GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Dyella japonica UNC79MFTsu3.2

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 N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein

Query= TCDB::Q9I405
         (244 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1562
          Length = 384

 Score =  157 bits (398), Expect = 2e-43
 Identities = 87/218 (39%), Positives = 141/218 (64%), Gaps = 10/218 (4%)

Query: 2   ISIKNVSKWYGDFQVLTDCSTEVAKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDIVVD 61
           +SI+ +++ YG F  L D S ++A+GE V + GPSGSGKS+L++ +  L+   +GD++ D
Sbjct: 3   LSIRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLRD 62

Query: 62  GTSIADPKTNLPKLRSRVGMVFQHFELFPHLSITENLTIAQIKVLGRSKEEATKKGLA-- 119
           GT +      LP  R  +G+VFQH+ LFPH+++ +N+    ++V  R++  + +   A  
Sbjct: 63  GTDLLA----LPAQRRDIGLVFQHYALFPHMTVADNIAFG-LRVRPRARRPSRRDIAARV 117

Query: 120 --LLERVGLKEHAHKHPGQLSGGQQQRVAIARALAMDPVVMLFDEPTSALDPEMVNEVLD 177
             LL RV L+E   ++P QLSGGQ+QRVA+ARALA++P ++L DEP  ALD ++   +  
Sbjct: 118 EDLLRRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRV 177

Query: 178 VMVQLAHE-GMTMMCVTHEMGFARKVANRVIFMDRGQI 214
            +  L    G+T + VTH+   A ++A+RV+ M+RG+I
Sbjct: 178 WLRDLQRSLGLTTVLVTHDQDEALELADRVVVMNRGRI 215


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: 214
Number of extensions: 15
Number of successful extensions: 4
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: 384
Length adjustment: 27
Effective length of query: 217
Effective length of database: 357
Effective search space:    77469
Effective search space used:    77469
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.

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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