Align 2-Deoxy-D-ribose porter, DeoP (characterized)
to candidate 6937507 Sama_1663 glucose/galactose transporter (RefSeq)
Query= TCDB::Q8XEV7 (438 letters) >FitnessBrowser__SB2B:6937507 Length = 415 Score = 191 bits (484), Expect = 5e-53 Identities = 127/405 (31%), Positives = 209/405 (51%), Gaps = 26/405 (6%) Query: 20 FQFILLSCLFPLWGCAAALNDILITQFKSVFSLSNFASALVQSAFYGGYFLIAIPASLVI 79 F L+ LF +WG LNDILI K+VFSL+ + L+Q F+G YFL+++PA +++ Sbjct: 22 FALTSLTTLFFMWGFITCLNDILIPHLKAVFSLNYAQAMLIQFCFFGAYFLVSVPAGVLV 81 Query: 80 KKTSYKVAILIGLTLYIVGCTLFFPASHMATYTMFLAAIFAIAIGLSFLETAANTYSSMI 139 K+ Y+ I++GL +GC LF+PA+ ATY +FL A+F +A G++ L+ AAN Y + + Sbjct: 82 KRLGYQKGIVVGLLTAALGCGLFYPAAVSATYGVFLGALFVLASGITVLQVAANPYVTAL 141 Query: 140 GPKAYATLRLNISQTFYPIGAAAGILLGKYLVFSEGESLEKQMAGMNAEQVHNFKVLMLE 199 GP A+ RL ++Q F +G G L+ S G +AE + L Sbjct: 142 GPVQTASSRLTLTQAFNSLGTTIAPAFGSVLILSVA-------VGASAEAEADAVKL--- 191 Query: 200 NTLEPYKYMIMVLVVVMVLFLLTRFPTCKVAQTASHKRPSALDTLRYLASNARFRRGIVA 259 PY + +L+V+ V+F L + P + T + ++ G + Sbjct: 192 ----PYLLLCGMLIVLAVVFALLKLP------HIHDQEDEVAATGQSALAHRHLVLGAIG 241 Query: 260 QFLYVGMQVAVWSFTIRLALE--LGDINERDASTFMVYSFACFFIGKFIANILMTRFNPE 317 F+YVG +VA+ SF + E + + E DA+ ++ + + +G+FI +M + + Sbjct: 242 IFVYVGGEVAIGSFLVNFLGESHVAGMAEADAAHYIAFYWGGAMVGRFIGAAVMQKVDAG 301 Query: 318 KVLILYSVIGALFLAYVALAPSFSAVYVAVLVSVLFGP-CWATIYAGTLDTVDNEHTEMA 376 KVL + + AL L VA+ S + A+L LF + TI++ L + T Sbjct: 302 KVLGFNATMAAL-LVLVAMNSSGALAMWAILAVGLFNSIMFPTIFSLALKNL-GPATAQG 359 Query: 377 GAVIVMAIVGAAVVPAIQGYVADMFHSLQLSFLVSMLCFVYVGVY 421 ++ +AIVG A+VP +QG +AD L SF++ +LC+ Y+ Y Sbjct: 360 SGILCLAIVGGALVPLLQGLLADSV-GLSASFILPVLCYGYILFY 403 Lambda K H 0.329 0.139 0.412 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: 401 Number of extensions: 22 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: 438 Length of database: 415 Length adjustment: 32 Effective length of query: 406 Effective length of database: 383 Effective search space: 155498 Effective search space used: 155498 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 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