Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 114 bits (286), Expect = 2e-30 Identities = 77/247 (31%), Positives = 134/247 (54%), Gaps = 18/247 (7%) Query: 7 LTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLE 66 + R + K++GR AL++ D ++ GE+LA++G +G+GK+++++ I+G PD G++ + Sbjct: 3 IAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFD 62 Query: 67 GKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAM 126 G+ + + S AR+ G V+Q AL +++A N+ G ++RK GK D+ + Sbjct: 63 GQDVTYAS-AAARRVGF--VFQQYALFKHMTVAKNIAFGLDVRK----GK-----DKPSK 110 Query: 127 EKQARAKLSELGLMTIQNI-NQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV- 184 + AR L L+ ++ + + LSGGQRQ VA++RA A V+++DEP AL Sbjct: 111 AEIARRVEELLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDAT 170 Query: 185 --KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSD 242 K RR L + D G+ + ++H+ E+ADR+ I GR + P + Sbjct: 171 VRKSLRRELRRVHDA--TGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAP 228 Query: 243 AVAFMTG 249 AF+ G Sbjct: 229 ETAFVCG 235 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: 171 Number of extensions: 7 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 260 Length of database: 339 Length adjustment: 26 Effective length of query: 234 Effective length of database: 313 Effective search space: 73242 Effective search space used: 73242 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: 48 (23.1 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