GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Herbaspirillum seropedicae SmR1

Align 2-aminoadipate:2-oxoglutarate aminotransferase (EC 2.6.1.39) (characterized)
to candidate HSERO_RS17885 HSERO_RS17885 aminotransferase

Query= reanno::Smeli:SMc04386
         (410 letters)



>FitnessBrowser__HerbieS:HSERO_RS17885
          Length = 393

 Score =  187 bits (475), Expect = 5e-52
 Identities = 124/395 (31%), Positives = 206/395 (52%), Gaps = 22/395 (5%)

Query: 13  QPASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGET 72
           Q A+R+  I    ++++  +AA ++++G+ +I +G GEPDF  P  V +AA+ A+  G+ 
Sbjct: 5   QLAARLQHIAPFHVMELSKKAAVLEQQGRHLIHMGIGEPDFTAPPAVVEAATRAMTEGKM 64

Query: 73  KYTALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPT 132
           +YT+  G P+L+ AI + ++   GL    + I V  GA   L  A  A ++   EV++P 
Sbjct: 65  QYTSATGLPQLRAAISDHYRSVYGLEIAPERIVVTAGASAALLLACAALVERDSEVLMPD 124

Query: 133 PYWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYS 192
           P +      V   EG+  LIA      F+L+A+ +       TR VLL SPSNP+G +  
Sbjct: 125 PSYPCNRHFVAAFEGRAKLIASGPEHRFQLSAQMVREHWGSATRGVLLASPSNPTGTSIL 184

Query: 193 AADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYA 252
             + R ++   +R    + +VD++Y+ + Y+G  F   +     L +  + +N  SK + 
Sbjct: 185 PDELRAIVGE-VRQRGGFTIVDEIYQGLSYEGAPFSALS-----LGDDVVVINSFSKYFN 238

Query: 253 MTGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQD--FLKERTESFQR 310
           MTGWR+G+   P  L+  +  +      C SSI+Q A+VA    PQ     +ER   F+R
Sbjct: 239 MTGWRLGWLVLPPALVPQVEKLAQNLLICASSIAQHAAVACFT-PQTLALYEERKAEFKR 297

Query: 311 RRDLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHV 370
           RRD +V  L ++      +P+GAFY ++ C+     +     ++  D      +L +A V
Sbjct: 298 RRDYIVPALESLGFTVPVMPDGAFYVYADCSA----LADDADQLSLD------MLNEAGV 347

Query: 371 AVVPGSAFG---LSPFFRISYATSEAELKEALERI 402
            +VPG  FG      + R+SYATS   L+EA+ R+
Sbjct: 348 VLVPGLDFGPFTARRYIRLSYATSMENLQEAVARL 382


Lambda     K      H
   0.318    0.134    0.393 

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: 362
Number of extensions: 20
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: 410
Length of database: 393
Length adjustment: 31
Effective length of query: 379
Effective length of database: 362
Effective search space:   137198
Effective search space used:   137198
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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