GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argJ in Herbaspirillum seropedicae SmR1

Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate HSERO_RS01730 HSERO_RS01730 N-acetylglutamate synthase

Query= CharProtDB::CH_000559
         (406 letters)



>FitnessBrowser__HerbieS:HSERO_RS01730
          Length = 411

 Score =  421 bits (1082), Expect = e-122
 Identities = 229/413 (55%), Positives = 287/413 (69%), Gaps = 9/413 (2%)

Query: 1   MAVNLTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAP 60
           MAVN        L  + GI L  A+AGV+K    D+ ++ +A  +TV  VFT NRFCAAP
Sbjct: 1   MAVNSPIPVPSDLKAVAGIELGHAEAGVRKANRKDVLVMKLAETATVAGVFTKNRFCAAP 60

Query: 61  VHIAKSHLFDEDG---VRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPF 117
           V I +++L        +RALVINTGNANAGTG +G   A +VCAA A+Q+G +  Q++PF
Sbjct: 61  VQICQANLAQLSAGKPIRALVINTGNANAGTGEEGLQRAKSVCAALAQQMGVEAQQILPF 120

Query: 118 STGVILEPLPADKIIAALPK----MQPAFWNEAARAIMTTDTVPKAASREGKVGDQHTVR 173
           STGVILEPLPAD+IIA LP+    ++   W  AA +IMTTDT PKAASR   +G +  V 
Sbjct: 121 STGVILEPLPADRIIAGLPQAIGNLKADNWFNAAESIMTTDTQPKAASRTLTIGGKQVVM 180

Query: 174 ATGIAKGSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSF 233
            TGI+KG+GMI PNMATMLGF+A DAK+ Q +L  + ++ AD +FN IT+DGDTSTNDSF
Sbjct: 181 -TGISKGAGMIKPNMATMLGFLAFDAKLPQALLNQLVKDAADHSFNCITIDGDTSTNDSF 239

Query: 234 VIIATGKNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTC 293
           +++ATG   + EI +     Y QL   +  L+  LA  IVRDGEGATKFI V VE+ K+ 
Sbjct: 240 ILMATGAG-ELEITSADSEEYQQLAAAVTDLSQHLAHQIVRDGEGATKFIEVAVEDGKSV 298

Query: 294 DEARQAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHG 353
           +E RQ AY+   SPLVKTAFFASDPNLG+ LAAIGYA + DLD   + ++LDD+ VA+ G
Sbjct: 299 EECRQIAYSIGHSPLVKTAFFASDPNLGRILAAIGYAGIDDLDVSKINLWLDDVWVAKDG 358

Query: 354 GRAASYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406
           GR   Y E  GQ VM K EI VR+KL RG A A+++TCDLSH YVSINADYRS
Sbjct: 359 GRNPDYREEDGQRVMKKAEIVVRVKLARGAAKASIWTCDLSHDYVSINADYRS 411


Lambda     K      H
   0.317    0.130    0.367 

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: 381
Number of extensions: 10
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: 406
Length of database: 411
Length adjustment: 31
Effective length of query: 375
Effective length of database: 380
Effective search space:   142500
Effective search space used:   142500
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.

Links

Downloads

Related tools

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