Align citrate transporter (characterized)
to candidate Ac3H11_3022 putative sugar transport protein
Query= CharProtDB::CH_014606 (431 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3022 Length = 543 Score = 183 bits (464), Expect = 1e-50 Identities = 100/314 (31%), Positives = 170/314 (54%), Gaps = 11/314 (3%) Query: 20 GNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGSGFLMRPIGAVVLGAYIDR 79 G E +DF+L+G A IAK FF +A + F +GF++RP GA+ G D Sbjct: 15 GTVFEWYDFYLYGSLAAIIAKQFFSGLDSGSAFIFALLAFAAGFIVRPFGAIFFGRLGDM 74 Query: 80 IGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGRLLQGFSAGVELGGVSVYL 139 IGR+ ++T+ IMG T ++ ++P Y +IG+ AP++++V RLLQG + G E GG + Y+ Sbjct: 75 IGRKYTFLVTILIMGLSTFIVGILPTYASIGVAAPIILIVLRLLQGLALGGEYGGAATYV 134 Query: 140 SEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDEISEWGWRIPFFIGCMIIP 199 +E A G +G YT+W + + + ++ ++ G +G + ++WGWR+PF + +++ Sbjct: 135 AEHAPHGRRGAYTAWIQTTATLGLFLSLMVILGTRTIVGEEAFADWGWRVPFIVSIVLLA 194 Query: 200 LIFVLRRSLQETEAFLQRKHRPDT-----REIFTTIAKNWRIITAGTLLVAMTTTTFY-- 252 + +R ++ E+ AF + K T +E F +I A L A +Y Sbjct: 195 ISVWIRLAMNESPAFQKMKAEGKTSKAPLKESFGEWKNLKIVILALVGLTAGQAVVWYSG 254 Query: 253 -FITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGRRPVLMGITLLA 311 F ++ T V +A + V++L+G FI + G++SD+IGR+P+++ LLA Sbjct: 255 QFYALFFLTQALKVDGATANILVAVSLLIGTPFFI---VFGSLSDKIGRKPIILAGCLLA 311 Query: 312 LVTTLPVMNWLTAA 325 +T PV LT A Sbjct: 312 ALTYFPVFGALTKA 325 Score = 44.3 bits (103), Expect = 9e-09 Identities = 26/90 (28%), Positives = 43/90 (47%), Gaps = 4/90 (4%) Query: 327 DFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVYVRTVGFSLAFSLATAIFGGLTPAIST 386 D +T +L++ M G + A L E+ P +R SL + + FGGL P + Sbjct: 441 DKVMVTAILVYLVLLVTMVYGPIAAMLVEMFPTRIRYTSMSLPYHIGNGWFGGLLPTTAF 500 Query: 387 ALVQLTGDKSSPGWWLMCAALCGLAATTML 416 A+V TG+ + W+ + A AAT ++ Sbjct: 501 AIVAQTGNMYNGLWYPIIIA----AATVVI 526 Lambda K H 0.328 0.141 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: 575 Number of extensions: 28 Number of successful extensions: 3 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: 431 Length of database: 543 Length adjustment: 34 Effective length of query: 397 Effective length of database: 509 Effective search space: 202073 Effective search space used: 202073 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: 52 (24.6 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