GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Pseudomonas stutzeri RCH2

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate GFF305 Psest_0306 adenosylmethionine-8-amino-7-oxononanoate transaminase

Query= curated2:Q8TUE8
         (395 letters)



>FitnessBrowser__psRCH2:GFF305
          Length = 467

 Score =  190 bits (482), Expect = 8e-53
 Identities = 140/420 (33%), Positives = 217/420 (51%), Gaps = 57/420 (13%)

Query: 27  MQTYGRQPLV-LSKGKGAVVQDIYGKEYIDCVAGIAVNNVGHCHPTVVKAIQAQAENLIH 85
           M+ + + PL+ + +G G  ++D  GK Y+D V+   VN  GH +P + + I+ Q + L H
Sbjct: 22  MKDHEQLPLIPIRRGDGVWLEDFDGKRYLDAVSSWWVNVFGHANPRINQRIKDQVDQLEH 81

Query: 86  VSNLYYT-EIQAEFAETLASIT--GMERVFFCNSGAESVEAAMKLA-----RVATG-KSA 136
           V    ++ +   E +E L ++T  G++RVF+ ++G+  +E A+K++         G K  
Sbjct: 82  VMLAGFSHQPVVELSERLVALTPAGLDRVFYTDNGSTGIEVALKMSFHYWRNSGRGQKQR 141

Query: 137 FVAAEHSFHGRTIGALSVTHKSMYRDPFMPPVSSETTFVPYSDA----------EAIRQA 186
           FV   +S+HG T+ A+SV   +++ D + P +  +T  VP  D           E  RQ 
Sbjct: 142 FVTLTNSYHGETVAAMSVGDVALFTDTYKP-LLLDTFKVPSPDCYLRPDGVSWEEHSRQM 200

Query: 187 IS----------ENTAAVILEP-IQGEGGINIPDPGYLKEVREICDETGALLIFDEVQTG 235
            +          ++ AAVI+EP IQG GG+ +  P YLK +RE CD     LI DE+  G
Sbjct: 201 FAHMEQTLAEHHQDIAAVIVEPLIQGAGGMRMYHPVYLKLLREACDRYEVHLIHDEIAVG 260

Query: 236 FGRTGTWFCKEQFGVEPDIMSMSKAIGGGF-PMGAIAAHNGI---------NFGRGQHAS 285
           FGRTGT F  EQ G+ PD + +SKA+ GG+ PM A+   + I               H+ 
Sbjct: 261 FGRTGTMFACEQAGITPDFLCLSKALTGGYLPMAAVLTTDRIYQAFYDDYSTLRAFLHSH 320

Query: 286 TFGGGPLACAAALASVKVIREEKLLERSKEMGAYFMKKLAGMV-RDDVVEVRGKGLMIGV 344
           T+ G PLACAAALA++ +  E+ ++E +K + A      A +V    V EVR  G+ + +
Sbjct: 321 TYTGNPLACAAALATLDIFAEDNVIEANKPLAARMASATAHLVDHPHVAEVRQTGMALAI 380

Query: 345 EI--------KYPCG-----KFVDFAREQGVLVNCTSDSVLRLVPPLVITKEQIDTVVDV 391
           E+         YP       K    A E+G L+     SV+  +PP  IT+EQID +  V
Sbjct: 381 EMVQDKASRTAYPWQERRGLKVYQHALERGALLR-PLGSVVYFLPPYCITEEQIDFLAAV 439


Lambda     K      H
   0.319    0.135    0.391 

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: 402
Number of extensions: 27
Number of successful extensions: 5
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: 395
Length of database: 467
Length adjustment: 32
Effective length of query: 363
Effective length of database: 435
Effective search space:   157905
Effective search space used:   157905
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 (21.7 bits)
S2: 51 (24.3 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