Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_017868944.1 LACPOB_RS0111380 ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_000349725.1:WP_017868944.1 Length = 372 Score = 249 bits (635), Expect = 1e-70 Identities = 145/369 (39%), Positives = 209/369 (56%), Gaps = 14/369 (3%) Query: 8 DVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRL 67 ++ +Y G +++I+L I D +F+ +VGPSGCGKST LR AGLE + +GE+ + Sbjct: 5 EIKHLYKKYPGRSNYTLKDINLSIKDKQFVAIVGPSGCGKSTLLRCFAGLEEINKGEVLV 64 Query: 68 EDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDML 127 + + + ++R++AMVFQ YALYPH +V NM++ L+ + + I Q+V E + L Sbjct: 65 NGKNFDKIDPRNRNVAMVFQDYALYPHMTVFKNMAYNLKIAKK-DKETIEQKVTEAAEKL 123 Query: 128 GISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQG 187 ++D L +KP QLSGGQ+QRVALGRA+VRDPE+FLMDEPLSNLDAKLR + R ++ L Sbjct: 124 KLTDYLQQKPAQLSGGQRQRVALGRAMVRDPEIFLMDEPLSNLDAKLRVKTRQDIIDLHR 183 Query: 188 ELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNL 247 +LG T+YVTHDQ EAM + D++ V+ DG L Q GTP + Y P+N+FVA FIG PSMN+ Sbjct: 184 QLGTITMYVTHDQAEAMALADQIVVMRDGILMQTGTPAELYDDPHNIFVARFIGSPSMNI 243 Query: 248 FDGSL-SGDTFRGDGFDYPLSGATRDQL--GGASGLTLGIRPEDVTV-------GERRSG 297 F G L S F+ Y L L + +G RPE E Sbjct: 244 FRGFLDSKAQFKVGKTTYNLKNIVPKSLLPVDEQEIFIGFRPEQTRPLLPSEEGKENDKD 303 Query: 298 QRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHL 357 + TF A++ E G ++L + Q G + T+ ++ Sbjct: 304 KFTFKAQLNYAEYMGAYTLLYLEAHERSIVAQIYRKIEGSPH---NRQVTMEVTPKDLYF 360 Query: 358 FDGETGDAL 366 F+ +TG + Sbjct: 361 FNADTGQRM 369 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: 358 Number of extensions: 13 Number of successful extensions: 2 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: 372 Length adjustment: 30 Effective length of query: 353 Effective length of database: 342 Effective search space: 120726 Effective search space used: 120726 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 24 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