Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 6936040 Sama_0245 cytochrome c biogenesis protein CcmA (RefSeq)
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__SB2B:6936040 Length = 217 Score = 62.8 bits (151), Expect = 7e-15 Identities = 60/233 (25%), Positives = 94/233 (40%), Gaps = 32/233 (13%) Query: 1 MTTQSMTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGF 60 MT + T L++ E LT + +++SFS N G+I I GPNGAGKT+L + G Sbjct: 1 MTLPTKTAHSLVSAEKLTCIREERILFDELSFSVNEGDIIQIEGPNGAGKTSLLRILAGL 60 Query: 61 YTPTVGRLTLRHADGKEFLLERMPGYRISQKASVARTF-QNIRLFGGMSVLENLIVAQHN 119 P G + YR + F +++ G ++ +++ + A+ N Sbjct: 61 SRPYAGSVF----------------YRDEEIGRCRDEFNEDLLYLGHLAGVKSELTAEEN 104 Query: 120 KLIRASGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEI 179 L L Y + V L +V L F + AG+L G RR + Sbjct: 105 LNFN---------LRLSGYDDFDTGEV------LAKVNLKGFEEALAGHLSAGQHRRTAL 149 Query: 180 ARAMCTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVV 232 AR + + LDEP ++ R EL L D +L DM ++ Sbjct: 150 ARLWHSNCKVWILDEPFTAIDKRGVAELEQLFLKHADNGGCVILTTHQDMGLI 202 Lambda K H 0.319 0.137 0.397 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: 138 Number of extensions: 6 Number of successful extensions: 2 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: 294 Length of database: 217 Length adjustment: 24 Effective length of query: 270 Effective length of database: 193 Effective search space: 52110 Effective search space used: 52110 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