Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate Ac3H11_1610 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1610 Length = 362 Score = 231 bits (590), Expect = 2e-65 Identities = 144/366 (39%), Positives = 210/366 (57%), Gaps = 20/366 (5%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 M+ L L DVTK Y G AV+ ++L ++ GEF+ L+GPSGCGK+TTL+M+AG E V Sbjct: 1 MSFLQLTDVTKFY-----GSTCAVQSMNLSVEKGEFVSLLGPSGCGKTTTLQMVAGFEAV 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T G + L R + A R + +VFQSYAL+PH +V N+SFGLE +P E + RV Sbjct: 56 TSGRIELAGRDITHAKANTRGLGIVFQSYALFPHMTVADNVSFGLEMRK-VPKAERKDRV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 + ++ + R P +LSGGQ+QRVAL RA+V +P V L+DEPLSNLDAKLR EM+ Sbjct: 115 AQALGLVHLEKHAGRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDAKLREEMQF 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 EL+++Q ++G TTV VTHDQ+EAM++ DRV V++ G Q+ P Y P F++ F+ Sbjct: 175 ELRQIQRKVGTTTVMVTHDQSEAMSISDRVVVMEAGRATQIDHPHRVYEHPRTRFISTFV 234 Query: 241 GEPSMNLFDGSL----SGDTFRGDG-FDYPLSGATRDQLGGASGLTLGIRPEDVTVGERR 295 G+ NL G + + T G G + + GA Q + + L +RPE + + Sbjct: 235 GK--ANLVPGQVTTASATHTHVGAGPIEVRVEGA---QFRPGAAVLLSVRPEKLQLVPTV 289 Query: 296 SGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAI 355 G+ D EV G++ + GD A G+ +E G+RT + +P+ + Sbjct: 290 QGR--IDGEVCERFFLGSQWLYRVGTGMGD--LMVLAPNDGRGALEEGERTGLDWPDHCM 345 Query: 356 HLFDGE 361 L + Sbjct: 346 RLLPAD 351 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: 384 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: 362 Length adjustment: 30 Effective length of query: 353 Effective length of database: 332 Effective search space: 117196 Effective search space used: 117196 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