGAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNK 402 +++ G TV+ Q T G+ AL+ LY+ +F SWGP+ WVLL E+F NK Sbjct: 409 VSM------IGLGTVLYSQDT-----GMAALLLMLLYIAAFAVSWGPVTWVLLSEIFPNK 457 Query: 403 IRAAALSVAAGVQWIANFIISTTFPP------LLDTVGLGPAYGLYATSAAISIFFIWFF 456 I+ A+++A VQW+AN ++S TFP L +T G AY +Y A +S FI F Sbjct: 458 IK-GAMAIAVAVQWLANLLVSWTFPMMNNNTYLTETFHNGFAYWVYGIMAVLSGIFILKF 516 Query: 457 VKETKGKTLEQM 468 V ETKGKTLE+M Sbjct: 517 VPETKGKTLEEM 528 Lambda K H 0.325 0.140 0.430 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: 661 Number of extensions: 36 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 468 Length of database: 543 Length adjustment: 34 Effective length of query: 434 Effective length of database: 509 Effective search space: 220906 Effective search space used: 220906 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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