GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3607958
          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:

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