Align 2-Deoxy-D-ribose porter, DeoP (characterized)
to candidate BWI76_RS22920 BWI76_RS22920 MFS transporter
Query= TCDB::Q8XEV7 (438 letters) >lcl|FitnessBrowser__Koxy:BWI76_RS22920 BWI76_RS22920 MFS transporter Length = 436 Score = 257 bits (656), Expect = 6e-73 Identities = 144/419 (34%), Positives = 232/419 (55%), Gaps = 3/419 (0%) Query: 15 NKTPLFQFILLSCLFPLWGCAAALNDILITQFKSVFSLSNFASALVQSAFYGGYFLIAIP 74 +K + F LL LF LW A LNDIL+ QF+ F+L+NF + L+QSAFY GYF+I IP Sbjct: 19 SKRYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFVIPIP 78 Query: 75 ASLVIKKTSYKVAILIGLTLYIVGCTLFFPASHMATYTMFLAAIFAIAIGLSFLETAANT 134 A +++KK SYK I+ GL LY G LF+PA+ + YT+FL +F IA GL LETAAN Sbjct: 79 AGILMKKLSYKAGIITGLFLYAFGAALFWPAAEVMNYTLFLIGLFIIAAGLGCLETAANP 138 Query: 135 YSSMIGPKAYATLRLNISQTFYPIGAAAGILLGKYLVFSE-GESLEKQMAGMNAEQVHNF 193 + +++GP++ RLN++QTF GA ++ G+ L+ S + + M EQ+ + Sbjct: 139 FVTVLGPESGGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMAPEQLSAY 198 Query: 194 KVLMLENTLEPYKYMIMVLVVVMVLFLLTRFPTCKVAQTASHKRPSALDTLRYLASNARF 253 K ++ + PY ++ V+++V +L +LT+FP + + + S +L L + Sbjct: 199 KHSLVLSVQTPYMIIVAVVLLVALLIMLTKFPALQSDDHSDATQSSFSASLARLVRVRHW 258 Query: 254 RRGIVAQFLYVGMQVAVWSFTIRLAL-ELGDINERDASTFMVYSFACFFIGKFIANILMT 312 R ++AQF YVG Q A WS+ IR A+ E+ + A+ ++ + CFFIG+F L++ Sbjct: 259 RWAVLAQFCYVGAQTACWSYLIRYAIEEIPGMTPGFAANYLTGTMVCFFIGRFSGTWLIS 318 Query: 313 RFNPEKVLILYSVIGALFLAYVALAPSFSAVYVAVLVSVLFGPCWATIYAGTLDTVDNEH 372 RF P KVL Y+++ + A + L S + TI++ + + + Sbjct: 319 RFAPHKVLAAYALLSMILCLISAFTGGHVGLLALTLCSAFMSIQYPTIFSLGIKNL-GQD 377 Query: 373 TEMAGAVIVMAIVGAAVVPAIQGYVADMFHSLQLSFLVSMLCFVYVGVYFWRESKVRGN 431 T+ + IVM I+G +V + G+V+D ++ + LV LCF + ++ S+ N Sbjct: 378 TKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELVPALCFAVIFIFARFRSQTAAN 436 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: 460 Number of extensions: 25 Number of successful extensions: 4 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: 436 Length adjustment: 32 Effective length of query: 406 Effective length of database: 404 Effective search space: 164024 Effective search space used: 164024 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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