GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Phaeobacter inhibens BS107

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate GFF900 PGA1_c09150 adenosylmethionine-8-amino-7-oxononanoate aminotransferase BioA

Query= curated2:Q8ZV07
         (383 letters)



>FitnessBrowser__Phaeo:GFF900
          Length = 432

 Score =  104 bits (260), Expect = 4e-27
 Identities = 105/393 (26%), Positives = 174/393 (44%), Gaps = 43/393 (10%)

Query: 26  DKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIWAVPLNFATPARERFIEEFSKLL- 84
           D G R ID  ++   +  GH NP I  A+  Q++ +  V     T   +  I+   KLL 
Sbjct: 43  DDGTRLIDAMSSWWCMMHGHRNPAITSAIHAQLDTLPHVMFGGLT--HDPAIDLGRKLLE 100

Query: 85  --PPKFGVVFLQNTGTEAVEVAIKIAKKVTR------KPTIVAFTNSFHGRTMGSLSIT- 135
             P     +F  ++G+ +VEVA+K+A +         +       + +HG T  ++S+  
Sbjct: 101 ITPESLTRIFYCDSGSVSVEVAMKMAVQYQHAIGQPERKEFATIRSGYHGDTWKAMSVCD 160

Query: 136 ----WNEKYKKAFEPLY----PHVRFGKFNVPHEVDKLIGE----------DTCCVVVEP 177
                +  ++ A    +    P VR  +          +GE               ++EP
Sbjct: 161 PDTGMHHLFQGALSVQHFVSRPPVRIHEDWSDDPAQNGLGELRAVLEAGQDKIAAFILEP 220

Query: 178 I-QGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQKYGVEPDIFTA 236
           + QG GG+    PE+L   R      G LLIFDE+ TGFGRTGA++A      EPDI   
Sbjct: 221 VVQGTGGMYFYHPEYLNQARALCDELGILLIFDEIATGFGRTGALFATNFCDAEPDIICL 280

Query: 237 GKPVAGG-LPIGLAVAREDFGDVFEPGE-----HGSTFAGNAVVMAAAAAASRLLREED- 289
           GK + GG +     +  +   +    G      HG T+  N +  AAA A+  LL  +D 
Sbjct: 281 GKGLTGGHISFACTMTNDRVAEGVGGGNPGIFMHGPTYMANPLACAAAKASLDLLTGQDW 340

Query: 290 ---VPGRAERIGAELAKALGDTGSRLAVRVKGMGLMLGLELRVKADQFIQPLLERGVMAL 346
              V G AE++ +ELA A  +  +   VRV G   ++ ++  V AD+      + GV   
Sbjct: 341 RGTVSGIAEQMQSELATA-RELPNVADVRVLGAIGVIEMKHAVSADEAHARAHDMGVFLR 399

Query: 347 TAGVNTLRFLPPYMISKEDVEVVHAAVTEVLKK 379
             G N +  +PP++ + + +  + A +  + ++
Sbjct: 400 PFGKN-IYTMPPFITTPDQLSQITAGMLRLARE 431


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: 396
Number of extensions: 20
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 383
Length of database: 432
Length adjustment: 31
Effective length of query: 352
Effective length of database: 401
Effective search space:   141152
Effective search space used:   141152
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