GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysY in Herbaspirillum seropedicae SmR1

Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.- (uncharacterized)
to candidate HSERO_RS19210 HSERO_RS19210 N-acetyl-gamma-glutamyl-phosphate reductase

Query= curated2:A0RWW0
         (348 letters)



>FitnessBrowser__HerbieS:HSERO_RS19210
          Length = 345

 Score =  243 bits (619), Expect = 7e-69
 Identities = 134/349 (38%), Positives = 195/349 (55%), Gaps = 7/349 (2%)

Query: 1   MKVGVVGASGYVGGETLRLLVNHPDVEIAAVTSRQHVGEYLHRVQPSLRGFTDLTFSELD 60
           +KVG+VG +GY G E LR+   HP+  + AVTSR+  G  +  + PSLRG  D+ FS  D
Sbjct: 2   IKVGIVGGTGYTGVELLRIFATHPEARVQAVTSRKEDGMPVAEMYPSLRGRVDVAFSSPD 61

Query: 61  YDRLSDSCDLVFTAVPHGTATDIVRALYDRDIKVIDLSADYRLHDPADYTKWYGWEHPHP 120
             RL+D CD+VF A PHG A      L    +KVIDL+AD+R+ D A + KWY   H   
Sbjct: 62  KARLTD-CDVVFFATPHGVAMAQAPELVAAGVKVIDLAADFRMQDVAAFEKWYKLPHSCT 120

Query: 121 DYLSKSVFGIPELHREEIRSAKLVSCPGCMAVTSILALAPPVREGLVDTEHIVVDSKIGS 180
           D L ++ +G+PEL+RE IR A++V  PGC   T  L  AP ++ G++D  H++ D K G 
Sbjct: 121 DLLKEAAYGLPELNREAIRKARVVGNPGCYPTTMQLGYAPLLKAGVIDASHLIADCKSGV 180

Query: 181 SGAG--AGAGTAHAMRAGVIRPYKPAKHRHTGEIEQELSGIAGKKIRVSMSPHAVDVVRG 238
           SGAG  A      +  +   + Y  + HRH+ E  + LS +   K+ +  +PH V ++RG
Sbjct: 181 SGAGRKAELSLLFSEASDNFKAYGVSGHRHSPETIERLSHLTSDKVGLLFTPHLVPMIRG 240

Query: 239 ILCTNHVFLTREASEKDLWKMYRQAYGEERFVRLIRDKKGLYKFPDPKFLVGSNFCDIGF 298
           +  T +  LT+E     L  ++  AY +E FV    D       P+ +    SN   +  
Sbjct: 241 MHSTLYARLTKEIDNAALQALFEDAYKDEPFV----DVLPFGAHPETRTTRASNMLRLAV 296

Query: 299 DLDEDNNRLVAISASDNLMKGAAGSAIQNMNIMAGLDEMSGLRYTPLTP 347
               D + +V +   DNL+KGA+G A+Q MN+M GLDE +GL+  P+ P
Sbjct: 297 HRPGDGDTVVVLVVQDNLVKGASGQAVQCMNLMFGLDETTGLQQVPVLP 345


Lambda     K      H
   0.320    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: 271
Number of extensions: 14
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: 348
Length of database: 345
Length adjustment: 29
Effective length of query: 319
Effective length of database: 316
Effective search space:   100804
Effective search space used:   100804
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: 49 (23.5 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