Alignments for a candidate for argD'B in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for argD'B in Phaeobacter inhibens BS107

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF2829 PGA1_c28750 aminotransferase class-III

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>FitnessBrowser__Phaeo:GFF2829
          Length = 440

 Score =  197 bits (500), Expect = 7e-55
 Identities = 152/428 (35%), Positives = 216/428 (50%), Gaps = 57/428 (13%)

Query: 26  VRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGK--FWHTGNGYTNEPV 83
           V G+G  L D  GK Y+D +GG AV+ LGH+   ++ A+ EQ GK  F HTG   T+EP 
Sbjct: 17  VAGDGCYLIDANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVGKLAFAHTGF-LTSEPA 75

Query: 84  LRLAKQLIDATFAD--RVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGR 141
             LA  LI     D  RV+F + G+EA EAA+KLAR+Y  +R  + +  ++A + ++HG 
Sbjct: 76  EALADLLISQAPGDLHRVYFVSGGSEATEAAIKLARQYHLERGDTTRRHVIARRQSYHGN 135

Query: 142 TLFTVSAGGQPAYSQDFAPLPPQIQHA---------------------IYNDLDSAKALI 180
           TL  ++AGG     Q FAPL   I H                      + N+L++    +
Sbjct: 136 TLGALAAGGNAWRRQQFAPLLIDISHIAPCYEYVDRGDGESRYDYGQRVANELEAEILRL 195

Query: 181 DDNTC-AVIVEPMQGE-GGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAY 238
              T  A + EP+ G   G VPA   + + +RE+CD +  LLI DEV  G+GRTG L+A 
Sbjct: 196 GPETVMAFMAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILDEVMCGMGRTGHLFAC 255

Query: 239 MHYGVTPDLLSTAKALGGGF-PIGALLASERCASVMTVGT----HGTTYGGNPLACAVAG 293
              GV PD+L  AK LG G+ PIGA+L S +    +  G+    HG TY G+P+A A   
Sbjct: 256 EADGVAPDILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQHGHTYIGHPVATAAGL 315

Query: 294 EVFATINTREVLNGVKQRHQWFCERLN-AINARYGLFK---EIRGLGLLIGCVLK----- 344
            V   +  R    G+ QR     E L+ A+ AR+G      ++RG GL  G  L      
Sbjct: 316 AVVRALLDR----GLVQRSAEMGETLHAALVARFGQHPHVGDLRGRGLFRGIELVADRES 371

Query: 345 ----DEYAGKAKAISNQAAEEGLMIL-IAG------ANVVRFAPALIISEDEVNSGLDRF 393
               D   G A  +   A E GL+   +AG       + +  AP  I+SED++    D+ 
Sbjct: 372 KTPFDPGLGIAGKLKKAAFEAGLICYPMAGTRDGRNGDHILLAPPFILSEDQIGEITDKL 431

Query: 394 ELACKRFL 401
           E+A  + L
Sbjct: 432 EVALDQVL 439


Lambda     K      H
   0.321    0.137    0.412 

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: 478
Number of extensions: 25
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: 406
Length of database: 440
Length adjustment: 32
Effective length of query: 374
Effective length of database: 408
Effective search space:   152592
Effective search space used:   152592
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis