Align Citrate:H+ symporter (characterized)
to candidate RR42_RS07835 RR42_RS07835 membrane protein
Query= TCDB::P16482 (444 letters) >FitnessBrowser__Cup4G11:RR42_RS07835 Length = 434 Score = 298 bits (762), Expect = 3e-85 Identities = 161/427 (37%), Positives = 244/427 (57%), Gaps = 6/427 (1%) Query: 3 TARCSMRASSTAPVRMMATAGGARIGAILRVTSGNFLEQFDFFLFGFYATYIAHTFFPAS 62 TA + +S++ A A A++ + GN LE FD ++GF+A I+ FFP Sbjct: 2 TAVSASGSSNSGAAASAAPASRHPWRAVISASIGNALEWFDLVVYGFFAVTISALFFPNH 61 Query: 63 SEFASLMMTFAVFGAGFLMRPIGAIVLGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSY 122 E SL++T FG F MRP+GA+V+G Y D+ GRR L +++ +M GT +I L+P+Y Sbjct: 62 DENTSLLLTLGTFGVSFFMRPLGAVVIGVYADRKGRRAALTLSILLMMVGTLIIALLPTY 121 Query: 123 QTIGLWAPLLVLIGRLLQGFSAGAELGGVSVYLAEIATPGRKGFYTSWQSGSQQVAIMVA 182 IG+ AP+ +++ R++QGFSAG E G + +LAE A P R+GFY+S+Q SQ + ++A Sbjct: 122 AAIGVMAPIGIVLARMIQGFSAGGEFGSATAFLAEHA-PNRRGFYSSFQVASQGLTTLLA 180 Query: 183 AAMGFALNAVLEPSAISDWGWRIPFLFGVLIVPFIFILRRKLEETQEF-TARRHHLAMRQ 241 A G L L P + WGWR+PFLFG+LI P + +RR ++ET EF A +R Sbjct: 181 AGFGAVLTTTLTPDQMQSWGWRVPFLFGLLIGPVAYYIRRHVDETPEFLQAETTDTPLRD 240 Query: 242 VFATLLANWQVVIAGMMMVAMTTTAFYLITVYAPTFGKKVLMLSASDSLLVTLLVAISNF 301 TL + ++ M +V + T + YL+ +Y PT+ K L L S + TL + Sbjct: 241 ---TLSHQKERLLLAMGVVIVATVSTYLV-LYMPTYAVKQLGLPPSAAFAATLATGVVQM 296 Query: 302 FWLPVGGALSDRFGRRSVLIAMTLLALATAWPALTMLANAPSFLMMLSVLLWLSFIYGMY 361 + P+ G SDR+GR + LL L + WP +L++ P F +ML+V + L + +Y Sbjct: 297 LFAPLVGHWSDRYGRIPPMRLAALLLLVSIWPLFWLLSHYPGFGVMLAVQVVLGLMMTLY 356 Query: 362 NGAMIPALTEIMPAEVRVAGFSLAYSLATAVFGGFTPVISTALIEYTGDKASPGYWMSFA 421 GA+ +EI P + R G SL+Y++A +FGGF P I T LI TG K +P +++ Sbjct: 357 FGALPALASEIFPVKTRTTGLSLSYNIAVTLFGGFAPFILTWLISATGSKLAPSFYLMVC 416 Query: 422 AICGLLA 428 A+ L A Sbjct: 417 AVVSLAA 423 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: 545 Number of extensions: 26 Number of successful extensions: 5 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: 434 Length adjustment: 32 Effective length of query: 412 Effective length of database: 402 Effective search space: 165624 Effective search space used: 165624 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