Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__PV4:5208351 Length = 342 Score = 109 bits (273), Expect = 1e-28 Identities = 67/215 (31%), Positives = 122/215 (56%), Gaps = 9/215 (4%) Query: 10 LRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLE 69 L E + + G L +D L +GEI ALLG +G GK+TL+KA+ G+ +G I + Sbjct: 4 LTIEQVHSDYQGQTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRISIN 63 Query: 70 GQAIS-PKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128 G+ +S P+ +++ +G ++Q+ L P+++VA+N+ G + L + + R E Sbjct: 64 GRLLSGPETFVPSERREVGMIFQDYALFPHLTVAENILFGVKG-----LDKAARQARLGE 118 Query: 129 LMASYGF-SLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQ-EVELLFD 186 ++A L R P + S QQ V+I RA+ ++L+LDEP +++D + E++ + Sbjct: 119 MLALVKLEGLGGRYP-HELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVE 177 Query: 187 LMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNG 221 + L+ RGVS +FVTH D+ + +D++ + ++G Sbjct: 178 IREILKQRGVSAVFVTHSKDEAFVFADKLALFKDG 212 Score = 70.5 bits (171), Expect = 9e-17 Identities = 59/217 (27%), Positives = 97/217 (44%), Gaps = 25/217 (11%) Query: 269 NYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRS 328 +Y + + DL + GEI L G G G+T + I G++P G I G+ L Sbjct: 12 DYQGQTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRISINGRL--LSG 69 Query: 329 PHQASVLGIGFCPEDRKTDGIIAA-------ASVRENIILALQAQRGWLRPISRKEQQEI 381 P F P +R+ G+I +V ENI+ ++ R E + Sbjct: 70 PET-------FVPSERREVGMIFQDYALFPHLTVAENILFGVKGLDKAARQARLGEMLAL 122 Query: 382 AERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAE- 440 + + LG R P LSGG QQ+V ++R L P+ L+LDEP ID E Sbjct: 123 VK--LEGLGGRYPHE------LSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEM 174 Query: 441 IIRLIETLCADGLALLVISSELEELVGYADRVIIMRD 477 ++ + E L G++ + ++ +E +AD++ + +D Sbjct: 175 MVEIREILKQRGVSAVFVTHSKDEAFVFADKLALFKD 211 Lambda K H 0.321 0.138 0.391 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: 397 Number of extensions: 29 Number of successful extensions: 7 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: 500 Length of database: 342 Length adjustment: 31 Effective length of query: 469 Effective length of database: 311 Effective search space: 145859 Effective search space used: 145859 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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