Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate PP_5137 PP_5137 ferric iron ABC transporter, ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Putida:PP_5137 Length = 352 Score = 228 bits (580), Expect = 2e-64 Identities = 126/281 (44%), Positives = 178/281 (63%), Gaps = 13/281 (4%) Query: 2 AGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIE 61 A IK+ I+K +G AL D++LDI GE V +GPSGCGK+TLLR +AGLE G + Sbjct: 8 AQIKVRNIHKRFGAFTALNDVSLDIAAGELVCLLGPSGCGKTTLLRCIAGLERQDRGTLY 67 Query: 62 IGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVL 121 IG RD++ + P RD ++FQSYAL+P++TV N+ +G+ +G E ++R+AE ++ Sbjct: 68 IGERDISDLSPQARDYGILFQSYALFPNLTVEANIAYGLTGSGREQ--ARQRVAEMLELV 125 Query: 122 QLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHK 181 L + PGQLSGGQ+QRVA+ RA+ +PS+ L DEP+S LDA++R + EL L + Sbjct: 126 GLSGSEKKYPGQLSGGQQQRVALARALAPSPSLLLLDEPMSALDARVREHLCTELRQLQR 185 Query: 182 QLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMNV 241 QLG T + VTH+Q EAM MAD+I V+N G++EQ +P ++Y P + FVAEF+G Sbjct: 186 QLGITTLMVTHNQDEAMLMADRIAVMNNGQVEQYATPQEIYDHPATPFVAEFVGQGNWLP 245 Query: 242 F--SSD---------VGLQDISLDASAAFVGCRPEHIEIVP 271 F SSD + L S AS+ + CRPE I + P Sbjct: 246 FQRSSDSHALVGDMNMRLAPGSAQASSGRLFCRPEAITVNP 286 Lambda K H 0.320 0.139 0.396 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: 308 Number of extensions: 12 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: 338 Length of database: 352 Length adjustment: 29 Effective length of query: 309 Effective length of database: 323 Effective search space: 99807 Effective search space used: 99807 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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