Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate GFF2021 Psest_2064 ABC-type uncharacterized transport system, duplicated ATPase component
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__psRCH2:GFF2021 Length = 553 Score = 163 bits (412), Expect = 1e-44 Identities = 93/270 (34%), Positives = 161/270 (59%), Gaps = 4/270 (1%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPP- 103 ++EV +L V + G ++ + V V+F + KGE L ++GESGSGK+ +ILR + P Sbjct: 10 LVEVRDLAVEFVTGE-QVQRVVEGVTFDIRKGETLALVGESGSGKSVTAHSILRLLPYPL 68 Query: 104 GKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHG 163 + G+++F+G D+ RK+ I+ V Q +LNP+ + + H Sbjct: 69 ARHPQGQILFHGQDLLKADEKAMRKIRGNRIAMVFQEPMTSLNPLHTVGKQINEVLEIHK 128 Query: 164 EADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEP 222 K R ELL+LVG+ +P + ++ YP +LSGG +QRV+IA++L P+L++ DEP Sbjct: 129 GLRGKAATARTLELLELVGIPEPRKRIRAYPHELSGGQRQRVVIAMALANEPELLIADEP 188 Query: 223 TSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEE 282 T+ALD+ Q +L+L+K + +G+ ++ ++HD+ + +IA+R+ VM +G V+E+ E+ Sbjct: 189 TTALDVTVQLKILELLKELQARLGMALLLISHDLNLVRRIAHRVCVMQRGRVVEQALCED 248 Query: 283 IIKSPLNPYTSLLVSSIPSLKGEVKVINVP 312 + ++P +PYT L+++ PS G V V P Sbjct: 249 LFRAPQHPYTQELLAAEPS-GGPVAVEEAP 277 Score = 146 bits (368), Expect = 1e-39 Identities = 86/236 (36%), Positives = 141/236 (59%), Gaps = 7/236 (2%) Query: 63 IKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIFSMT 122 IKAV+ V+F + KG+ LGI+GESGSGK+TL AILR + G+I F G + SM+ Sbjct: 303 IKAVDGVNFSLPKGQTLGIVGESGSGKSTLGLAILRLLGSRGEIR-----FQGQHLQSMS 357 Query: 123 IDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIERASELLKLVG 182 + R L + + V Q +L+P + + +I H + K + E L VG Sbjct: 358 QRQVRPLR-RQMQVVFQDPFGSLSPRMSVGQIVGEGLHIHRMGNAKEQEQAIIEALVEVG 416 Query: 183 LDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLIKNIN 242 LDP YP + SGG +QR+ IA +L+L P LIL+DEPTSALD Q +++L++++ Sbjct: 417 LDP-ETRHRYPHEFSGGQRQRIAIARALVLKPALILLDEPTSALDRTVQRQVVELLRSLQ 475 Query: 243 QEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSS 298 + +T ++++HD+ + ++++++V+ +G V+E+G +I +P +PYT L+ S Sbjct: 476 AKYNLTYLFISHDLAVVRALSHQMMVVKQGQVVEQGAAADIFAAPQHPYTQQLLES 531 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: 414 Number of extensions: 20 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 362 Length of database: 553 Length adjustment: 33 Effective length of query: 329 Effective length of database: 520 Effective search space: 171080 Effective search space used: 171080 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: 51 (24.3 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