Aligments for a candidate for argD in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Aligments for a candidate for argD in Herbaspirillum seropedicae SmR1

Align 4-aminobutyrate aminotransferase GabT; (S)-3-amino-2-methylpropionate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.22 (characterized)
to candidate HSERO_RS19685 HSERO_RS19685 4-aminobutyrate aminotransferase

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__HerbieS:HSERO_RS19685
          Length = 456

 Score =  228 bits (580), Expect = 4e-64
 Identities = 147/425 (34%), Positives = 230/425 (54%), Gaps = 25/425 (5%)

Query: 8   MQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVE 67
           +  R++++ RG G++ PI  D+A      D +G  ++D + G+ V + G  +P+VV A+ 
Sbjct: 33  LSARTESMARGGGRM-PIAMDQAFGVTFKDPDGNTFIDLSAGVGVSSVGRCNPRVVEAIR 91

Query: 68  AQLKKLSHTCFQVLAYEPYL--ELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAA 125
            Q + L H+     +    L  ++ EIM   + GD    T     GS+A+E AVK A+  
Sbjct: 92  KQSESLMHSMEVNSSKRTELAAKISEIMPDGLRGDCI--TFFTQGGSDALEAAVKFAKRV 149

Query: 126 TKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPL-------HGI 178
           T R   IAF G YHG  + + ALT     Y  G G   G V  A YP          H  
Sbjct: 150 TGRHQIIAFHGGYHGIWNASNALTTGT-AYRKGFGPFMGGVIHAPYPYAYRFPFDTSHKS 208

Query: 179 SEDDAIASIHRIFKND-AAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLI 237
           +E  A   +  +      A +D+AA+++EPVQGEGG+   SP F+Q LR  CD  G +LI
Sbjct: 209 AEQIAGEYVDYLLNTPYTAADDVAAVIVEPVQGEGGYVPPSPEFLQILRKACDRSGALLI 268

Query: 238 ADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGT 297
            DEVQ+GAGRTG ++A+E  GV PD+ TF K I G  P+AG+  R+++   +  G    T
Sbjct: 269 VDEVQAGAGRTGKMWAVEHSGVKPDMLTFGKGIGGDMPMAGLVMRSDLAAKIPDGSQPNT 328

Query: 298 YAGNPIACVAALEVLKVFEQE--NLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMI 355
           +A N I+   AL  + + +    +L+ +A+ LG + ++ + +     P +G+VRG G MI
Sbjct: 329 FAANSISAAVALTNISILQDPRLDLVNRAHTLGLEAQERIRSF--NSPWVGEVRGRGLMI 386

Query: 356 AIELFEDGDHNKPDAKLTAEIVARARD----KGLILLSCGPYYNVLRILVPLTIEDAQIR 411
            IEL E+ +  +P   L+ E + +  D     G++++ CG Y NV+R++  LTI  + + 
Sbjct: 387 GIELVENRETREP---LSREKLGKLMDYVVGHGVLMIPCGRYTNVMRVMPSLTIPRSLMF 443

Query: 412 QGLEI 416
           +GL+I
Sbjct: 444 KGLDI 448


Lambda     K      H
   0.320    0.137    0.401 

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: 525
Number of extensions: 31
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: 426
Length of database: 456
Length adjustment: 32
Effective length of query: 394
Effective length of database: 424
Effective search space:   167056
Effective search space used:   167056
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis