Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate BWI76_RS06690 BWI76_RS06690 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__Koxy:BWI76_RS06690 Length = 369 Score = 202 bits (515), Expect = 9e-57 Identities = 117/295 (39%), Positives = 181/295 (61%), Gaps = 17/295 (5%) Query: 20 SDYALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQE 79 S L + ++ EDG +GPSGCGK+T+L +++GL S G+VL + P Sbjct: 15 STVTLHQVNLDIEDGEFAVFVGPSGCGKSTLLRMIAGLEEVSEGEVLIGDEVMNDVVPAH 74 Query: 80 RNIAQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGL 139 R +A VFQ +Y MTVAEN+ + L+ KVP+ +I+++V ++A+ L++S L+++ L Sbjct: 75 RGVAMVFQSYALYPHMTVAENMGYGLKVNKVPKDEIRRQVEMVAKTLQLSHLLDRKPKQL 134 Query: 140 AADAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHD 199 + +Q++++GR +VR + +FDEPL+ +D L+ ++R + ++HHELK T++YVTHD Sbjct: 135 SGGQRQRVAIGRAIVR-NPRVFMFDEPLSNLDAELRVEMRLHIAKLHHELKTTMVYVTHD 193 Query: 200 QVEALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLP----AHRDGE 255 QVEA+T AD++VVM GK Q+GS +L+ P + FV FIGSP MNFLP A + G+ Sbjct: 194 QVEAMTLADKIVVMNYGKVEQMGSPMSLYYNPVNKFVAGFIGSPKMNFLPATVTAWQPGQ 253 Query: 256 NLSV---AGHRLASPVGRA--LPAGALQVGIRPEYLALAQPQQAGALPGTVVQVQ 305 LSV H L + + P A+ +GIRPE+L+ GTVV+ Q Sbjct: 254 -LSVKMAQDHNLTLNITTSPLQPGAAVTLGIRPEHLS------TDVNIGTVVEFQ 301 Lambda K H 0.320 0.136 0.395 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: 317 Number of extensions: 16 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: 358 Length of database: 369 Length adjustment: 29 Effective length of query: 329 Effective length of database: 340 Effective search space: 111860 Effective search space used: 111860 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