Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 238 bits (607), Expect = 2e-67 Identities = 125/252 (49%), Positives = 174/252 (69%), Gaps = 8/252 (3%) Query: 4 LTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEG 63 +T ++VTK + G + AV+ +SL +++GEF L+GPSGCGK+T LRM+AG ET TEG Sbjct: 15 ITFENVTKRF-----GKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEG 69 Query: 64 ELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEET 123 + ++ + ++ V R + MVFQSYA++PH +V N+++GL+ +P E RV E Sbjct: 70 RILIDGQDISNVPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDN-VPKAEREARVAEA 128 Query: 124 TDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQ 183 +++ + L RKP QLSGGQ+QRVAL RA+V+ P V L+DEPLS LDAKLR +MRTEL Sbjct: 129 LELVQLGGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELC 188 Query: 184 RLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEP 243 LQ ++G+T + VTHDQ EA+ + R AV+ G LQQV TP D Y PN+ FVA FIG+ Sbjct: 189 TLQEKVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIGQ- 247 Query: 244 SMNLFDGSLSGD 255 +NLF+G L+ D Sbjct: 248 -VNLFEGVLAVD 258 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: 376 Number of extensions: 19 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: 381 Length adjustment: 30 Effective length of query: 353 Effective length of database: 351 Effective search space: 123903 Effective search space used: 123903 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