Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 325 bits (834), Expect = 1e-93 Identities = 180/377 (47%), Positives = 244/377 (64%), Gaps = 24/377 (6%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 MA L LRNV KTY AG + I++ I +GEF+++VGPSGCGKSTL+ +AGLE I+GG Sbjct: 1 MAKLSLRNVQKTY-AGNVKVVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAISGG 59 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 + IGD+ V+ + P +RDIAMVFQ+YALYP MSV +N+ +GLKIR M +++I+ V A Sbjct: 60 EVHIGDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLKIRGMDKSEIEQRVKHAA 119 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 +L++ LL RKP LSGGQ+QRVAMGRA+ R P ++LFDEPLSNLDAKLRV+MR E+K Sbjct: 120 GILELAPLLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLELKE 179 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 +H+RL+TT++YVTHDQ+EAMTL D++ V+ G ++Q GTP E+Y PA+ FVASFIGSPP Sbjct: 180 LHRRLRTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFIGSPP 239 Query: 241 MNFVP------------LRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRP 288 MN VP +R+++K G A G + L+ E L LGLRP Sbjct: 240 MNLVPVTRTNGGQGEAQMRVEQKPGAQGAPATLG--HLPMGLHLPERAL------LGLRP 291 Query: 289 EQIMLAAGEGDSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQ 348 E I A A EV++ E G D+ + L V RL ++ G+ L + Sbjct: 292 EHIEPCAAHEAIA---EIEVRLVEALGADSYAYGTLGGQPVVVRLDSNMPVSSGDRLPIT 348 Query: 349 FDPSKVLLFDANTGERL 365 + FDA++G+R+ Sbjct: 349 AAAEHLHFFDADSGKRI 365 Lambda K H 0.318 0.135 0.382 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: 398 Number of extensions: 16 Number of successful extensions: 3 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: 386 Length of database: 367 Length adjustment: 30 Effective length of query: 356 Effective length of database: 337 Effective search space: 119972 Effective search space used: 119972 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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