GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Herbaspirillum seropedicae SmR1

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__HerbieS:HSERO_RS05420
          Length = 426

 Score =  217 bits (553), Expect = 4e-61
 Identities = 143/383 (37%), Positives = 205/383 (53%), Gaps = 34/383 (8%)

Query: 28  DLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMP-QTLPT 86
           D    R   A +WD EG  +ID   G  V N GH +P++++A++ Q +       Q +P 
Sbjct: 27  DFYAERAANAELWDVEGRRFIDFAAGIAVLNTGHRHPKLLDAMRAQMDKFTHTAYQIVPY 86

Query: 87  PMRGEFYRTLTAILP---PELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGR 143
               E    +  + P   P+    F  ++G EA E A+K ARAHTGR   +A   GF GR
Sbjct: 87  ASYVELAERINRLTPGNYPKKTAFF--STGAEAVENAIKIARAHTGRPGVIAFAGGFHGR 144

Query: 144 TMGSLSVTWE-PKYREPFLPLVEPVEFIPY----------NDVEALKRAVDEE-----TA 187
           TM  +++T +   Y+  F P    V   PY          + +EA+K     +      A
Sbjct: 145 TMMGMALTGKVAPYKLGFGPFPGDVFHAPYPSALHGITSEDALEAVKGLFKSDIEAKRVA 204

Query: 188 AVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVP 247
           A+ILEPVQGEGG   A  +F+R  R +  E G LLI DE+Q+G GRTGK FA EH+ ++P
Sbjct: 205 AIILEPVQGEGGFYAAPADFMRGLRALCDEHGILLIADEVQSGYGRTGKLFAMEHYDVLP 264

Query: 248 DILTLAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLW 307
           D++T+AK+L GG+PL A   R E+  +   GG G T+ GNPLA+A+ +A +  +E  +L 
Sbjct: 265 DLMTMAKSLAGGMPLSAVNGRAEIMDAPAPGGLGGTYAGNPLAIASALAVLDVMEEEQLV 324

Query: 308 ERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVGLELKEKA-----APYIARLEK---E 357
            R   LG    E L+ + S  P+I EVRG+G MV +E  + A     A Y  ++++    
Sbjct: 325 TRGQRLGDKLQEHLKELRSSVPQIAEVRGVGAMVAVEFADPATGKPDAEYTKKVQQHALN 384

Query: 358 HRVLALQAGP--TVIRFLPPLVI 378
           + +L L  G    VIRFL PL I
Sbjct: 385 NGLLLLTCGSYGNVIRFLFPLTI 407


Lambda     K      H
   0.319    0.137    0.402 

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: 423
Number of extensions: 23
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: 395
Length of database: 426
Length adjustment: 31
Effective length of query: 364
Effective length of database: 395
Effective search space:   143780
Effective search space used:   143780
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 (21.7 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