Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_900167125.1:WP_078717009.1 Length = 370 Score = 234 bits (598), Expect = 2e-66 Identities = 143/358 (39%), Positives = 214/358 (59%), Gaps = 22/358 (6%) Query: 4 LTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEG 63 + L+ V K + E + ++ LDI GEFL ++GPSGCGK+T LR++AG E+ + G Sbjct: 8 IRLEHVAKEFDGE-----TVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSG 62 Query: 64 ELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEET 123 E+ L+ R + V R + VFQSYAL+PH SV N++FGL S G+P EI +RV + Sbjct: 63 EIILDGRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMS-GIPKVEIGERVAKA 121 Query: 124 TDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQ 183 M+G++ R+P LSGGQQQRVA+ RA+V P V L+DEPLS LD KLR +MRTEL+ Sbjct: 122 LRMVGLAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELK 181 Query: 184 RLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEP 243 +L+ E+G+T ++VTHDQ EA +M DRV V+++G + QVGTP++ Y +P N+FVA F+GE Sbjct: 182 QLRREMGITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVGE- 240 Query: 244 SMNLFDGSLSGDTFRG------DGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERR-- 295 N+F+G ++G + G +G LS Q G + + +RPED+ V Sbjct: 241 -TNVFEG-VAGQSDGGILQALVEGRTCELSSHRGFQPG--DRIRVLLRPEDLLVEREEPE 296 Query: 296 -SGQRTFDAEVVVVEPQGNENAVHLRFVDGDE--GTQFTATTTGQSRVEAGDRTTVSF 350 + ++ +G+ + ++ G E T+F + +AG+R VS+ Sbjct: 297 DDDKLWLPGRIMETVYKGSTWDMVVQLDSGHEILVTEFFDEDADKMNFQAGERVVVSW 354 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: 464 Number of extensions: 23 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: 370 Length adjustment: 30 Effective length of query: 353 Effective length of database: 340 Effective search space: 120020 Effective search space used: 120020 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 Apr 09 2024. 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