Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate GFF204 HP15_203 oligopeptide/dipeptide ABC transporter, ATPase subunit
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Marino:GFF204 Length = 332 Score = 204 bits (520), Expect = 2e-57 Identities = 115/315 (36%), Positives = 190/315 (60%), Gaps = 6/315 (1%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +LEV +L+V + + A+ +SF ++KGE LG++GESG+GK+ +IL I PG Sbjct: 3 LLEVKDLDVRFAVRGGDLT-ALRGISFSLDKGERLGLVGESGAGKSVAAFSILNLIAKPG 61 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 I G+++F G D+ +M+ E R++ I+ + Q LNPVL I ++H + Sbjct: 62 YIAGGQILFEGRDLAAMSERELRRIRGNRIAMIFQDPMMTLNPVLTIGTQMVEAILAHRK 121 Query: 165 ADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223 KK A + L+ V + P + L YP +LSGGM+QRV+IA++LLL+P++I+ DEPT Sbjct: 122 ISKKEARAIALDRLQKVQIPSPEKRLDQYPHELSGGMRQRVIIAIALLLDPEIIIADEPT 181 Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283 +ALD+ Q ++ L+ N+ ++ V ++ +THD+ ++Q+ R+LVMY G ++E+G T EI Sbjct: 182 TALDVTIQAEIMDLLLNLCEQENVALMLITHDLGVVSQVTQRMLVMYSGRIIEQGPTREI 241 Query: 284 IKSPLNPYTSLLVSSIPSL--KGEVKVINVPLDEP-LVSKEKGCPFLARCSKAFGRCKEE 340 I +PYT L++++P + GE ++ +P P L + GCPF RC+ A +CK+ Sbjct: 242 INDAQHPYTQGLINALPQMGEPGE-RLFQIPGSMPSLKNVPSGCPFHPRCNFATEQCKQA 300 Query: 341 LPEIRLVYDRKVRCH 355 +PE + V C+ Sbjct: 301 MPEYVRSGNVNVACY 315 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: 257 Number of extensions: 12 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: 332 Length adjustment: 29 Effective length of query: 333 Effective length of database: 303 Effective search space: 100899 Effective search space used: 100899 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