Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate CCNA_03483 CCNA_03483 ABC transporter ATP-binding protein
Query= uniprot:A0A166R419 (517 letters) >FitnessBrowser__Caulo:CCNA_03483 Length = 314 Score = 99.4 bits (246), Expect = 2e-25 Identities = 77/229 (33%), Positives = 118/229 (51%), Gaps = 24/229 (10%) Query: 8 AVLSVSGIGKTYAQ--PVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTGQM 65 +++SV G+ KTYA L IDL + +GE+ AL G NGAGK+TL II G+V P+ G + Sbjct: 9 SIISVQGLTKTYASGHQALKRIDLDIRQGEIFALLGPNGAGKTTLISIICGIVNPSQGVI 68 Query: 66 RFQGRDYRPGSRSQAEELGIRMVMQELN------LLPTLSVAENLFLDNLPSHGGWISRK 119 G D R+ ++G+ V QEL+ + T+S + LF K Sbjct: 69 LADGHDVVRDYRAARTKIGL--VPQELHTDAFETVWATVSFSRGLF------------GK 114 Query: 120 QLRKAAIEAMAQVGLDAIDP-DTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTA 178 A IE + + L D D+ + L G ++ V IA+ L + +L LDEPTA + Sbjct: 115 PRNDALIEQILR-DLSLWDKKDSKIMALSGGMKRRVMIAKALSHEPTILFLDEPTAGVDV 173 Query: 179 REVEMLFEQITRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLVCVE 227 ++E + +L+ GV+II +H +EE +A RI V+ G ++ VE Sbjct: 174 ELRRDMWEMVRKLRESGVTIILTTHYIEEAEEMADRIGVINKGEIILVE 222 Score = 80.1 bits (196), Expect = 1e-19 Identities = 52/224 (23%), Positives = 113/224 (50%), Gaps = 20/224 (8%) Query: 262 LTVKGLTRS-----DKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGADTADSGTVAL 316 ++V+GLT++ ++ + ++R GEIF + G GAG+T L+ +I G G + Sbjct: 11 ISVQGLTKTYASGHQALKRIDLDIRQGEIFALLGPNGAGKTTLISIICGIVNPSQGVILA 70 Query: 317 GASAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGNMPVISSGGFVNNGD 376 V R+ +G L+ ++ + +++ A ++ S G Sbjct: 71 DGHDVVRDYRAARTKIG----LVPQELHTDAF---ETVWATVSF-------SRGLFGKPR 116 Query: 377 EMSLAQRQINAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCTVMLFDEPTRGIDVGA 436 +L ++ + + + +++++ LSGG +++V+I + L + T++ DEPT G+DV Sbjct: 117 NDALIEQILRDLSLWDKKDSKIMA-LSGGMKRRVMIAKALSHEPTILFLDEPTAGVDVEL 175 Query: 437 KFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLI 480 + D++ ++ +L G +++ + + E + DRIGV++ G +I Sbjct: 176 RRDMWEMVRKLRESGVTIILTTHYIEEAEEMADRIGVINKGEII 219 Lambda K H 0.319 0.137 0.384 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: 355 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 517 Length of database: 314 Length adjustment: 31 Effective length of query: 486 Effective length of database: 283 Effective search space: 137538 Effective search space used: 137538 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