Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate H281DRAFT_01031 H281DRAFT_01031 peptide/nickel transport system ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Burk376:H281DRAFT_01031 Length = 377 Score = 182 bits (462), Expect = 1e-50 Identities = 104/303 (34%), Positives = 171/303 (56%), Gaps = 15/303 (4%) Query: 26 YALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFK 85 +A+ +VS +++ G+ ++GESG GK+TLGR+++ L T G V+Y G +I + + Sbjct: 41 HAVNEVSFAVHTGETFAIVGESGCGKSTLGRMLLRLIDATQGRVLYQGEDITHWQGAKLR 100 Query: 86 KYRKDVQLIPQDPYSTLPFNKTVEEILVAPI-LRWEKINKDELRKRLINLLELVKLTPAE 144 + R+D+Q+I QDP+++L TV +I+ P+ + E R+R+ LL V L PA Sbjct: 101 RLRRDMQIIFQDPFASLNPGMTVGQIIGEPVAFHGLASSGSECRERVAQLLTKVGLQPA- 159 Query: 145 EFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLN 204 + +YPH+ SGGQ+QR+ IAR+L+ P++IV DEPV+ +D S++ ++N L +K L Sbjct: 160 -YAQRYPHEFSGGQRQRIGIARALAGEPKLIVGDEPVSALDVSVQAQVINLLESLKAELG 218 Query: 205 LTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIKLTPS 264 LT++ + HD+ + R H+ D+ VM+ G IVE A ++E+ PLHPYT L++ P+ Sbjct: 219 LTLIMVAHDLAVIR---HMSDR--VAVMYLGEIVELAQVDELFDAPLHPYTQALLRAIPA 273 Query: 265 IDNLYKEINVKINYE-----RVEKGCPYRLRCPFAMDICKNEEP--KLFKYSHEVACFLY 317 + + + GC + RCP A C E P + +VAC + Sbjct: 274 SSPHERRTKPALQGDLPSPTAPPPGCRFHTRCPHAKPRCVQERPLSETLPGGRQVACHFW 333 Query: 318 GKV 320 V Sbjct: 334 RDV 336 Lambda K H 0.321 0.141 0.410 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: 15 Number of successful extensions: 4 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: 324 Length of database: 377 Length adjustment: 29 Effective length of query: 295 Effective length of database: 348 Effective search space: 102660 Effective search space used: 102660 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