Align 2-Deoxy-D-ribose porter, DeoP (characterized)
to candidate BWI76_RS23685 BWI76_RS23685 MFS transporter
Query= TCDB::Q8XEV7 (438 letters) >FitnessBrowser__Koxy:BWI76_RS23685 Length = 444 Score = 333 bits (855), Expect = 5e-96 Identities = 179/416 (43%), Positives = 261/416 (62%), Gaps = 6/416 (1%) Query: 13 YLNKTPLFQFILLSCLFPLWGCAAALNDILITQFKSVFSLSNFASALVQSAFYGGYFLIA 72 YL TP QF+L+ CLF LWG A LNDILI QFK F L++ +ALVQS F+ GYF +A Sbjct: 24 YLPHTPWLQFLLVCCLFALWGMAGNLNDILIAQFKKGFDLTDTQTALVQSIFFLGYFFVA 83 Query: 73 IPASLVIKKTSYKVAILIGLTLYIVGCTLFFPASHMATYTMFLAAIFAIAIGLSFLETAA 132 +PA+ +IK+ SYK AI+IGL LY +GC LF PA+ + TY FLA + IA GLSFLET+A Sbjct: 84 LPAAALIKRYSYKAAIIIGLCLYALGCFLFVPAAQIMTYGAFLACLGVIACGLSFLETSA 143 Query: 133 NTYSSMIGPKAYATLRLNISQTFYPIGAAAGILLGKYLVFSEGESLEKQMAGMNAEQVHN 192 NTYSS++GP +T R+N SQ F +G +G+L+G+ +VF E + +Q+ M A Sbjct: 144 NTYSSLLGPIQSSTQRINFSQIFNSLGVISGVLIGQVMVFGENDPSHEQLLAMPAAAADA 203 Query: 193 FKVLMLENTLEPYKYMIMVLVVVMVLFLLTRFPTCKVAQTASHKRP--SALDTLRYLASN 250 + M+ + PY + VLVV+ ++F+ +FP+CK + + P S TL+ L + Sbjct: 204 ARHQMVGQVVGPYLIIGSVLVVLALVFVFIKFPSCKGTPSQQQQIPTESMGSTLKRLFAI 263 Query: 251 ARFRRGIVAQFLYVGMQVAVWSFTIR-LALELGDINERDASTFMVYSFACFFIGKFIANI 309 RFR GI++QFLYVG QV VWSFTIR + L +E A+ +++ S + +GK +A Sbjct: 264 PRFRLGILSQFLYVGAQVGVWSFTIRFVQLVQQGTSEHSATYWLLASLVIYAVGKTVATW 323 Query: 310 LMTRFNPEKVLILYSVIGALFLAYVALAPSFSAVYVAVLVSVLFGPCWATIYAGTLDTVD 369 LM R NP +L +++ + L + S AVY +LVS PCW T + + + Sbjct: 324 LMNRLNPALLLGTFALAATVLLLIAVFSSSMLAVYALILVSFCMAPCWPTNFGLVIKGMG 383 Query: 370 NEHTEMAGAVIVMAIVGAAVVPAIQGYVADM-FHSLQLSFLVSMLCFVYVGVY-FW 423 + T+ AG+++VM+I+G AV+P + G ++DM ++Q++F+ +LCFVYV Y FW Sbjct: 384 KD-TQTAGSIVVMSIIGGAVIPLVMGIISDMNGGNMQIAFIAPLLCFVYVAFYGFW 438 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: 464 Number of extensions: 31 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: 444 Length adjustment: 32 Effective length of query: 406 Effective length of database: 412 Effective search space: 167272 Effective search space used: 167272 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