GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Phaeobacter inhibens BS107

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate GFF2829 PGA1_c28750 aminotransferase class-III

Query= curated2:P30900
         (393 letters)



>FitnessBrowser__Phaeo:GFF2829
          Length = 440

 Score =  206 bits (525), Expect = 8e-58
 Identities = 142/436 (32%), Positives = 223/436 (51%), Gaps = 55/436 (12%)

Query: 2   IASVLPTYTRAPL-AFVRGEGSWLWTADGSRYLDLGAGIAVNALGHAAPDLVATLTEQAG 60
           ++ V P +T+A L   V G+G +L  A+G RYLD   G AV+ LGH+  +++A + EQ G
Sbjct: 1   MSHVFPRHTKADLPTAVAGDGCYLIDANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVG 60

Query: 61  KLWHVSNLYRIPEQ-ERLADMLVAKTFADT--VFFTNSGTEACELAVKMVRKHFYDKGQP 117
           KL      +   E  E LAD+L+++   D   V+F + G+EA E A+K+ R++  ++G  
Sbjct: 61  KLAFAHTGFLTSEPAEALADLLISQAPGDLHRVYFVSGGSEATEAAIKLARQYHLERGDT 120

Query: 118 ERTEILTFSGAFHGRSSAAIAAAGTEKMVKGFGPLL-------PGFVHLPWGDLDA---- 166
            R  ++    ++HG +  A+AA G     + F PLL       P + ++  GD ++    
Sbjct: 121 TRRHVIARRQSYHGNTLGALAAGGNAWRRQQFAPLLIDISHIAPCYEYVDRGDGESRYDY 180

Query: 167 -------VKAAVT----ETTAAILIEPIQGE-GGIRPAPEGFLRALREICDETGTLLVFD 214
                  ++A +     ET  A + EP+ G   G  PA EG+ + +REICD+ G LL+ D
Sbjct: 181 GQRVANELEAEILRLGPETVMAFMAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILD 240

Query: 215 EVQCGVARTGKLFAHEWAGVTPDVMMVAKGIGGGF-PLGAVLATEDAASGMIAGT----H 269
           EV CG+ RTG LFA E  GV PD++ +AKG+G G+ P+GA+L +      +  G+    H
Sbjct: 241 EVMCGMGRTGHLFACEADGVAPDILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQH 300

Query: 270 GSTYGGNPLGCAIGAKMIEIVTAPGFLDEVSRKAGFLRQWLEGLVAAHPDIFEEVRGQGL 329
           G TY G+P+  A G  ++  +   G +   +     L   L      HP +  ++RG+GL
Sbjct: 301 GHTYIGHPVATAAGLAVVRALLDRGLVQRSAEMGETLHAALVARFGQHPHV-GDLRGRGL 359

Query: 330 MLGLRL------KLP-------PGDVVKAAYAQNLLTVPAA--------DNVLRLLPALT 368
             G+ L      K P        G + KAA+   L+  P A        D++L L P   
Sbjct: 360 FRGIELVADRESKTPFDPGLGIAGKLKKAAFEAGLICYPMAGTRDGRNGDHIL-LAPPFI 418

Query: 369 ISEDDMAEAVRRLDAA 384
           +SED + E   +L+ A
Sbjct: 419 LSEDQIGEITDKLEVA 434


Lambda     K      H
   0.320    0.136    0.409 

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: 443
Number of extensions: 16
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: 393
Length of database: 440
Length adjustment: 31
Effective length of query: 362
Effective length of database: 409
Effective search space:   148058
Effective search space used:   148058
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