GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Pseudomonas stutzeri RCH2

Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate GFF305 Psest_0306 adenosylmethionine-8-amino-7-oxononanoate transaminase

Query= SwissProt::Q8ZPV2
         (408 letters)



>FitnessBrowser__psRCH2:GFF305
          Length = 467

 Score =  163 bits (412), Expect = 1e-44
 Identities = 126/410 (30%), Positives = 194/410 (47%), Gaps = 50/410 (12%)

Query: 22  PFIPVR-GEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIG-NGYT 79
           P IP+R G+G  L D  GK Y+D      VN  GHA+P + + + +Q ++  H+   G++
Sbjct: 29  PLIPIRRGDGVWLEDFDGKRYLDAVSSWWVNVFGHANPRINQRIKDQVDQLEHVMLAGFS 88

Query: 80  NEPALRLAKKLIDATFA--ERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNA 137
           ++P + L+++L+  T A  +RVF+ ++G+   E ALK++  Y  +     K   V   N+
Sbjct: 89  HQPVVELSERLVALTPAGLDRVFYTDNGSTGIEVALKMSFHYWRNSGRGQKQRFVTLTNS 148

Query: 138 FHGRTLFTVSAGGQPTYSQDFAPL--------PPDI------------RHAAYNDLNSAS 177
           +HG T+  +S G    ++  + PL         PD                 +  +    
Sbjct: 149 YHGETVAAMSVGDVALFTDTYKPLLLDTFKVPSPDCYLRPDGVSWEEHSRQMFAHMEQTL 208

Query: 178 ALIDDNTCAVIVEP-VQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELY 236
           A    +  AVIVEP +QG GG+      +L+ LRE CDR++  LI DE+  G GRTG ++
Sbjct: 209 AEHHQDIAAVIVEPLIQGAGGMRMYHPVYLKLLREACDRYEVHLIHDEIAVGFGRTGTMF 268

Query: 237 AYMHYGVTPDILTTAKALGGGF-PIGAMLTTQ-------DYASVMTPGTHGTTYGGNPLA 288
           A    G+TPD L  +KAL GG+ P+ A+LTT        D  S +    H  TY GNPLA
Sbjct: 269 ACEQAGITPDFLCLSKALTGGYLPMAAVLTTDRIYQAFYDDYSTLRAFLHSHTYTGNPLA 328

Query: 289 TAVAGKVLDII---NTPEMQNGVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLLGCVLQT 345
            A A   LDI    N  E    +  R  +    L    V     +E+R  G+ L   +  
Sbjct: 329 CAAALATLDIFAEDNVIEANKPLAARMASATAHL----VDHPHVAEVRQTGMALAIEMVQ 384

Query: 346 EFAGKAKL---------IAQEAAKAGVMVLIAGGDVVRFAPALNVSDEEI 386
           + A +            + Q A + G + L   G VV F P   +++E+I
Sbjct: 385 DKASRTAYPWQERRGLKVYQHALERGAL-LRPLGSVVYFLPPYCITEEQI 433


Lambda     K      H
   0.320    0.137    0.413 

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: 432
Number of extensions: 22
Number of successful extensions: 4
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: 408
Length of database: 467
Length adjustment: 32
Effective length of query: 376
Effective length of database: 435
Effective search space:   163560
Effective search space used:   163560
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 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