Align Dicarboxylate (succinate, fumarate, malate) transporter, vcINDY (characterized)
to candidate WP_046007904.1 OLEAN_RS02400 anion transporter
Query= TCDB::Q9KNE0 (462 letters) >NCBI__GCF_000967895.1:WP_046007904.1 Length = 443 Score = 380 bits (977), Expect = e-110 Identities = 195/417 (46%), Positives = 286/417 (68%), Gaps = 6/417 (1%) Query: 48 GISMLAFIAVLWLTEALHVTVTAILVPVMAVFFGIFETQAALNNFANSIIFLFLGGFALA 107 G+ +L+ IA WL E ++VTA+LVPV+AV F + + + AL +FA+ IIFLFLGGFALA Sbjct: 29 GLIILSLIAHAWLAELFPLSVTALLVPVLAVAFNVMDLKVALLSFAHPIIFLFLGGFALA 88 Query: 108 AAMHHQGLDKVIADKVLAMAQGKMSVAVFMLFGVTALLSMWISNTATAAMMLPLVLGVLS 167 A +H LD+ A ++ A+ V +LF +TA LSMWISNTAT MMLP+ LG++S Sbjct: 89 ATLHEHKLDQHFAHILMLKAKNNGLVICLILFSLTAFLSMWISNTATTVMMLPIALGLMS 148 Query: 168 KVDADKQRSTYVFVLLGVAYSASIGGIATLVGSPPNAIAAAEVGLSFTDWMKFGLPTAMM 227 ++ +K ++ + F+LLG+AYSA+IGGIAT+VGSPPNAIAA+ +GLSF +W+ LP +++ Sbjct: 149 HLEYEKHKTVFAFLLLGIAYSANIGGIATIVGSPPNAIAASALGLSFYEWLIIALPISLV 208 Query: 228 MLPMAIAILYFLLKPTLNGMFELDRAPVN---WDKGKVVTLGIFGLTVFLWIFSSPINAA 284 +LP+ ILY LKP L +F+ + A V W + +++ + IF T LWIF I Sbjct: 209 LLPLMWGILYTYLKPNLT-LFKSEIAEVQSFAWSRQRILAIIIFITTASLWIFGDFIQGI 267 Query: 285 LGGFKSFDTLVALGAILMLSFARVVHWKEIQKTADWGVLLLFGGGLCLSNVLKQTGTSVF 344 LG FD+ +A+ AI++L ++ + WK + WGVLLLFGGGL LS VL TG +++ Sbjct: 268 LGKIADFDSWIAIIAIVVLHASKSLSWKAFENNTQWGVLLLFGGGLALSAVLSATGANLY 327 Query: 345 LANALSDMVSHMGIFVVILVVATFVVFLTEFASNTASAALLIPVFATVAEAFGMSPVLLS 404 LA L + + + ++ ++L+V F++F+TE +SNTA +AL+IP F +A+ G+ ++ Sbjct: 328 LAQQLEMLSAGLSLYWLLLLVILFIIFMTEISSNTALSALMIPTFMGMADVMGLDTTMIV 387 Query: 405 VLIAVAASCAFMLPVATPPNAIVFASGHIKQSEMMRVGLYLNIACIGLLTAIAMLFW 461 IA+AASCAF+LPVATPPNAIVF+SG+I Q+ MM+VGL LN+ ++T + +FW Sbjct: 388 SAIAIAASCAFILPVATPPNAIVFSSGYIPQNTMMKVGLILNLIFSMIIT--SYMFW 442 Score = 48.5 bits (114), Expect = 4e-10 Identities = 39/152 (25%), Positives = 75/152 (49%), Gaps = 9/152 (5%) Query: 90 NNFANSIIFLFLGGFALAAAMHHQGLDKVIADKVLAMAQGKMSVAVFMLFGVTALLSMW- 148 NN ++ LF GG AL+A + G + +A ++ ++ G +S+ +L + ++ M Sbjct: 299 NNTQWGVLLLFGGGLALSAVLSATGANLYLAQQLEMLSAG-LSLYWLLLLVILFIIFMTE 357 Query: 149 -ISNTATAAMMLPLVLGVLSKVDADKQRSTYVFVLLGVAYSASIGGIATLVGSPPNAIAA 207 SNTA +A+M+P +G+ + D ++ +A +AS I V +PPNAI Sbjct: 358 ISSNTALSALMIPTFMGMADVMGLDT-----TMIVSAIAIAASCAFILP-VATPPNAIVF 411 Query: 208 AEVGLSFTDWMKFGLPTAMMMLPMAIAILYFL 239 + + MK GL ++ + + +++L Sbjct: 412 SSGYIPQNTMMKVGLILNLIFSMIITSYMFWL 443 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: 614 Number of extensions: 30 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 462 Length of database: 443 Length adjustment: 33 Effective length of query: 429 Effective length of database: 410 Effective search space: 175890 Effective search space used: 175890 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 24 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