Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate AO356_07270 AO356_07270 peptide ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07270 Length = 322 Score = 174 bits (442), Expect = 2e-48 Identities = 102/313 (32%), Positives = 174/313 (55%), Gaps = 5/313 (1%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +LE+ NLNV + G++ + V+ + VEKGE+L I+GESGSGK+ + A++ I PG Sbjct: 3 LLEIKNLNVRF--GDATAVPVVDGLDLSVEKGEVLAIVGESGSGKSVTMMALMGLIEHPG 60 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 + + + F+G ++ ++ + R+++ KD++ V Q ALNP + H + Sbjct: 61 IVTADALNFDGKNMLKLSNRQRRQIVGKDLAMVFQDPMTALNPSYTVGFQIEEVLRLHLK 120 Query: 165 ADKKRVIERASELLKLVGLDPARV-LKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223 K +RA ELL+ V + A + YP QLSGGM QRV IA+++ PKL++ DEPT Sbjct: 121 MSGKAARKRAIELLEKVEIPGAASRMDAYPHQLSGGMSQRVAIAMAIAGEPKLLIADEPT 180 Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283 +ALD+ Q ++ L+ + +E + +V +THD+ +A+ A R+ VMY G +E G+ ++ Sbjct: 181 TALDVTIQAQIMDLLLALQKEQDMGLVLITHDLAVVAETAQRVCVMYAGQAVEVGQVPQL 240 Query: 284 IKSPLNPYTSLLVSSIPS-LKGEVKVINVPLDEP-LVSKEKGCPFLARCSKAFGRCKEEL 341 P +PY+ L+++IP G ++ +P P + +GC RC C+++ Sbjct: 241 FDIPAHPYSEALLAAIPEHSMGAERLATLPGIVPGRYDRPQGCLLSPRCPYVQDNCRQQR 300 Query: 342 PEIRLVYDRKVRC 354 P + + RC Sbjct: 301 PALDAKSNSLARC 313 Lambda K H 0.319 0.138 0.391 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: 277 Number of extensions: 8 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: 362 Length of database: 322 Length adjustment: 29 Effective length of query: 333 Effective length of database: 293 Effective search space: 97569 Effective search space used: 97569 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