Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Synpcc7942_2236 Synpcc7942_2236 ATPase
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__SynE:Synpcc7942_2236 Length = 554 Score = 153 bits (386), Expect = 1e-41 Identities = 93/270 (34%), Positives = 158/270 (58%), Gaps = 19/270 (7%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +LE+ L + + E A+ + V+ GE +GI+GESGSGK+ AI + P Sbjct: 5 LLEIRQLQICFGEAI-----ALQGLDLVVQPGESVGIVGESGSGKSVACLAI-PGLLPKT 58 Query: 105 KIISGKVIFNGM------DIFSMTIDEFRKLLWKDISYVPQASQNALNPVLP-----ISE 153 SG++ F + D+ ++ E R+L + ++ Q ++LNPV + Sbjct: 59 ARCSGQIAFRSVAGQSSRDLLTLPERELRQLRGDRLGFIFQEPLSSLNPVFSAGFQLLEA 118 Query: 154 IFYHEAISHGEADKKRVIERASEL-LKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLL 212 I H +S EA ++RVI E+ L A++L+ YP QLSGG +QR+MIA++L Sbjct: 119 IQQHLPLSQAEA-QQRVIALLQEVQLIREPSQAAQILRRYPHQLSGGQRQRLMIAIALAA 177 Query: 213 NPKLILMDEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKG 272 NP L+L DEPT+ALD Q +L+L++ + Q+ + +++V+HD+ IA++A+R++V+Y+G Sbjct: 178 NPDLLLADEPTTALDATVQASVLQLLRRLQQQRQMAMIFVSHDLGVIAEVADRVVVLYRG 237 Query: 273 YVMEEGKTEEIIKSPLNPYTSLLVSSIPSL 302 V+E+G+ +++ SP +PYT LV+ P + Sbjct: 238 QVVEQGRVADVLNSPQHPYTQGLVACRPQI 267 Score = 122 bits (305), Expect = 3e-32 Identities = 81/263 (30%), Positives = 140/263 (53%), Gaps = 11/263 (4%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +L+V L + Y G S +AV ++SF + G LG++GESG GK++L ++ + Sbjct: 300 LLQVEQLGITY-RGRSTAFQAVQNLSFTLPAGLTLGLVGESGCGKSSLARCLVGLVPA-- 356 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPI-SEIFYHEAISHG 163 S I+ + R+ L + + V Q AL+P + S I I Sbjct: 357 ---SEGQIWLDQQPLDLRSSRDRQRLRQTVQMVFQDPAAALDPRWTVGSAILEPLRIKQP 413 Query: 164 EADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223 D+ + L+ V L P + YP + SGG +QR+ IA +L+ P+L++ DE Sbjct: 414 RRDRTADQRLLKQWLQRVDL-PTDIGDRYPHEFSGGQRQRICIARALIGQPRLLICDESV 472 Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283 SALD+ Q +L L+K + E+G+T ++++HD+ + +++R+LVM +G + E+ TE++ Sbjct: 473 SALDVSVQAQILNLLKQLQAELGLTYLFISHDLAVVRYMSDRILVMNQGQLEEDSPTEQL 532 Query: 284 IKSPLNPYTSLLVSSIPSLKGEV 306 + P + YT L+++IP GEV Sbjct: 533 FQRPQSDYTRRLIAAIP---GEV 552 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: 401 Number of extensions: 13 Number of successful extensions: 3 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: 554 Length adjustment: 33 Effective length of query: 329 Effective length of database: 521 Effective search space: 171409 Effective search space used: 171409 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