Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Synpcc7942_2236 Synpcc7942_2236 ATPase
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__SynE:Synpcc7942_2236 Length = 554 Score = 129 bits (324), Expect = 2e-34 Identities = 76/239 (31%), Positives = 134/239 (56%), Gaps = 6/239 (2%) Query: 25 FYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIF 84 F A++++S ++ G L ++GESG GK++L R +VGL + G++ D + + Sbjct: 317 FQAVQNLSFTLPAGLTLGLVGESGCGKSSLARCLVGLVPASEGQIWLDQQPLDLRSSRDR 376 Query: 85 KKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAE 144 ++ R+ VQ++ QDP + L TV ++ P LR ++ +D + + L ++ Sbjct: 377 QRLRQTVQMVFQDPAAALDPRWTVGSAILEP-LRIKQPRRDRTADQRLLKQWLQRVDLPT 435 Query: 145 EFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLN 204 + +YPH+ SGGQ+QR+ IAR+L PR+++ DE V+ +D S++ ILN L +++ L Sbjct: 436 DIGDRYPHEFSGGQRQRICIARALIGQPRLLICDESVSALDVSVQAQILNLLKQLQAELG 495 Query: 205 LTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIKLTP 263 LT +FI+HD+ + RY +VM G++ E + E++ + P YT LI P Sbjct: 496 LTYLFISHDLAVVRYM-----SDRILVMNQGQLEEDSPTEQLFQRPQSDYTRRLIAAIP 549 Score = 125 bits (314), Expect = 2e-33 Identities = 81/278 (29%), Positives = 155/278 (55%), Gaps = 28/278 (10%) Query: 3 LMELKGVSVIFEDKVGLFKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQ 62 L+E++ + + F + + AL+ + L + G+ + ++GESG+GK+ I GL Sbjct: 5 LLEIRQLQICFGEAI---------ALQGLDLVVQPGESVGIVGESGSGKSVACLAIPGLL 55 Query: 63 KPT---SGEVVY------DGYNIWKNKRKIFKKYRKD-VQLIPQDPYSTLPFNKTVEEIL 112 T SG++ + ++ + ++ R D + I Q+P S+L + L Sbjct: 56 PKTARCSGQIAFRSVAGQSSRDLLTLPERELRQLRGDRLGFIFQEPLSSLNPVFSAGFQL 115 Query: 113 VAPILRWEKINKDELRKRLINLLELVKL----TPAEEFLGKYPHQLSGGQKQRLSIARSL 168 + I + +++ E ++R+I LL+ V+L + A + L +YPHQLSGGQ+QRL IA +L Sbjct: 116 LEAIQQHLPLSQAEAQQRVIALLQEVQLIREPSQAAQILRRYPHQLSGGQRQRLMIAIAL 175 Query: 169 SVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGN 228 + NP +++ADEP T +DA+++ +L L ++ + + M+F++HD+ + + D+ Sbjct: 176 AANPDLLLADEPTTALDATVQASVLQLLRRLQQQRQMAMIFVSHDLGV---IAEVADR-- 230 Query: 229 TIVMFAGRIVERADLEEILKDPLHPYTNDLIKLTPSID 266 +V++ G++VE+ + ++L P HPYT L+ P I+ Sbjct: 231 VVVLYRGQVVEQGRVADVLNSPQHPYTQGLVACRPQIN 268 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: 441 Number of extensions: 15 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: 554 Length adjustment: 32 Effective length of query: 292 Effective length of database: 522 Effective search space: 152424 Effective search space used: 152424 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