Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Synpcc7942_1305 Synpcc7942_1305 ATPase
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__SynE:Synpcc7942_1305 Length = 536 Score = 167 bits (422), Expect = 7e-46 Identities = 87/239 (36%), Positives = 149/239 (62%), Gaps = 5/239 (2%) Query: 27 ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86 A+ +SL + G+ L ++GESG GK+TL R I+ L +P+ G+V++ G ++ + + + Sbjct: 299 AVDGLSLEVWPGETLGLIGESGCGKSTLLRTILQLLRPSQGKVLFQGQDLTQLPDRRLRS 358 Query: 87 YRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEEF 146 R+++QLI QDP + L T+ + + P+ +++++ +LE V LTPA + Sbjct: 359 LRRELQLIFQDPAACLNPRLTIGDAIADPLKIQGLARGAAAKQQVLAILEQVGLTPAPTW 418 Query: 147 LGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLT 206 + +YPHQLSGGQ+QR++IAR+L P++++ DEPV+M+DA+++ +L + E+K +LNLT Sbjct: 419 IDRYPHQLSGGQQQRVAIARALITRPKLVLCDEPVSMLDATVQAQVLALMQELKQQLNLT 478 Query: 207 MVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIKLTPSI 265 +F+THD+ +AR F V+ G+IVE ++L P HPYT L+ P + Sbjct: 479 YLFVTHDLRVAREFC-----DRVAVLQRGKIVEIGPAAQVLTQPEHPYTRSLLASLPEL 532 Score = 124 bits (311), Expect = 5e-33 Identities = 76/239 (31%), Positives = 140/239 (58%), Gaps = 12/239 (5%) Query: 27 ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTS---GEVVYDGYNIWKNKRKI 83 AL+ +SL + G+ L ++GESG GK+TLGR I+ L P S G++ G + + + + Sbjct: 20 ALQQLSLELAAGERLGLVGESGCGKSTLGRAILRLLPPGSHQQGDIRLAGQALGQLQGRS 79 Query: 84 FKKYRK-DVQLIPQDPYSTLPFNKTVEEILVAPI-LRWEKINKDELRKRLINLLELVKLT 141 +++R V L+ QDP + L +T+ + L+ + + +++ + +++ ++ LE V++ Sbjct: 80 LQRFRGGQVGLVFQDPMTRLDPLQTIGDHLLETLQVHRPHLSRRQAKQQALSWLERVRI- 138 Query: 142 PAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKN 201 PA + +YPHQ SGG +QR++IA +L + PR++VADEP T +D ++ IL L + + Sbjct: 139 PANRW-SQYPHQFSGGMRQRVAIALALLLQPRLVVADEPTTSLDVTVAAEILQELTRLCS 197 Query: 202 RLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIK 260 N +++ I+HD+P+ + V++ G++VE +L P HPYT L++ Sbjct: 198 EENTSLLLISHDLPMVAAYC-----DRIAVLYQGQLVETGPTTAVLTRPQHPYTQTLLQ 251 Lambda K H 0.321 0.141 0.410 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: 404 Number of extensions: 17 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: 324 Length of database: 536 Length adjustment: 31 Effective length of query: 293 Effective length of database: 505 Effective search space: 147965 Effective search space used: 147965 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: 50 (23.9 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