GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Dinoroseobacter shibae DFL-12

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 3607958 Dshi_1366 aminotransferase class-III (RefSeq)

Query= reanno::pseudo3_N2E3:AO353_08585
         (454 letters)



>lcl|FitnessBrowser__Dino:3607958 Dshi_1366 aminotransferase
           class-III (RefSeq)
          Length = 441

 Score =  270 bits (690), Expect = 7e-77
 Identities = 151/425 (35%), Positives = 232/425 (54%), Gaps = 20/425 (4%)

Query: 22  PFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAASKQMR 81
           PF+  +Q K   PR+   A G+Y   +EG ++LDG AGLWC   G+ R  + +A   Q  
Sbjct: 18  PFTANRQFKSN-PRMFVAADGMYYTTAEGRQVLDGTAGLWCCNAGHKRPRIVEAIQAQAA 76

Query: 82  ELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKGQ 141
           EL Y   F Q  HP   ELA  + +IAP+GM+HVF+T SGSE  ++ L++   Y   +G+
Sbjct: 77  ELDYAPAF-QMGHPRAFELANRLVEIAPDGMDHVFYTNSGSEAVESALKIALAYHRARGE 135

Query: 142 PNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWFGEGGDMTPEEF 201
             +  +I R  GYHG    G S+GG+    +     + G+ H+P  +           E 
Sbjct: 136 AGRTRLIGRERGYHGVNFGGISVGGIVNNRKHFGTLLTGVDHLPHTHIPENQWSRGMPEL 195

Query: 202 GIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEILAKYDILFVADE 261
           G   A+ LE  I   G +T+ A I EP+ G+ GV++PP  Y  R+++I   + I+ + DE
Sbjct: 196 GAHLADDLERIIALHGAETIAAVIVEPMAGSTGVLLPPKGYLQRLRKITQDHGIVLIFDE 255

Query: 262 VICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEGG----DF 317
           VI GFGR G  FG+  +G+ PDM+T AKGLT+G IPMG ++    + +   +G     + 
Sbjct: 256 VITGFGRVGAAFGAQRFGVTPDMITCAKGLTNGVIPMGAVLCGSHIHDAFMQGPENLIEL 315

Query: 318 NHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELNDHPLVGEVRGVG 377
            HG+TYSG+P+A+A  L  +   RE+ +      +  PY Q+ L  L     V ++R +G
Sbjct: 316 FHGYTYSGNPIASAAGLATLETYREDDLFARA-LDLEPYWQEALHSLKGARHVIDIRNLG 374

Query: 378 LLGAIEL--VQDKATRARYVGKGVGMICRQF--CFDNGLIMRAVGDTMIIAPPLVITKAE 433
           L+GAIEL  +    T+  +         + F   +D G+++R  GD + ++PPL+I  A+
Sbjct: 375 LIGAIELEPISGHPTKRAF---------QAFLDAYDKGVLIRTTGDIIALSPPLIIETAQ 425

Query: 434 IDELV 438
           ID +V
Sbjct: 426 IDRIV 430


Lambda     K      H
   0.320    0.140    0.428 

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: 550
Number of extensions: 31
Number of successful extensions: 6
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: 454
Length of database: 441
Length adjustment: 33
Effective length of query: 421
Effective length of database: 408
Effective search space:   171768
Effective search space used:   171768
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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