Align 2-Deoxy-D-ribose porter, DeoP (characterized)
to candidate 7025147 Shewana3_2310 glucose/galactose transporter (RefSeq)
Query= TCDB::Q8XEV7 (438 letters) >FitnessBrowser__ANA3:7025147 Length = 423 Score = 211 bits (537), Expect = 4e-59 Identities = 130/417 (31%), Positives = 221/417 (52%), Gaps = 25/417 (5%) Query: 20 FQFILLSCLFPLWGCAAALNDILITQFKSVFSLSNFASALVQSAFYGGYFLIAIPASLVI 79 F + L+ LF +WG LNDILI K+VFSL+ + L+Q F+G YFL++IPA ++ Sbjct: 24 FALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCFFGAYFLVSIPAGQLV 83 Query: 80 KKTSYKVAILIGLTLYIVGCTLFFPASHMATYTMFLAAIFAIAIGLSFLETAANTYSSMI 139 K+ Y+ I+ GL + +GC LF+PA+ ATY +FL A+F +A G++ L+ AAN Y + + Sbjct: 84 KRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASGITILQVAANPYVNAL 143 Query: 140 GPKAYATLRLNISQTFYPIGAAAGILLGKYLVFSEGESLEKQMAGMNAEQVHNFKVLMLE 199 G A+ RLN++Q F +G G L+ S S+ ++A NAE +V+ L Sbjct: 144 GSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAASVSSELAQANAEA----EVVKL- 198 Query: 200 NTLEPYKYMIMVLVVVMVLFLLTRFPTCKVAQTASHKRPSALDTLRYLASNARFRR---- 255 PY + L V+ ++F P + H + +A + +L + + Sbjct: 199 ----PYLLLAAALAVLAIIFAKLDLPVIR-----EHSQAAAEEVQTHLGKTSALQSMHLV 249 Query: 256 -GIVAQFLYVGMQVAVWSFTIRLALE--LGDINERDASTFMVYSFACFFIGKFIANILMT 312 G V F+YVG +V++ SF + E + + E A+ ++ Y + +G+FI + +M Sbjct: 250 LGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVGRFIGSAVMQ 309 Query: 313 RFNPEKVLILYSVIGALFLAYVALAPSFSAVYVAVLVSVLFGP-CWATIYAGTLDTVDNE 371 + P ++ ++ A L VA+ S S A+L LF + TI++ L + Sbjct: 310 KI-PAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSLALRDL-GP 367 Query: 372 HTEMAGAVIVMAIVGAAVVPAIQGYVADMFHSLQLSFLVSMLCFVYVGVYFWRESKV 428 HT ++ +AIVG A+VP +QG +AD +QL+F++ ++C+ ++ Y + SK+ Sbjct: 368 HTSQGSGILCLAIVGGAIVPLLQGVLADNL-GIQLAFILPVVCYGFILFYGAKGSKM 423 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: 392 Number of extensions: 15 Number of successful extensions: 3 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: 423 Length adjustment: 32 Effective length of query: 406 Effective length of database: 391 Effective search space: 158746 Effective search space used: 158746 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