GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Methylocystis bryophila S285

Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate WP_245300308.1 B1812_RS21480 diaminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P50457
         (421 letters)



>NCBI__GCF_002117405.1:WP_245300308.1
          Length = 454

 Score =  205 bits (521), Expect = 3e-57
 Identities = 144/415 (34%), Positives = 210/415 (50%), Gaps = 28/415 (6%)

Query: 15  PRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTH 74
           PRG+ +      +S     ++DVE  EYID  +G      GH H  +V AV   L     
Sbjct: 27  PRGLPIAL----KSGGGVRVRDVEDREYIDCLSGAGTQPLGHNHEVVVDAVRDALSGAVP 82

Query: 75  TAYQIVPY---ESYV-TLAEKINALAPVSGQAKTAFF-TTGAEAVENAVKIARAHTGRPG 129
                +P    + ++  L + + A  P     K  F   +GA+A+E A+K+ R  TGR G
Sbjct: 83  LQTLDLPTPLKDRFIGDLFDSLPAEFP--NNFKIQFCGPSGADAIEAALKLVRTATGRRG 140

Query: 130 VIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLH-------GISTQDS 182
           +++F G +HG T   ++LTG+  P K         V  +PYPSD            ++ S
Sbjct: 141 ILSFRGAYHGMTSGALSLTGESGP-KAAINGGAAEVQFLPYPSDYRCPFGLGGHAGSEMS 199

Query: 183 LDAIERLFKSDIEAKQV-AAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQ 241
              IE L +  +    + AA+I E VQGEGG N AP   +  IR + +  GI +I DEVQ
Sbjct: 200 ARYIENLLEDPLSGVPLPAAMILEVVQGEGGINPAPDSWLRKIREITEFRGIPLILDEVQ 259

Query: 242 SGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNP 301
           +G  RTG+L+A  H    PD++ ++K++ GG+PLS V+     +D   PG   GT+ GN 
Sbjct: 260 TGLGRTGRLYAFQHAGITPDVLVLSKAIGGGLPLSVVIYRRE-LDHWQPGAHAGTFRGNQ 318

Query: 302 LAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEF--- 358
           LA AA  A +  I  + L   A ++G RL++ L   +     I  VRG G M+ VE    
Sbjct: 319 LAFAAGAATIRFISAQRLECNAEEMGCRLQDALRSIQSETRCIGHVRGRGLMVGVEIVRA 378

Query: 359 --NDPQTGEPSAA--IAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFD 409
              D   G PS++  +AQK+Q   L +GL+L   G  G+VIRFL PL +  A+ D
Sbjct: 379 DHTDRLAGPPSSSPQMAQKLQNECLRRGLILERGGRLGSVIRFLPPLIVTPAEID 433


Lambda     K      H
   0.319    0.134    0.388 

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: 509
Number of extensions: 27
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 421
Length of database: 454
Length adjustment: 32
Effective length of query: 389
Effective length of database: 422
Effective search space:   164158
Effective search space used:   164158
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 Apr 09 2024. 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