Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_607 Length = 517 Score = 447 bits (1150), Expect = e-130 Identities = 247/499 (49%), Positives = 339/499 (67%), Gaps = 9/499 (1%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +L+ G+ K F G+ L +V +L GEI AL+G+NGAGKSTLIK LTGV A G + L Sbjct: 18 VLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRL 77 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEME----- 123 GQA+ P + AQ+LGI TVYQEVNL PN+SVA+N+F GR P R G+ + ++ Sbjct: 78 GGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYP-RCGIAQGFRIDWATLH 136 Query: 124 KRATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVEL 183 +RA +L+A G +DV L+ + VA+QQ+VAI RA+ + ++VLILDEPT+SLD EV+ Sbjct: 137 QRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQK 196 Query: 184 LFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243 LF+++R+LR G+S++FVTHFL+QVY VSDRITVLRNGS+VG +L L+ MLG Sbjct: 197 LFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAMLG 256 Query: 244 RELDTHALQRAGRTLLSDKPVAAFK--NYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTE 301 R+L + Q A + + + G+ + P DL++R GE+VGLAGLLGSGRTE Sbjct: 257 RDLAAASEQPAPAPAVDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGSGRTE 316 Query: 302 TAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIIL 361 A ++FG++ D G I G+ +P A G+ CPE+RKTDGI+A SVRENI L Sbjct: 317 LARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVRENIAL 376 Query: 362 ALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRP 421 ALQA+ G + +SR EQ E+AER+++ LGI+T + ++PI LSGGNQQK +L+RW+ P Sbjct: 377 ALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWMAIEP 436 Query: 422 QFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQV 481 + LILDEPTRGIDV A EI+ I L G+A+L ISSE+ E+V A R++++RDR++V Sbjct: 437 RLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVLRDRRKV 496 Query: 482 AEIPLAELSVPAIMNAIAA 500 E+P A S A+ + IAA Sbjct: 497 GELP-AGSSEDAVYDLIAA 514 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: 628 Number of extensions: 25 Number of successful extensions: 7 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: 517 Length adjustment: 34 Effective length of query: 466 Effective length of database: 483 Effective search space: 225078 Effective search space used: 225078 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