Align Dicarboxylate (succinate, fumarate, malate) transporter, vcINDY (characterized)
to candidate 7023217 Shewana3_0451 anion transporter (RefSeq)
Query= TCDB::Q9KNE0 (462 letters) >FitnessBrowser__ANA3:7023217 Length = 466 Score = 539 bits (1388), Expect = e-158 Identities = 273/445 (61%), Positives = 346/445 (77%), Gaps = 4/445 (0%) Query: 20 RNSLIVLADVALFLALYHFLPFEHNVVLGISMLAFIAVLWLTEALHVTVTAILVPVMAVF 79 + LI++AD+ L ALY+ LPF+ V G+++L F A+LWLTEA+H+++TAILVP++AVF Sbjct: 23 KKMLILVADIFLLFALYYGLPFDQGVNTGLAILVFAAILWLTEAIHISITAILVPILAVF 82 Query: 80 FGIFETQAALNNFANSIIFLFLGGFALAAAMHHQGLDKVIADKVLAMAQGKMSVAVFMLF 139 FG+FET+ A++NFAN II+LF GGF LAAA+HHQ +D +IA K+L ++GK+S+A MLF Sbjct: 83 FGVFETKEAMSNFANPIIYLFFGGFVLAAALHHQKIDTLIAQKLLLASKGKLSIACLMLF 142 Query: 140 GVTALLSMWISNTATAAMMLPLVLGVLSKVDADKQRSTYVFVLLGVAYSASIGGIATLVG 199 GVTALLSMWISNTAT AMMLPL LG+L ++D STYVF+LLG+AYSA+IGGI TLVG Sbjct: 143 GVTALLSMWISNTATTAMMLPLALGILQQLDRKLYHSTYVFLLLGIAYSANIGGIGTLVG 202 Query: 200 SPPNAIAAAEVGLSFTDWMKFGLPTAMMMLPMAIAILYFLLKPTLNGMFELDRAPVNWDK 259 SPPNAIAAA+VGLSF+DW+KFG+PT ++MLPM + LY+ KP L+ EL Sbjct: 203 SPPNAIAAAQVGLSFSDWLKFGIPTVILMLPMMLLALYWYFKPDLSAKCELAVEDQKLTF 262 Query: 260 GKVVTLGIFGLTVFLWIFSSPINAALGGFKSFDTLVALGAILMLSFARVVHWKEIQKTAD 319 +TL IF TV WIFS P+ ALGG FDT+VALGA+++L+ +V WK+I+ T D Sbjct: 263 QGKLTLVIFLATVCCWIFSVPLAKALGGITQFDTVVALGAVVLLAGLGLVGWKKIESTTD 322 Query: 320 WGVLLLFGGGLCLSNVLKQTGTSVFLANALSDMV--SHMGIFVVILVVATFVVFLTEFAS 377 WGVL+LFGGGL LS VLK TGTSVFLA+ ++D+ +HM +FV V FVV LTEFAS Sbjct: 323 WGVLILFGGGLTLSAVLKSTGTSVFLAHWMTDIFGSTHMSLFV--FAVIAFVVMLTEFAS 380 Query: 378 NTASAALLIPVFATVAEAFGMSPVLLSVLIAVAASCAFMLPVATPPNAIVFASGHIKQSE 437 NTASAALL+PVFA +AEA G+SPV+LSVLI +AASCAFMLPVATPPNAIV+ SGHIKQSE Sbjct: 381 NTASAALLVPVFAAIAEALGVSPVMLSVLIGIAASCAFMLPVATPPNAIVYGSGHIKQSE 440 Query: 438 MMRVGLYLNIACIGLLTAIAMLFWQ 462 M+RVG+ +N + +L IA FW+ Sbjct: 441 MVRVGMIINFLSMIVLGIIAHTFWE 465 Lambda K H 0.329 0.139 0.417 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: 705 Number of extensions: 26 Number of successful extensions: 6 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: 462 Length of database: 466 Length adjustment: 33 Effective length of query: 429 Effective length of database: 433 Effective search space: 185757 Effective search space used: 185757 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