Align Citrate:H+ symporter (characterized)
to candidate WP_017597434.1 D471_RS0103990 MFS transporter
Query= TCDB::P16482 (444 letters) >NCBI__GCF_000341125.1:WP_017597434.1 Length = 433 Score = 192 bits (489), Expect = 1e-53 Identities = 120/381 (31%), Positives = 190/381 (49%), Gaps = 10/381 (2%) Query: 36 GNFLEQFDFFLFGFYATYIAHT-FFPASSE-FASLMMTFAVFGAGFLMRPIGAIVLGAYI 93 G +E FDF+++ A + T FFP + LM +FA F GF RP+G +V G + Sbjct: 22 GTTIEWFDFYVYATAAGLVFGTLFFPGDIDPMVGLMASFATFAVGFFARPLGGVVFGHFG 81 Query: 94 DKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLLVLIGRLLQGFSAGAELGGVSV 153 D++GR+ L+ TL +M TF + L+P+Y +G APLL+++ R +QG + G E GG + Sbjct: 82 DRLGRKSALVTTLLMMGVATFCVGLLPTYAQVGFVAPLLLVVLRFVQGIAVGGEWGGAVL 141 Query: 154 YLAEIATPGRKGFYTSW-QSGSQQVAIMVAAAMGFALNAVLEPSAISDWGWRIPFLFGVL 212 E A RK FY S+ Q G+ A++ A F L + + WGWR+PFL L Sbjct: 142 MAVESAPEERKTFYGSFAQLGNPAGALL--ATGSFGLITAWDSDLLYTWGWRLPFLASCL 199 Query: 213 IVPFIFILRRKLEETQEFTARRHHLAMR----QVFATLLANWQVVIAGMMMVAMTTTAFY 268 +V ++R K+EE+ F A R + A + TL +W+ V+ G+ ++ + +Y Sbjct: 200 LVLVGLVVRLKVEESPVFEAARENRAAEPEGPPLRETLRTSWRAVLLGIGVLPVAVGGYY 259 Query: 269 LITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVGGALSDRFGRRSVLIAMTLLAL 328 ++T + +G +S L L A F L DRFG ++ Sbjct: 260 VVTTFLQAYGVTEAGISEQLILSGLTLAAFVELFATLATAWLGDRFGTARIVTVGLAAVA 319 Query: 329 ATAWPALTMLANAPSFLMMLSVLLWLSFIYGMYNGAMIPALTEIMPAEVRVAGFSLAYSL 388 A P +L + L++L + L + +Y G + L ++ P VR G S++Y + Sbjct: 320 VLALPQFLVLETGSAVLIVLMLCLMRVAMAAVY-GPIARVLAQMYPPRVRYTGISVSYQV 378 Query: 389 ATAVFGGFTPVISTALIEYTG 409 A A+FGG +P+ TAL TG Sbjct: 379 AGALFGGLSPLACTALFALTG 399 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: 526 Number of extensions: 29 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: 444 Length of database: 433 Length adjustment: 32 Effective length of query: 412 Effective length of database: 401 Effective search space: 165212 Effective search space used: 165212 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 Apr 09 2024. 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