Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 164 bits (414), Expect = 4e-45 Identities = 93/275 (33%), Positives = 150/275 (54%), Gaps = 12/275 (4%) Query: 27 ISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNG----VSAQDRDI 82 ++L + GE L+GPSGCGK+T LR +AGL+ ++ G + + + ++ V+ + R I Sbjct: 22 LNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSIAINGKTVSADGCFVAPEKRSI 81 Query: 83 AMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPGQLSG 142 M+FQ YAL+PH +V N+ FG+ + L R+EE ++ + L R P +LSG Sbjct: 82 GMIFQDYALFPHLTVADNILFGVRQ---LDKQSRSVRLEEMLSLVKLEGLGKRYPHELSG 138 Query: 143 GQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTHDQTE 202 GQQQRV++ RA+ +P++ L+DEP SN+DA++R + E++ + V+ V+VTH + E Sbjct: 139 GQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEIRAILKARNVSAVFVTHSKDE 198 Query: 203 AMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGDTFRGDGF 262 A D +A+ + G + Q G P Y PN +VA F+G + N D L Sbjct: 199 AFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLG--ASNYLDVRLEAGQLISTLG 256 Query: 263 DYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSG 297 +PL +D + +RPE + + R G Sbjct: 257 AFPL---PQDFKAASETGRWLLRPEQLLIEARADG 288 Lambda K H 0.316 0.136 0.384 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: 325 Number of extensions: 15 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: 383 Length of database: 341 Length adjustment: 29 Effective length of query: 354 Effective length of database: 312 Effective search space: 110448 Effective search space used: 110448 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: 42 (22.0 bits) S2: 49 (23.5 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