Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Synpcc7942_1305 Synpcc7942_1305 ATPase
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__SynE:Synpcc7942_1305 Length = 536 Score = 157 bits (398), Expect = 5e-43 Identities = 92/250 (36%), Positives = 146/250 (58%), Gaps = 14/250 (5%) Query: 58 GNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMD 117 G I++AV+ +S V GE LG+IGESG GK+TL+ IL+ +RP GKV+F G D Sbjct: 292 GGGEIVRAVDGLSLEVWPGETLGLIGESGCGKSTLLRTILQLLRPS----QGKVLFQGQD 347 Query: 118 IFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYH----EAISHGEADKKRVIER 173 + + R L +++ + Q LNP L I + + ++ G A K++V+ Sbjct: 348 LTQLPDRRLRSLR-RELQLIFQDPAACLNPRLTIGDAIADPLKIQGLARGAAAKQQVLA- 405 Query: 174 ASELLKLVGLDPARV-LKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQE 232 +L+ VGL PA + YP QLSGG +QRV IA +L+ PKL+L DEP S LD Q Sbjct: 406 ---ILEQVGLTPAPTWIDRYPHQLSGGQQQRVAIARALITRPKLVLCDEPVSMLDATVQA 462 Query: 233 LLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYT 292 +L L++ + Q++ +T ++VTHD+ + +R+ V+ +G ++E G +++ P +PYT Sbjct: 463 QVLALMQELKQQLNLTYLFVTHDLRVAREFCDRVAVLQRGKIVEIGPAAQVLTQPEHPYT 522 Query: 293 SLLVSSIPSL 302 L++S+P L Sbjct: 523 RSLLASLPEL 532 Score = 129 bits (324), Expect = 2e-34 Identities = 80/255 (31%), Positives = 135/255 (52%), Gaps = 6/255 (2%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +L + L+V Y A+ +S + GE LG++GESG GK+TL AILR + PPG Sbjct: 3 LLSIDQLSVTYPGSEQ---PALQQLSLELAAGERLGLVGESGCGKSTLGRAILRLL-PPG 58 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHG- 163 G + G + + ++ + V Q L+P+ I + H Sbjct: 59 SHQQGDIRLAGQALGQLQGRSLQRFRGGQVGLVFQDPMTRLDPLQTIGDHLLETLQVHRP 118 Query: 164 EADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223 +++ ++A L+ V + PA YP Q SGGM+QRV IAL+LLL P+L++ DEPT Sbjct: 119 HLSRRQAKQQALSWLERVRI-PANRWSQYPHQFSGGMRQRVAIALALLLQPRLVVADEPT 177 Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283 ++LD+ +L+ + + E +++ ++HD+ +A +R+ V+Y+G ++E G T + Sbjct: 178 TSLDVTVAAEILQELTRLCSEENTSLLLISHDLPMVAAYCDRIAVLYQGQLVETGPTTAV 237 Query: 284 IKSPLNPYTSLLVSS 298 + P +PYT L+ S Sbjct: 238 LTRPQHPYTQTLLQS 252 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: 361 Number of extensions: 13 Number of successful extensions: 5 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: 536 Length adjustment: 32 Effective length of query: 330 Effective length of database: 504 Effective search space: 166320 Effective search space used: 166320 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