Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 201408 SO2258 lipoprotein releasing system ATP-binding protein LolD (NCBI ptt file)
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__MR1:201408 Length = 230 Score = 83.6 bits (205), Expect = 3e-21 Identities = 67/218 (30%), Positives = 107/218 (49%), Gaps = 24/218 (11%) Query: 3 QEPILTARGLVKRY--GRVTALDRADFDL--YPGEILAVIGDNGAGKSSMIKAISGAVTP 58 Q+ +L + + K Y G VT +D DL + GE LA++G +G+GKS+++ + P Sbjct: 2 QDVLLQVQAVSKSYHDGDVTTQVLSDVDLQVFKGEQLAIVGTSGSGKSTLLHIMGTLDKP 61 Query: 59 DEGEIRLEGKPIQFRSPMEARQAGIET-----VYQNLALSPALSIADNMFLGREIRKPGI 113 G++ L G+ + S ARQA I +YQ L P + +N+ Sbjct: 62 SSGKVLLAGEDLYQVS--SARQAQIRNQDLGFIYQFHHLLPEFTALENV----------A 109 Query: 114 MGKWFRSLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVV 173 M + + DR + A+ L +GL ++ LSGG+RQ VA+ARA K+V Sbjct: 110 MPAFIQGRDRTLAQADAKVLLERVGLG--HRMSHIPAELSGGERQRVAIARALINKPKLV 167 Query: 174 IMDEPTAALGVKESRRVLELILDVRRR-GLPIVLISHN 210 + DEPT L K V ELI ++ + G V+++H+ Sbjct: 168 LADEPTGNLDAKSGEAVYELIRELANQLGTAFVVVTHD 205 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: 113 Number of extensions: 5 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: 230 Length adjustment: 24 Effective length of query: 236 Effective length of database: 206 Effective search space: 48616 Effective search space used: 48616 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: 46 (22.3 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