Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_010529853.1 ON01_RS04720 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_000224785.1:WP_010529853.1 Length = 365 Score = 308 bits (790), Expect = 1e-88 Identities = 168/369 (45%), Positives = 234/369 (63%), Gaps = 16/369 (4%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA + ++ + K Y +++AV++ +LDI D EF+V VGPSGCGKSTTLRM+AGLE + Sbjct: 1 MAEMRMEQIHKTYDK----NVLAVDDFNLDIKDKEFIVFVGPSGCGKSTTLRMIAGLEEI 56 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T G+L ++D+ +N ++ +DRDIAMVFQ+YALYPH +V NM+FGL+ DEI +RV Sbjct: 57 TGGDLYIDDKRMNDIAPKDRDIAMVFQNYALYPHMNVYDNMAFGLKLRK-FKKDEIDRRV 115 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 + ++LG+ + LDRKP LSGGQ+QRVALGRAIVRD +VFLMDEPLSNLDAKLR +MR Sbjct: 116 KNAANILGLENYLDRKPKALSGGQRQRVALGRAIVRDAKVFLMDEPLSNLDAKLRVQMRA 175 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E+Q+L L TT+YVTHDQTEAMTM R+ V+ DG +QQVG P + Y +P N+FV GFI Sbjct: 176 EIQKLHQRLQTTTIYVTHDQTEAMTMATRLVVMKDGVIQQVGAPKEVYDQPENIFVGGFI 235 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPL----SGATRDQLGGASGLTLGIRPEDV---TVGE 293 G PSMN G+L F + + R++ + LGIRPED+ Sbjct: 236 GSPSMNFLTGTLKDGHFANEDATIKIPEGKMKTLREKGYVDKEIILGIRPEDIHDEPAFI 295 Query: 294 RRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPED 353 + + + V E G E+ ++ + G F A +S + G++ ++F + Sbjct: 296 EATPETRITVTIDVAELMGAESYLYSKLA----GQDFIARVDSRSDITGGEKIDLAFDMN 351 Query: 354 AIHLFDGET 362 + FD E+ Sbjct: 352 KVLFFDAES 360 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: 416 Number of extensions: 15 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: 365 Length adjustment: 30 Effective length of query: 353 Effective length of database: 335 Effective search space: 118255 Effective search space used: 118255 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