Align CbtB, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate AZOBR_RS31010 AZOBR_RS31010 ABC transporter permease
Query= TCDB::Q97VF8 (333 letters) >FitnessBrowser__azobra:AZOBR_RS31010 Length = 325 Score = 125 bits (315), Expect = 1e-33 Identities = 105/336 (31%), Positives = 161/336 (47%), Gaps = 27/336 (8%) Query: 5 WLIRRLASVIIAIFVTIVISWALLEFSPYSPANYIMQFINPQDFAQKPEL----YASLID 60 +++RRLA + +V++ ++L F+ I NP D PE A+ I Sbjct: 4 FILRRLAQSAV-----VVVAMSVLVFAG------IFAIGNPIDVLISPEADAFERAAAIA 52 Query: 61 YLNTLRPHGNPLINAVNYIWNTLHGNLGFSIISNVPVAELIAVALPWTLFIVVTSILISF 120 L +P I V+ + L G+LG S + VP L+ P TL + + ++L++ Sbjct: 53 RLGLDKPMHEQFIRFVD---SALDGDLGTSFVHGVPALGLVLQRFPATLELALCAMLVAV 109 Query: 121 FLGIRLGQKLGYLRGTKTDSVA---TVSLSILR-SVPIYIYAVLLIYILAFIYHIFPTGG 176 LGI LG G K DS+A ++ SIL S+P + ++LI A P GG Sbjct: 110 VLGI----PLGLWAGLKPDSLAGRVIMTGSILGFSLPTFWVGMMLIMAFAVTLGWLPAGG 165 Query: 177 AYSIHVTPGFNLPFI-ASVLYHAFLPILTLTIVNLVGWILQMRANTIYVLGEDFVNFAEI 235 G F+ A L H LP + L + L I RA T V +D+V FA Sbjct: 166 RGETASLFGVQWSFLTADGLAHLILPAVNLALFKLSLVIRLARAGTREVALQDYVKFARA 225 Query: 236 SGVKKDIIEKKYIGKNAILPLYTSLIISIGFSFSGSVFVEQTFSYPGVGNLLINSITSND 295 G+ + +I KN ++P+ T L + +G + SV E F++PG+G LLI+SI D Sbjct: 226 KGLAPARVVGVHILKNIMIPVVTVLGLELGSVIAFSVVTESVFAWPGMGKLLIDSILQLD 285 Query: 296 YPTEMGVFIIIIVAVIVGNLIADLTYSFLDPRAKVG 331 P + ++ ++ +V NLI DL YS LDPR ++G Sbjct: 286 RPVVIAYLLVTVLLFVVINLIVDLVYSLLDPRIRLG 321 Lambda K H 0.327 0.144 0.429 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: 233 Number of extensions: 14 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: 333 Length of database: 325 Length adjustment: 28 Effective length of query: 305 Effective length of database: 297 Effective search space: 90585 Effective search space used: 90585 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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