Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Dsui_2068 Dsui_2068 ABC-type metal ion transport system, ATPase component
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__PS:Dsui_2068 Length = 278 Score = 108 bits (270), Expect = 1e-28 Identities = 82/268 (30%), Positives = 136/268 (50%), Gaps = 25/268 (9%) Query: 5 PILTARGLVKRY----GRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60 P L RG+ K + G+ + D D+ PGEI +IG +GAGKS++++ + PD Sbjct: 9 PALALRGVSKSFRTPDGQQVGVHPTDLDVAPGEIHGIIGFSGAGKSTLLRLANLLERPDA 68 Query: 61 GEIRLEGKPIQFRSPMEARQA--GIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWF 118 G++ + G+ + SP + R A I ++Q+ L ++ADN+ I Sbjct: 69 GQVVVHGQDLMTLSPADLRTARQRIGMIFQHFNLLHNRTVADNVAFPLRI---------- 118 Query: 119 RSLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEP 178 D A + ++ + L +GL + A LSGGQ+Q VA+ARA A V++ DEP Sbjct: 119 AGADEARINERVKTCLEFVGLSEKAGVYPA--QLSGGQKQRVAIARALAPEPHVLLADEP 176 Query: 179 TAALGVKESRRVLELILDVRRR-GLPIVLISHNMPHVFEVADRIHIHRLGR---RLCVIN 234 T+AL + ++ +LE++ DV RR G+ I+L+SH M + + R+ + G+ RL + N Sbjct: 177 TSALDPRTTQSLLEVLADVNRRLGVTILLVSHEMGVIRRLCHRVSVMEAGQIVERLTIAN 236 Query: 235 ---PKDYTMSDAVAFMTGAKEPPREAIA 259 P D ++ + A+ EA A Sbjct: 237 GRIPPDSQLAQWLREYGDAEGDAEEAAA 264 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: 167 Number of extensions: 3 Number of successful extensions: 2 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: 278 Length adjustment: 25 Effective length of query: 235 Effective length of database: 253 Effective search space: 59455 Effective search space used: 59455 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: 47 (22.7 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