Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 214 bits (544), Expect = 4e-60 Identities = 128/309 (41%), Positives = 178/309 (57%), Gaps = 16/309 (5%) Query: 19 GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78 G A+ ++ L+I DGE L L+GPSG GK+T LR +AGLE G++ + + + SA Sbjct: 13 GRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFDGQDVTYASAA 72 Query: 79 DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDD---EIRQRVEETTDMLGISDLLDR 135 R + VFQ YAL+ H +V N++FGL+ G EI +RVEE ++ + L R Sbjct: 73 ARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELLKLVELEGLGGR 132 Query: 136 KPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVY 195 P QLSGGQ+QRVAL RA+ P V L+DEP LDA +R +R EL+R+ GVTT++ Sbjct: 133 YPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRRVHDATGVTTIF 192 Query: 196 VTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGD 255 VTHDQ EA+ + DRVA+L++G ++Q+GTP + P FV GF+GE N FDG +SG Sbjct: 193 VTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVGE--ANRFDGQVSGG 250 Query: 256 TFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTFDAEVVVVEPQGNEN 315 F+ P S A +D GA+ T +RP D + E F+ + + QG Sbjct: 251 RFKAGALTVPAS-ALKD---GAA--TAYVRPHDFALDE-----AGFEVLIERAQVQGALT 299 Query: 316 AVHLRFVDG 324 AV DG Sbjct: 300 AVTALTSDG 308 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: 383 Number of extensions: 21 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: 339 Length adjustment: 29 Effective length of query: 354 Effective length of database: 310 Effective search space: 109740 Effective search space used: 109740 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