GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Dinoroseobacter shibae DFL-12

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 3607958 Dshi_1366 aminotransferase class-III (RefSeq)

Query= curated2:Q8TUZ5
         (389 letters)



>FitnessBrowser__Dino:3607958
          Length = 441

 Score =  191 bits (486), Expect = 3e-53
 Identities = 134/413 (32%), Positives = 208/413 (50%), Gaps = 46/413 (11%)

Query: 19  PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYNE 78
           P   V  +G      EG + +D  AG+     GH  P +VEA++ Q   L +        
Sbjct: 29  PRMFVAADGMYYTTAEGRQVLDGTAGLWCCNAGHKRPRIVEAIQAQAAELDYAPAFQMGH 88

Query: 79  PQA-EAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF------TGCTKFIAFEGGF 131
           P+A E A  L E AP  ++ VF+ NSG+E+VE A+K+A  +       G T+ I  E G+
Sbjct: 89  PRAFELANRLVEIAPDGMDHVFYTNSGSEAVESALKIALAYHRARGEAGRTRLIGRERGY 148

Query: 132 HGRTMGALSATWKPEFREPFEPLVPEFEHVPYGDV-----------------NAVEKAID 174
           HG   G +S       R+ F  L+   +H+P+  +                 + +E+ I 
Sbjct: 149 HGVNFGGISVGGIVNNRKHFGTLLTGVDHLPHTHIPENQWSRGMPELGAHLADDLERIIA 208

Query: 175 ----DDTAAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFA 230
               +  AAVIVEP+ G  GV +PP+G+L+ LR++  +HG++LI DEV +G GR G  F 
Sbjct: 209 LHGAETIAAVIVEPMAGSTGVLLPPKGYLQRLRKITQDHGIVLIFDEVITGFGRVGAAFG 268

Query: 231 FEHEDVLPDIVCLAKGLGGGV-PVGATIAREEVAEAFEPGD-------HGSTFGGNPLAC 282
            +   V PD++  AKGL  GV P+GA +    + +AF  G        HG T+ GNP+A 
Sbjct: 269 AQRFGVTPDMITCAKGLTNGVIPMGAVLCGSHIHDAFMQGPENLIELFHGYTYSGNPIAS 328

Query: 283 AAVCAAVSTVLEENLPEAA---ERKGKLAMRILSEAEDVVEEVRGRGLMMGVEV-----G 334
           AA  A + T  E++L   A   E   + A+  L  A  V+ ++R  GL+  +E+      
Sbjct: 329 AAGLATLETYREDDLFARALDLEPYWQEALHSLKGARHVI-DIRNLGLIGAIELEPISGH 387

Query: 335 DDERAKDVAREMLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADALRA 387
             +RA     +  D+G L+  T+GD+I L PPL+I   ++++ +  L + L A
Sbjct: 388 PTKRAFQAFLDAYDKGVLIR-TTGDIIALSPPLIIETAQIDRIVETLGEVLAA 439


Lambda     K      H
   0.318    0.137    0.405 

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: 401
Number of extensions: 21
Number of successful extensions: 7
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: 389
Length of database: 441
Length adjustment: 31
Effective length of query: 358
Effective length of database: 410
Effective search space:   146780
Effective search space used:   146780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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