Align citrate transporter (characterized)
to candidate N515DRAFT_3073 N515DRAFT_3073 Arabinose efflux permease
Query= CharProtDB::CH_014606 (431 letters) >FitnessBrowser__Dyella79:N515DRAFT_3073 Length = 551 Score = 186 bits (472), Expect = 2e-51 Identities = 106/318 (33%), Positives = 168/318 (52%), Gaps = 11/318 (3%) Query: 14 ILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGSGFLMRPIGAVVL 73 IL + G E +DF+L+G A I K FF +E +A + F +GF +RP GA+V Sbjct: 19 ILASSLGTVFEWYDFYLYGSLAVLIGKHFFSGLNETSAFIFALLAFAAGFAVRPFGAIVF 78 Query: 74 GAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGRLLQGFSAGVELG 133 G D +GR+ +IT+ IMG T L+ ++P Y T+G++APVL++V RLLQG + G E G Sbjct: 79 GRLGDLVGRKYTFLITIIIMGLSTFLVGVLPSYSTVGMIAPVLLIVLRLLQGLALGGEYG 138 Query: 134 GVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDEISEWGWRIPFFI 193 G + Y++E A G +G YTS+ + + ++ L+ G + LG +WGWRIPF I Sbjct: 139 GAATYVAEHAPDGKRGLYTSFIQITATFGLFLSLLVILGTRMALGDKVFEDWGWRIPFLI 198 Query: 194 GCMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIA----KNWRII----TAGTLLVA 245 +++ + +R LQE+ F Q K + T A KN +++ T A Sbjct: 199 SSVLVAVSVYIRLQLQESPVFQQMKAEGKHSKAPLTEAFGHWKNLKVVILALLGATAGQA 258 Query: 246 MTTTTFYFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGRRPVLM 305 + T F +Y T + +A + +++G F++ G +SDRIGR+ +++ Sbjct: 259 VVWYTGQFYALYFLTQSLKIDGTTANLLIAAALIIGTPFFVFF---GWLSDRIGRKSIVL 315 Query: 306 GITLLALVTTLPVMNWLT 323 LLA +T P+ LT Sbjct: 316 AGCLLAALTYFPIFKGLT 333 Score = 37.4 bits (85), Expect = 1e-06 Identities = 21/77 (27%), Positives = 33/77 (42%) Query: 331 MTLVLLWFSFFFGMYNGAMVAALTEVMPVYVRTVGFSLAFSLATAIFGGLTPAISTALVQ 390 + ++L + M G + A L E+ P +R SL + + FGG P I LV Sbjct: 455 LVILLAILVLYVTMVYGPIAAWLVEMFPTRIRYTSMSLPYHIGNGWFGGFVPTIGFMLVA 514 Query: 391 LTGDKSSPGWWLMCAAL 407 GD W+ + A+ Sbjct: 515 WKGDIYYGLWYPIIVAV 531 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: 629 Number of extensions: 34 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: 551 Length adjustment: 34 Effective length of query: 397 Effective length of database: 517 Effective search space: 205249 Effective search space used: 205249 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