GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Calditerrivibrio nitroreducens DSM 19672

Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate WP_013451594.1 CALNI_RS07435 glutamate-1-semialdehyde-2,1-aminomutase

Query= SwissProt::Q8ZPV2
         (408 letters)



>NCBI__GCF_000183405.1:WP_013451594.1
          Length = 422

 Score =  135 bits (341), Expect = 2e-36
 Identities = 117/342 (34%), Positives = 163/342 (47%), Gaps = 31/342 (9%)

Query: 22  PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTNE 81
           P    RG+GS+++D  GKEYID+         GHA   +   +     +    G     E
Sbjct: 30  PIFIDRGKGSKIYDVDGKEYIDYVCSWGPLIHGHADDDIITEVERVLKKGTTFGAPTVLE 89

Query: 82  PALRLAKKLIDATFA-ERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHG 140
             L LAKK+++   + E V   +SG EA  +A++LAR Y     G  K  I+ F+  +HG
Sbjct: 90  --LELAKKVVEMVPSIEMVRMVSSGTEAVMSAIRLARGYT----GRDK--IIKFEGCYHG 141

Query: 141 RT--LFTVSAGGQPTYSQDFAP-LPPDI-RH---AAYNDLNSASALIDDNT---CAVIVE 190
            +  L   +  G  T+ Q  +P +P D+ +H   A YNDLNS   L  +N      VIVE
Sbjct: 142 HSDSLLVKAGSGALTFGQPSSPGVPADLAKHTLIADYNDLNSVKQLFINNKNQIACVIVE 201

Query: 191 PVQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDILTT 250
           PV G  GV+   + FL GLR+LC    ALLIFDEV TG  R     A  ++ V PDI T 
Sbjct: 202 PVAGNMGVVLPEEGFLSGLRDLCSNEGALLIFDEVITGF-RLAPGGAQEYFNVMPDITTL 260

Query: 251 AKALGGGFPIGA---MLTTQDYASVMTPGTHGTTYGGNPLATAVAGKVLDIINTP---EM 304
            K LGGG P+GA        +  S + P     T  GNPLA A     L+ +N     E+
Sbjct: 261 GKILGGGLPVGAYGGRKEIMEKISPLGPVYQAGTLSGNPLAMAAGIANLNKLNENFYYEL 320

Query: 305 QNGVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLLGCVLQTE 346
           +   +   + F      L + +  F+EI      + C+  TE
Sbjct: 321 RKKSQYLWNGFKNNCRELKLNYA-FNEIES----MSCMFFTE 357


Lambda     K      H
   0.320    0.137    0.413 

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: 428
Number of extensions: 28
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: 408
Length of database: 422
Length adjustment: 31
Effective length of query: 377
Effective length of database: 391
Effective search space:   147407
Effective search space used:   147407
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: 50 (23.9 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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