Align D-gluconate TRAP transporter, large permease component (characterized)
to candidate H281DRAFT_05541 H281DRAFT_05541 TRAP transporter, DctM subunit
Query= reanno::psRCH2:GFF2081 (425 letters) >FitnessBrowser__Burk376:H281DRAFT_05541 Length = 647 Score = 244 bits (624), Expect = 4e-69 Identities = 139/416 (33%), Positives = 237/416 (56%), Gaps = 7/416 (1%) Query: 5 VFLSSLLGFMTLGMPIAFALLLTGSVLMWYLDFWDVQLL--AQNLQAGADSFPLLAVPFF 62 + L+ +G + +G+PIAF L L S L++++ + ++ +Q + AG D F LLA+PFF Sbjct: 224 MLLAGFVGGLMVGVPIAFVLAL--SALLYFISDPSLPMIVYSQQVMAGMDHFVLLAIPFF 281 Query: 63 ILAGELMNAGGISRRIIAMAQAYFGHKRGGLGYVAIAASVLLASMSGSALADTAALATLL 122 +LAG +M G+S R+I + FG RG + +AI A+ + +SGS LAD AA+ ++ Sbjct: 282 VLAGLVMEVNGMSSRLIELLVRIFGRVRGSMNLIAILATAFFSGVSGSKLADIAAVGGIV 341 Query: 123 LPMMRERGYPLSSSSGLVAAGGIIAPIIPPSMPFVIYGVVTGTSISQLFLAGMVPGLIMG 182 +P +R + ++ ++AA G++A IPP + +I G V SI LFLAG+VP ++M Sbjct: 342 VPAVRRTKQDPNETAAVLAASGVMAETIPPCINMIIIGFVANISIGGLFLAGIVPAVVMA 401 Query: 183 MGLIVAWTLIARRIDEPKQEKASAAERRRVLVDGAAALMLPVIIVGGLRGGLFTPTEAAV 242 + L + ++I EPK S R+L AL++ ++I G+ G+ T TE + Sbjct: 402 IALATLVVIFGKKI-EPKTAFESRRPICRLLGGALVALVMVIMIGKGVTSGVATSTEVSS 460 Query: 243 VAAVYALAVSTLLYRELNWAGLVEVLTRASRTTASVMFLCAAATVSAYMITLAQLPDEIA 302 A VYAL + +REL + + RA+ A ++F+ AAA+ A+ +T+ Q+P ++ Sbjct: 461 FAVVYALVIGGFTFRELTPGAIAALFVRAAAMAAGILFIIAAASSVAFALTILQIPAMLS 520 Query: 303 AMLGPLAQD--PKLLMVAIMLLMIAVGMVLDLTPTILILGPVLAPIAIKAGIDPVYFGVM 360 A + LA + + +L+MI G +L+ P ++I GP+L PIA+ G++P++FG + Sbjct: 521 AGMLALAHNYGSVAFLAVSVLIMIVFGAILEGAPALIIFGPLLVPIAVHVGVNPLHFGTI 580 Query: 361 FVLIGSIGLITPPVGTVLNVVGGIGRLRMETLVRGVMPFFLIYLVIVGLLIAVPSI 416 V +GL +PP G L + R+E + R + + + +V++ LL+ VPSI Sbjct: 581 AVTAMGLGLFSPPFGLGLCATCAMTGTRIEDVSRRMFKYLALLVVMLVLLVLVPSI 636 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: 738 Number of extensions: 45 Number of successful extensions: 4 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: 647 Length adjustment: 35 Effective length of query: 390 Effective length of database: 612 Effective search space: 238680 Effective search space used: 238680 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: 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