GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Pseudomonas stutzeri RCH2

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate GFF4018 Psest_4091 diaminobutyrate--2-oxoglutarate aminotransferase

Query= curated2:Q8ZV07
         (383 letters)



>FitnessBrowser__psRCH2:GFF4018
          Length = 425

 Score =  176 bits (446), Expect = 1e-48
 Identities = 119/370 (32%), Positives = 203/370 (54%), Gaps = 32/370 (8%)

Query: 28  GQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIWAVP-LNFATPARERFIEEFSKL-LP 85
           G+RYID     G +  GH +P + +A+ + +E       L+  T A+ERF+E F++L L 
Sbjct: 35  GKRYIDFLAGAGTLNYGHNHPVLKQALLEYIENDGITHGLDMYTAAKERFLETFNRLILE 94

Query: 86  PK----FGVVFLQNTGTEAVEVAIKIAKKVTRKPTIVAFTNSFHGRTMGSLSITWNEKYK 141
           P+    + + F   TGT AVE A+K+A+KVT +  I++FTN FHG ++G+L+ T N+ ++
Sbjct: 95  PRGMGDYRMQFTGPTGTNAVEAAMKLARKVTGRNNIISFTNGFHGCSIGALAATGNQHHR 154

Query: 142 --------KAFEPLYPHVRFGKFNVPHEVDKLIGEDT------CCVVVEPIQGEGGVNPA 187
                         Y +    K N    +DKL+ + +        V+VE +QGEGG+N A
Sbjct: 155 GGSGISLTDVSRMPYANYFGDKTNTIGMMDKLLSDPSSGIDKPAAVIVEVVQGEGGLNTA 214

Query: 188 TPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQKYGVEPDIFTAGKPVAG-GLPI 246
           + E+++ L +  ++   LLI D++Q G GRTG  ++F++ G++PDI T  K ++G GLP 
Sbjct: 215 STEWMRKLEKLCRKHEMLLIVDDIQAGCGRTGTFFSFEEMGIQPDIVTLSKSLSGYGLPF 274

Query: 247 GLAVAREDFGDVFEPGEHGSTFAGNAVVMAAAAAASRLLREED-----VPGRAERIGAEL 301
            + + R++  D ++PGEH  TF GN      AAAA     + D     V  + +RI   +
Sbjct: 275 AMVLLRQEL-DQWKPGEHNGTFRGNNHAFVTAAAAVEHFWQNDAFANSVKAKGKRIADGM 333

Query: 302 AKALGDTGSRLAVRVKGMGLMLGLEL--RVKADQFIQPLLERGVMALTAGVNT--LRFLP 357
            + +   G   ++ +KG G+M+G+       A    +   E G++  T+G ++  ++ L 
Sbjct: 334 QRIIRRHGPD-SLYLKGRGMMIGISCPDGEIAAAVCRHAFENGLVIETSGAHSEVVKCLC 392

Query: 358 PYMISKEDVE 367
           P +IS+E ++
Sbjct: 393 PLIISEEQID 402


Lambda     K      H
   0.320    0.138    0.408 

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: 351
Number of extensions: 23
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: 383
Length of database: 425
Length adjustment: 31
Effective length of query: 352
Effective length of database: 394
Effective search space:   138688
Effective search space used:   138688
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