GapMind for Amino acid biosynthesis

 

Alignments 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.

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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