GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Cupriavidus basilensis 4G11

Align Amino acid ABC transporter ATP binding protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized)
to candidate RR42_RS02590 RR42_RS02590 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q9I405
         (244 letters)



>FitnessBrowser__Cup4G11:RR42_RS02590
          Length = 244

 Score =  417 bits (1072), Expect = e-121
 Identities = 210/244 (86%), Positives = 223/244 (91%)

Query: 1   MISIKNVSKWYGDFQVLTDCSTEVAKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 60
           MI I NVSKWYG FQVLTDC+T+VAKGEVVVVCGPSGSGKSTLIK VNALEPFQKGDI V
Sbjct: 1   MIEINNVSKWYGAFQVLTDCTTKVAKGEVVVVCGPSGSGKSTLIKTVNALEPFQKGDITV 60

Query: 61  DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLSITENLTIAQIKVLGRSKEEATKKGLAL 120
           DGTS+  PKTNLPKLRSRVGMVFQ+FELFPHLSITENLTIAQ KVLGRSKEEA  KGL  
Sbjct: 61  DGTSVGSPKTNLPKLRSRVGMVFQNFELFPHLSITENLTIAQTKVLGRSKEEAMAKGLKY 120

Query: 121 LERVGLKEHAHKHPGQLSGGQQQRVAIARALAMDPVVMLFDEPTSALDPEMVNEVLDVMV 180
           L+RVGLK  A K PGQLSGGQQQRVAIARAL+MDP+ MLFDEPTSALDPEMVNEVLDVMV
Sbjct: 121 LDRVGLKAQAAKFPGQLSGGQQQRVAIARALSMDPICMLFDEPTSALDPEMVNEVLDVMV 180

Query: 181 QLAHEGMTMMCVTHEMGFARKVANRVIFMDRGQIVEDCEKEEFFGDVSARSERAQQFLAK 240
           QLA EGMTMMCVTHEMGFARKVANRVIFMD+G+IVEDC KEEFFG++ ARSERA+QFL+K
Sbjct: 181 QLAQEGMTMMCVTHEMGFARKVANRVIFMDQGKIVEDCAKEEFFGNIDARSERAKQFLSK 240

Query: 241 ILPH 244
           IL H
Sbjct: 241 ILHH 244


Lambda     K      H
   0.320    0.135    0.389 

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: 268
Number of extensions: 3
Number of successful extensions: 1
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: 244
Length of database: 244
Length adjustment: 24
Effective length of query: 220
Effective length of database: 220
Effective search space:    48400
Effective search space used:    48400
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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