Align Citrate:H+ symporter (characterized)
to candidate BWI76_RS21415 BWI76_RS21415 MFS transporter
Query= TCDB::P16482 (444 letters) >FitnessBrowser__Koxy:BWI76_RS21415 Length = 432 Score = 235 bits (599), Expect = 2e-66 Identities = 136/387 (35%), Positives = 207/387 (53%), Gaps = 18/387 (4%) Query: 26 RIGAILRVTSGNFLEQFDFFLFGFYATYIAHTFFPASSEFASLMMTFAVFGAGFLMRPIG 85 RI AI+ +SGN +E FDF+++ F + Y AH FFP+ + L+ T VF AGFLMRPIG Sbjct: 20 RIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTAGVFAAGFLMRPIG 79 Query: 86 AIVLGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLLVLIGRLLQGFSAG 145 + G D+ GR+ +++++ +M G+ +I +P Y TIG WAP L+L+ RL QG S G Sbjct: 80 GWIFGRIADRRGRKTSMLISVCMMCFGSLVIACLPGYATIGTWAPALLLLARLFQGLSVG 139 Query: 146 AELGGVSVYLAEIATPGRKGFYTSWQ----SGSQQVAIMVAAAMGFALNAVLEPSAISDW 201 E G + Y++E+A G+KGFY S+Q G Q +A++V AL +L A+ W Sbjct: 140 GEYGTSATYMSEVAVEGKKGFYASFQYVTLIGGQLLAVLVVV----ALQQILSDEALHAW 195 Query: 202 GWRIPFLFGVLIVPFIFILRRKLEETQEFTARRHHLAMRQVFATLLANWQVVIAGMMMVA 261 GWRIPF G ++ LRR+L+ET + R L F L N + I + A Sbjct: 196 GWRIPFALGAVLAIVALWLRRQLDETSKQETRA--LKEAGSFKGLWRNRKAFIMVLGFTA 253 Query: 262 MTTTAFYLITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVGGALSDRFGRRSVLI 321 + +FY T Y + ++A + ++ P+ GALSD+ GRR+ ++ Sbjct: 254 AGSLSFYTFTTYMQKYLVNTAGMTAGTASMIMTAALFVYMLVQPLFGALSDKIGRRTSML 313 Query: 322 AMTLLALATAWPALTMLANAPS----FLMMLSVLLWLSFIYGMYNGAMIPALTEIMPAEV 377 +L P L L N S F +++ LL +SF Y +G + E+ PA+V Sbjct: 314 CFGVLVTVFTVPILNALQNVSSPYAAFALVICALLIVSF-YTSISGIL---KAEMFPAQV 369 Query: 378 RVAGFSLAYSLATAVFGGFTPVISTAL 404 R G L+Y++A A+FGG ++ +L Sbjct: 370 RALGVGLSYAVANALFGGSAEYVALSL 396 Lambda K H 0.329 0.139 0.421 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: 511 Number of extensions: 27 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: 444 Length of database: 432 Length adjustment: 32 Effective length of query: 412 Effective length of database: 400 Effective search space: 164800 Effective search space used: 164800 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 (21.9 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