Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Smeli:SM_b20713 Length = 513 Score = 376 bits (966), Expect = e-109 Identities = 200/493 (40%), Positives = 314/493 (63%), Gaps = 5/493 (1%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +L EG+ K FPGV ALD+V+F L+RG + AL+GENGAGKSTL+K L G+Y+ D+G + L Sbjct: 23 LLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKL 82 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPK-RFGLLRRKEMEKRAT 127 G I K+ A + GI ++QE+NL+P M+VA+N++I REPK RFG + EM + Sbjct: 83 RGAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRFGFVDHGEMRRMTA 142 Query: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187 +L LD + SVA +Q+V I +A+ + VLI+DEPT++L +EV LF++ Sbjct: 143 KLFERLKIDLDPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFEI 202 Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELD 247 +R LR +G+ ++++TH ++++++++D +V R+G ++G + E+ + ++++MM+GRE+ Sbjct: 203 IRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMVGREI- 261 Query: 248 THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIF 307 T + + V + KN G +VR GEI+G+AGL+GSGR+ AE +F Sbjct: 262 TQMFPKEEVPI--GDVVLSVKNLTLNGVFRDVSFDVRAGEILGVAGLVGSGRSNVAETLF 319 Query: 308 GIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQR 367 G+ PA SGT I GK + S ++A + F EDRK G + + EN+ +A+ + Sbjct: 320 GVTPASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDILENMQIAVLQDK 379 Query: 368 GWLRP-ISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLIL 426 R +S +E E R+L ++TP+ ++ +E LSGGNQQKVL+ RWLLT P+ LIL Sbjct: 380 FVKRGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQKVLIGRWLLTNPRILIL 439 Query: 427 DEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPL 486 DEPTRGIDVGA AEI RL+ L +G+A+++ISSE+ E++G +DR+++M + + + Sbjct: 440 DEPTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVMHEGRVTGILDR 499 Query: 487 AELSVPAIMNAIA 499 AE + +M A Sbjct: 500 AEATQIKVMELAA 512 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: 590 Number of extensions: 26 Number of successful extensions: 8 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: 500 Length of database: 513 Length adjustment: 34 Effective length of query: 466 Effective length of database: 479 Effective search space: 223214 Effective search space used: 223214 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: 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