Align Citrate-proton symporter; Citrate carrier protein; Citrate transporter; Citrate utilization determinant; Citrate utilization protein A (characterized)
to candidate SMa1328 SMa1328 MtbA protein
Query= SwissProt::P0A2G3 (434 letters) >FitnessBrowser__Smeli:SMa1328 Length = 440 Score = 194 bits (492), Expect = 6e-54 Identities = 123/396 (31%), Positives = 197/396 (49%), Gaps = 24/396 (6%) Query: 17 ILRVTSGNFLEQFDFFLFGFYATYIARTFFPAESEFASLMLTFAVFGSGFLMRPVGAIVL 76 I+ + GN +E +DF++FG A ++ FF A+L+ T A+F +GFL+RP+GA + Sbjct: 13 IVAASVGNIIEWYDFYIFGSLAAVLSVKFFEQSHPVAALLSTIALFTAGFLIRPLGAFLF 72 Query: 77 GAYIDRIGRRKGLMVTLAIMGCGTLLIALVPGYQTIGLAAPALVLLGRLLQGFSAGVELG 136 G DR+GR+ ++TL MG GT I L+P Y++IGL A L+ R++QG G E G Sbjct: 73 GWMGDRVGRKYTFLITLTGMGLGTGAIGLIPTYESIGLTAAFLLFSLRMIQGLCLGGEYG 132 Query: 137 GVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYSLNITLGHDAISEWGWRIPFFI 196 G Y++E +G+YT W S + IVV+ + + G +A W WR+PF + Sbjct: 133 GAITYVAEHVPDERRGYYTGWLQTSPTLGIVVSLAVIIAARTYFGSEAFDAWAWRVPFLV 192 Query: 197 GCMIIPLIFVLRRSLQETEAFLQRKHRPDT-----REIFATIAKNWRIITAGTLLVAMTT 251 +++ + +R LQET F + K + RE F ++ N + + T+++ Sbjct: 193 SFLLVGIAIYIRLQLQETPIFQEIKAKGQMTQNPWREAF--LSSNIKYVGIATIVLIGQG 250 Query: 252 TTFY---FITVYTPTYGRTVLNLSARDSLIVTMLVGVSNFIWLP---IGGAISDRIGRRA 305 +Y F +Y + +S D L +VG + + P + G +SD IGR+ Sbjct: 251 VVWYSGQFWALY------FLQQVSKVDPLNSAYIVGAALLLATPSLILFGWLSDIIGRKP 304 Query: 306 VLMGITLLALITTWPVMQWLTAAPDFTRMTLVLLWFSFFF-----GMYNGAMVAALTEVM 360 V++G LLA +T +P+ WL A + + F F GM G + A L E Sbjct: 305 VILGGMLLAALTYYPLYLWLGAVTQPDNINYPIAIFIIFILVCYVGMVYGPVGAFLAEYF 364 Query: 361 PVYVRTVGFSLAFSLATAIFGGLTPAISTALVKLTG 396 P +R S+ + + GGL P I++A TG Sbjct: 365 PGRIRYTSVSVPYHIGNGWGGGLVPFITSAAFAATG 400 Lambda K H 0.329 0.140 0.432 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: 532 Number of extensions: 23 Number of successful extensions: 3 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: 434 Length of database: 440 Length adjustment: 32 Effective length of query: 402 Effective length of database: 408 Effective search space: 164016 Effective search space used: 164016 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