GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Collimonas arenae Ter10

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_128083232.1 CAter10_RS21330 4-aminobutyrate--2-oxoglutarate transaminase

Query= BRENDA::P42588
         (459 letters)



>NCBI__GCF_001584165.1:WP_128083232.1
          Length = 420

 Score =  211 bits (536), Expect = 5e-59
 Identities = 147/398 (36%), Positives = 212/398 (53%), Gaps = 32/398 (8%)

Query: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAM--LAKTLAA 135
           D +G+ FID   G  + N GHR+P +V+A+Q QL K   H+   + P  +   LA+ + A
Sbjct: 31  DVEGRRFIDFAAGIAVLNTGHRHPKLVAAIQEQLGKFT-HTAYQIVPYGSYVELAERINA 89

Query: 136 LTPGK-LKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKS 194
           +TPG   K + F ++G E+VE A+K+A+A     G+   IA SGAFHG+++  ++ T K 
Sbjct: 90  VTPGDHAKKTTFFSTGAEAVENAVKIARA---ATGRSAVIAFSGAFHGRTMMGMALTGKV 146

Query: 195 T-FRKPFMPLLPGFRHVPFG------NIEAMRTALNECKKTGDD---VAAVILEPIQGEG 244
             ++  F P      HVPF       +IE    AL    K   D   VAA+ILEP+QGEG
Sbjct: 147 VPYKVGFGPFPAEVYHVPFPVELHGVSIENSLAALQSLFKADVDPKRVAAIILEPVQGEG 206

Query: 245 GVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGG 304
           G    PP ++ A+RKLCDE G L+++DEVQTG  RTGK+FA EH  V PD++ +AK+L G
Sbjct: 207 GFYAAPPAFMQALRKLCDEHGILLVVDEVQTGFARTGKLFAVEHSGVIPDLMTMAKSLAG 266

Query: 305 GVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGD 364
           G MP+ A     E+       P     T+ GNPLA A+ALA ++V+ E+ L  +A   G 
Sbjct: 267 G-MPLSAVCGRAEIMDAA--APGGLGGTYAGNPLAVASALAVLDVIEEEKLVERANVLGG 323

Query: 365 MLLDGFRQLAREYPDLVQEARGKGMLMAIEFV-------DNEIGYNFASEMFRQRVLVAG 417
            L      L  + P  + + RG G ++A+EF        D +      +E  +  +L+  
Sbjct: 324 RLKQVLEGLRADVPQ-IADIRGLGAMVAVEFTQPGSKQPDADFTKKVQAEALKNGLLLLS 382

Query: 418 TLNNAKTIRIEPPLT----LTIEQCELVIKAARKALAA 451
               +  IR   PLT    L  E   ++ KA R   AA
Sbjct: 383 CGVYSNAIRFLFPLTIEDALMDEALAILSKAMRTVAAA 420


Lambda     K      H
   0.320    0.135    0.393 

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: 435
Number of extensions: 18
Number of successful extensions: 5
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: 459
Length of database: 420
Length adjustment: 32
Effective length of query: 427
Effective length of database: 388
Effective search space:   165676
Effective search space used:   165676
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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