GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Herbaspirillum seropedicae SmR1

Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate HSERO_RS03330 HSERO_RS03330 branched-chain amino acid aminotransferase

Query= BRENDA::P54691
         (305 letters)



>FitnessBrowser__HerbieS:HSERO_RS03330
          Length = 306

 Score =  179 bits (455), Expect = 6e-50
 Identities = 109/298 (36%), Positives = 171/298 (57%), Gaps = 17/298 (5%)

Query: 11  EDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSAKFL 70
           + + + + DA + V TH LHYG   F G+R    P+  GT + FRL  H  RL  SAK  
Sbjct: 13  DGELIDWRDATVHVLTHTLHYGMGVFEGVRAYKTPD--GTAI-FRLQEHTRRLRNSAKIF 69

Query: 71  HYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVY--SSGLGIAPRLHNLEKDFLVYGLE 126
             ++    + + +     V++NQ + S YIRPL++  S  LG++ + + +     V    
Sbjct: 70  QMEVPYDHDTLAQAQRQVVRENQLE-SCYIRPLIWIGSEKLGVSAKGNQIH--VAVAAWS 126

Query: 127 MGDYLAADGVS----CRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDEAILM 182
            G YL  DG++     + SS+ R       +R K    YI S LA  EA+  G+DEA+L+
Sbjct: 127 WGAYLGEDGLNKGIRVKTSSFSRHHVNVSLVRAKACGYYINSILANQEALADGYDEALLL 186

Query: 183 NSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPIDKSE 242
           +++G V E +G NVF+V+NG+I TP +    L+GITRD++LT+A DLGI   ++ I + E
Sbjct: 187 DTEGYVSEGSGENVFIVKNGKIYTP-DLASCLDGITRDAVLTMARDLGIEVIEKRITRDE 245

Query: 243 LMIADEVFLSGTAAKITPVKRIENFTLGGDR--PITEKLRSVLTAVTENREPKYQDWV 298
           +  ADE F +GTAA+ITP++ ++   +G     P+TEKL+++   V   R P+Y+ W+
Sbjct: 246 MYCADEAFFTGTAAEITPIRELDRRVIGSGARGPVTEKLQTLFFDVVAGRAPQYKHWL 303


Lambda     K      H
   0.320    0.138    0.406 

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: 223
Number of extensions: 12
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: 305
Length of database: 306
Length adjustment: 27
Effective length of query: 278
Effective length of database: 279
Effective search space:    77562
Effective search space used:    77562
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: 48 (23.1 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