Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_011383734.1 AMB_RS06730 nitrate ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_000009985.1:WP_011383734.1 Length = 452 Score = 137 bits (345), Expect = 6e-37 Identities = 103/302 (34%), Positives = 151/302 (50%), Gaps = 36/302 (11%) Query: 2 ARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVT 61 A L L V K + + +E + +++GE + L+G SG GKST LR+MAGL Sbjct: 9 ALLDLRGVRKTFLTPDRRERTVLEGVDFKLEEGEIVALLGKSGSGKSTLLRIMAGLIKAN 68 Query: 62 EGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVE 121 GE++ ++ G + + I+MVFQS+AL+P +V N+ GLE + G+ E +R Sbjct: 69 GGEVKYRGHLMTGPA---KGISMVFQSFALFPWLTVEENVELGLE-AAGVAKAEREERAN 124 Query: 122 ETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTE 181 E D++G+ P +LSGG +QRV RA+V P+V L+DEP S LD +R + Sbjct: 125 EAIDLIGLGGYESAYPKELSGGMRQRVGFARALVMRPDVLLLDEPFSALDVLTSETLRED 184 Query: 182 LQRLQGELGVTT---VYVTHDQTEAMTMGDRVAVL--DDGELQ---QVGTPLDCYHRPNN 233 L L E + T + V+H+ EA++M DRV V D G ++ +V P RP + Sbjct: 185 LLELWDERKIPTKGILLVSHNIEEAVSMADRVLVFSSDPGRVRAEIRVNLP-----RPRD 239 Query: 234 LFVAGF--IGEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTV 291 A F I + L ++ RG G LG A LTLG R D T Sbjct: 240 TESAAFRQIVDEVYTLMTANV-----RGGG------------LGAAEQLTLGYRLPDTTP 282 Query: 292 GE 293 G+ Sbjct: 283 GK 284 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: 470 Number of extensions: 27 Number of successful extensions: 5 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: 452 Length adjustment: 31 Effective length of query: 352 Effective length of database: 421 Effective search space: 148192 Effective search space used: 148192 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: 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