Align D-gluconate TRAP transporter, large permease component (characterized)
to candidate AZOBR_RS23855 AZOBR_RS23855 C4-dicarboxylate ABC transporter
Query= reanno::psRCH2:GFF2081 (425 letters) >FitnessBrowser__azobra:AZOBR_RS23855 Length = 425 Score = 263 bits (671), Expect = 1e-74 Identities = 146/417 (35%), Positives = 224/417 (53%), Gaps = 2/417 (0%) Query: 3 VVVFLSSLLGFMTLGMPIAFALLLTGSVLMWYLDFWDVQLLAQNLQAGADSFPLLAVPFF 62 V + + M G+PIAFA+ + G D + + Q + + + SFPLLAVPFF Sbjct: 1 VTLLAVTFFALMAFGLPIAFAIGIAGFSFFATNDIIPMSIGVQQVASASQSFPLLAVPFF 60 Query: 63 ILAGELMNAGGISRRIIAMAQAYFGHKRGGLGYVAIAASVLLASMSGSALADTAALATLL 122 +LAG +MN GI+ R+I + GGL V I S L+ +SGSA+AD A A +L Sbjct: 61 VLAGHMMNRTGITSRLINCSNVLVSWMSGGLAQVCIVLSTLMGGVSGSAVADAAMEARIL 120 Query: 123 LPMMRERGYPLSSSSGLVAAGGIIAPIIPPSMPFVIYGVVTGTSISQLFLAGMVPGLIMG 182 P + RGY ++ +A G +I IPPS+ ++YG V SI +LFLAG++PG +M Sbjct: 121 GPSLIARGYSKGFTAAAIAVGSLITATIPPSLGLILYGFVGNVSIGRLFLAGVIPGFMMM 180 Query: 183 MGLIVAWTLIARR--IDEPKQEKASAAERRRVLVDGAAALMLPVIIVGGLRGGLFTPTEA 240 GL++ LIARR E+ + R + D AL+ PV ++ +RGGLFTP+E Sbjct: 181 AGLMLTVWLIARRRGYRPEMAERPTLRAVWRAVADAKWALLFPVALLFAIRGGLFTPSEV 240 Query: 241 AVVAAVYALAVSTLLYRELNWAGLVEVLTRASRTTASVMFLCAAATVSAYMITLAQLPDE 300 A VYA V LL++EL WA + E L A T +M + + + Y I Q P Sbjct: 241 GAFAVVYAAVVGFLLHKELTWAAVAEALQEAVVDTGLIMLIILFSGMVGYAIIFEQAPQT 300 Query: 301 IAAMLGPLAQDPKLLMVAIMLLMIAVGMVLDLTPTILILGPVLAPIAIKAGIDPVYFGVM 360 IA + L P L++ I++ + G+ ++ T +L+L P+ PI G+DPV+FG++ Sbjct: 301 IAEAMTQLTSSPLLVVALILIFLFIAGLFVESTVLVLLLTPIFLPIVTPLGVDPVHFGIL 360 Query: 361 FVLIGSIGLITPPVGTVLNVVGGIGRLRMETLVRGVMPFFLIYLVIVGLLIAVPSII 417 + I ++G +TPPVG + V + +E V +PF +++V +L P ++ Sbjct: 361 MMTIVTLGSMTPPVGVAMYTVCSLLDCPIEEYVVESLPFVGTIVLLVAVLTLWPGLV 417 Lambda K H 0.328 0.142 0.413 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: 537 Number of extensions: 27 Number of successful extensions: 2 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: 425 Length of database: 425 Length adjustment: 32 Effective length of query: 393 Effective length of database: 393 Effective search space: 154449 Effective search space used: 154449 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 (21.7 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