GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Pseudomonas fluorescens FW300-N2C3

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate AO356_10715 AO356_10715 4-aminobutyrate aminotransferase

Query= BRENDA::A0A140N9B6
         (406 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_10715
          Length = 425

 Score =  211 bits (536), Expect = 4e-59
 Identities = 141/399 (35%), Positives = 207/399 (51%), Gaps = 38/399 (9%)

Query: 22  PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTG-NGYTN 80
           P      + + + D +G+E+IDFAGGIAV   GH HP++  A+  Q +K  HT       
Sbjct: 25  PIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTAQLNKLTHTCFQVLAY 84

Query: 81  EPVLRLAKKL---IDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNA 137
           EP + + +K+   +   FA +     +G+EA E A+K+AR        + ++G++AF  A
Sbjct: 85  EPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARA------ATGRAGVIAFTGA 138

Query: 138 FHGRTLFTVSAGGQPA-YSQDFAPLPADIRHAAY-NDINSASALIDDSTC---------- 185
           +HGRT+ T+   G+   YS     +P  I  A Y N+++  S  IDDS            
Sbjct: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS--IDDSIASIERIFKNDA 196

Query: 186 ------AVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYM 239
                 A+I+EP+QGEGG   A   F++ LR LC++H  LLI DEVQTG GRTG  +A  
Sbjct: 197 EPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAME 256

Query: 240 HYGVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELI 299
             GV  DL T AK++ GGFP+  +    E    +  G  G TY G+P+A A A  V+E+ 
Sbjct: 257 QMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVF 316

Query: 300 NTPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVL--NAD-YAGQAKQISQ 356
               +L+  K   +  V  L  I  +Y +  EVR LG +I   L  N D +   A  ++Q
Sbjct: 317 EEEHLLDRCKAVGERLVTGLKAIQKKYPVIGEVRALGAMIAVELFENGDTHKPNAAAVAQ 376

Query: 357 EAAKA---GVMVLIAG--GNVVRFAPALNVSEEEVTTGL 390
             AKA   G+++L  G  GNV+R    L   +E++  GL
Sbjct: 377 VVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGL 415


Lambda     K      H
   0.319    0.135    0.406 

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: 447
Number of extensions: 19
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: 406
Length of database: 425
Length adjustment: 31
Effective length of query: 375
Effective length of database: 394
Effective search space:   147750
Effective search space used:   147750
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: 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