GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Shewanella sp. ANA-3

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 7025958 Shewana3_3106 beta alanine--pyruvate transaminase (RefSeq)

Query= curated2:Q8TUZ5
         (389 letters)



>FitnessBrowser__ANA3:7025958
          Length = 446

 Score =  191 bits (486), Expect = 3e-53
 Identities = 137/417 (32%), Positives = 212/417 (50%), Gaps = 48/417 (11%)

Query: 19  PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYNE 78
           P  L   EG    D  GN+ +D  AG+     GH    + EAV +Q+  + +  +     
Sbjct: 32  PRLLAQAEGMYYTDINGNKVLDSTAGLWCCNAGHGRREISEAVSKQIREMDYAPSFQMGH 91

Query: 79  PQA-EAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF------TGCTKFIAFEGGF 131
           P A E A  L E +P+ LNKVFF NSG+ESV+ A+K+A  +         T+FI  E G+
Sbjct: 92  PLAFELAERLTELSPEGLNKVFFTNSGSESVDTALKMALCYHRANGQASRTRFIGRELGY 151

Query: 132 HGRTMGALSATWKPEFREPFE-PLVPEFEHVPYG-DVN-----------AVEKAI----- 173
           HG   G +S       R+ F   L+   +H+P+  D+              EKA      
Sbjct: 152 HGVGFGGISVGGLSNNRKAFSGQLLQGVDHLPHTLDIQNSAFSRGLPSLGAEKAEVLEQL 211

Query: 174 -----DDDTAAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQF 228
                 ++ AAVIVEP+ G AGV +PP+G+L+ LRE+  ++G+LLI DEV +  GR G  
Sbjct: 212 VTLHGAENIAAVIVEPMSGSAGVILPPQGYLKRLREITQKYGILLIFDEVITAFGRVGAA 271

Query: 229 FAFEHEDVLPDIVCLAKGL-GGGVPVGATIAREEVAEAFEPGD-------HGSTFGGNPL 280
           FA +   V+PDI+  AK +  G +P+GA   ++ + +    G        HG T+ G+P+
Sbjct: 272 FASQRWGVIPDIITTAKAINNGAIPMGAVFVQDFIHDTCMQGPTELIEFFHGYTYSGHPV 331

Query: 281 ACAAVCAAVSTVLEENLPEAA---ERKGKLAMRILSEAEDVVEEVRGRGLMMGVEV---- 333
           A AA  A +S    E L E +   ER  + A+  L    +V+ ++R  GL+ G ++    
Sbjct: 332 AAAAALATLSIYENEQLFERSFELERYFEDAVHSLKGLPNVI-DIRNTGLVAGFQLAPNS 390

Query: 334 -GDDERAKDVAREMLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADALRASG 389
            G  +R   V      +G LV  T GD+I + PPL++ + ++++ +  L+DA+ A G
Sbjct: 391 QGAGKRGYSVFEHCFHQGTLVRAT-GDIIAISPPLIVEKHQIDQIVNSLSDAIHAVG 446


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: 410
Number of extensions: 27
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 1
Length of query: 389
Length of database: 446
Length adjustment: 31
Effective length of query: 358
Effective length of database: 415
Effective search space:   148570
Effective search space used:   148570
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