Align D-gluconate TRAP transporter, large permease component (characterized)
to candidate 3607682 Dshi_1091 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= reanno::psRCH2:GFF2081 (425 letters) >FitnessBrowser__Dino:3607682 Length = 424 Score = 281 bits (718), Expect = 3e-80 Identities = 157/426 (36%), Positives = 245/426 (57%), Gaps = 5/426 (1%) Query: 1 MTVVVFLSSLLGFMTLGMPIAFALLLTGSVLMWYLDFWDVQLLAQNLQAGADSFPLLAVP 60 MT+++ L +L + LG+P+AFAL G + M L + + Q++ + D F LLAVP Sbjct: 1 MTIILILVALFVLLLLGVPVAFALGGMG-LAMLILGGFSPLMAPQSILSTLDGFILLAVP 59 Query: 61 FFILAGELMNAGGISRRIIAMAQAYFGHKRGGLGYVAIAASVLLASMSGSALADTAALAT 120 F+L L+ GG+ R + A QA+ GH GGL I + L A++SGS++A A + T Sbjct: 60 LFLLMSNLLLKGGVGRDLFAAVQAWVGHWPGGLAVATILSCALFAAISGSSVATAATIGT 119 Query: 121 LLLPMMRERGYPLSSSSGLVAAGGIIAPIIPPSMPFVIYGVVTGTSISQLFLAGMVPGLI 180 + +P M RGY GL+AAGG + +IPPS+P ++YG VT S+ LFLAG+ PGL+ Sbjct: 120 VAIPEMINRGYEKKFVYGLLAAGGTLGILIPPSIPMIVYGFVTEQSVIALFLAGIGPGLL 179 Query: 181 MGMGLIVAWTLIARRIDEPKQE--KASAAERRRVLVDGAAALMLPVIIVGGLRGGLFTPT 238 + + L V + ++ R+ KA+ AER ++ L +++ GL G FTPT Sbjct: 180 L-VTLFVLFAMLHARLSGTYTPVPKATMAERMSASKRALPSVALAALVIVGLYSGAFTPT 238 Query: 239 EAAVVAAVYALAVSTLLYRELNWAGLVEVLTRASRTTASVMFLCAAATVSAYMITLAQLP 298 EAA + + ALA+ TL R L W E + ++ TTA+++ + A A V I L ++P Sbjct: 239 EAAAIGSAAALAIVTLWLRTLTWVTFWEAVRESAITTAAILLIVAGAKVFGKAIALYRIP 298 Query: 299 DEIAAMLGPLAQDPKLLMVAIMLLMIAVGMVLDLTPTILILGPVLAPIAIKAGIDPVYFG 358 +I+A L + P + +V + L+++ +G+V + ILI+ PVL P A+ G DP++FG Sbjct: 299 QDISAFLTQVIDGPIMFIVVVSLVLLLMGLVFEALSMILIMTPVLLPAAMGLGFDPIWFG 358 Query: 359 VMFVLIGSIGLITPPVGTVLNVVGGIGRLRMETLVRGVMPFFLIYLVIVGLLIAVPSI-I 417 + V++ LITPPVG L V+ + R + + RGV PF ++ LV VG+L A P + + Sbjct: 359 IYMVIMVECALITPPVGLNLYVIQSVARTTLSNVARGVWPFLILMLVTVGVLYAFPQLAL 418 Query: 418 TVPLAW 423 +P W Sbjct: 419 YIPFQW 424 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: 512 Number of extensions: 21 Number of successful extensions: 5 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: 424 Length adjustment: 32 Effective length of query: 393 Effective length of database: 392 Effective search space: 154056 Effective search space used: 154056 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 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