Align 2-Deoxy-D-ribose porter, DeoP (characterized)
to candidate BWI76_RS22920 BWI76_RS22920 MFS transporter
Query= TCDB::Q8XEV7 (438 letters) >FitnessBrowser__Koxy:BWI76_RS22920 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:
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