Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Pedo557:CA265_RS10520 Length = 568 Score = 105 bits (262), Expect = 2e-27 Identities = 73/241 (30%), Positives = 130/241 (53%), Gaps = 21/241 (8%) Query: 2 AQEPILTARGLVKRY-------GRVT----ALDRADFDLYPGEILAVIGDNGAGKSSMIK 50 AQEP+L + L Y G+ T A+D+ +F+++PGE L ++G++G GK+++ + Sbjct: 305 AQEPLLQIKNLCTWYPIHNGLFGKTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGR 364 Query: 51 AISGAVTPDEGEIRLEGKPIQF--RSPMEARQAGIETVYQNLALSPALSIADNMFLGREI 108 I + P GEI G+ I ++ + + I+ ++Q+ P S+ + +G+ I Sbjct: 365 TILRLIQPTSGEIIFNGENITHIGKTALRKLRKDIQIIFQD----PYASLNPKLSIGQSI 420 Query: 109 RKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAF 168 +P + K +R + + +++ L ++GL ++ N+ SGGQRQ V +ARA A Sbjct: 421 LEPLQVHKLYR--NDSERKQKVLELLDKVGLKE-EHFNRYPHEFSGGQRQRVVIARALAL 477 Query: 169 GSKVVIMDEPTAALGVKESRRVLELILDVRRR-GLPIVLISHNMPHVFEVADRIHIHRLG 227 K +I DE +AL V +VL LI D++ GL + ISH++ V ++DRI + G Sbjct: 478 QPKFIICDESVSALDVSVQAQVLNLIKDLQSEFGLTYIFISHDLAVVKHISDRILVMNKG 537 Query: 228 R 228 + Sbjct: 538 K 538 Score = 76.6 bits (187), Expect = 1e-18 Identities = 59/212 (27%), Positives = 109/212 (51%), Gaps = 16/212 (7%) Query: 21 ALDRADFDLYPGEILAVIGDNGAGKS----SMIKAISGAVTPDEGEIRLEGKPIQFRSPM 76 A+ + F + G +L ++G++G+GKS S+++ GEI E + S Sbjct: 22 AVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDERAAKITGEIDFEDISLLNLSSN 81 Query: 77 EARQA---GIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAK 133 E RQ I ++Q P S+ G ++ + ++ R +D+A +K A Sbjct: 82 EIRQIRGNQISMIFQ----EPMTSLNPVFTCGYQVAEAIML---HRKVDQAEAKKHTIAL 134 Query: 134 LSELGLMTIQNINQAV-ETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLE 192 +E+ L + I ++ +SGGQ+Q V +A A + K++I DEPT AL V + +L+ Sbjct: 135 FNEVQLPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTTALDVTVQKTILQ 194 Query: 193 LILDVRR-RGLPIVLISHNMPHVFEVADRIHI 223 L+L +++ R + ++ ISH++ V E+AD + + Sbjct: 195 LLLKLKQERNMAMIFISHDLGVVNEIADEVAV 226 Lambda K H 0.321 0.136 0.383 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: 285 Number of extensions: 14 Number of successful extensions: 4 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: 260 Length of database: 568 Length adjustment: 30 Effective length of query: 230 Effective length of database: 538 Effective search space: 123740 Effective search space used: 123740 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