Alignments for a candidate for argC in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Trichormus variabilis ATCC 29413

Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_011317314.1 AVA_RS02170 N-acetyl-gamma-glutamyl-phosphate reductase

Query= reanno::Smeli:SMc01801
         (310 letters)



>NCBI__GCF_000204075.1:WP_011317314.1
          Length = 322

 Score =  295 bits (754), Expect = 1e-84
 Identities = 158/314 (50%), Positives = 213/314 (67%), Gaps = 9/314 (2%)

Query: 2   KPKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDD 61
           KPKIFIDGE GTTGLQI  R+  R D+EL+SI  ++R++A  R  LLNS D+AILCLPDD
Sbjct: 3   KPKIFIDGEAGTTGLQIYSRLNERDDIELVSIAASKRKDADERAKLLNSVDVAILCLPDD 62

Query: 62  ASREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPTG 121
           A+REAV++V  +++V+I+D STA+R A  W YGF E++  Q ++I +A+ V+NPGCYPTG
Sbjct: 63  AAREAVSLVH-SSQVKILDASTAYRTAQGWVYGFPELNPGQREKIANAQFVSNPGCYPTG 121

Query: 122 AIALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGA----PHFLYG 177
            +A +RPL   GILP  +P+T+NAVSGY+GGGK +I Q  D  +    GA    P  +YG
Sbjct: 122 FLACVRPLIAQGILPSSFPITINAVSGYSGGGKSLI-QKYDSFHEQQKGATSDYPFGIYG 180

Query: 178 LTLKHKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVD 237
           L   HKHV EM  H  L   P+F P+VG F QGM+VQ+PL L  L    + E IH+A+  
Sbjct: 181 LQFGHKHVKEMHQHSGLASPPLFIPAVGDFEQGMLVQIPLPLWTLDNPPSGEEIHQAIAQ 240

Query: 238 HYAGQSIVEVVPLDESAKL---ARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGK 294
           +Y G+  V+V    + + L     +DAT + G++ +++FVF         LVA LDNLGK
Sbjct: 241 YYQGEKFVQVASFKDPSLLRDGTFLDATAVNGTNIVQVFVFANDNTKEALLVARLDNLGK 300

Query: 295 GASGAAVQNMDLML 308
           GASGAAVQN+++ML
Sbjct: 301 GASGAAVQNLNIML 314


Lambda     K      H
   0.319    0.136    0.395 

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: 287
Number of extensions: 10
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: 310
Length of database: 322
Length adjustment: 27
Effective length of query: 283
Effective length of database: 295
Effective search space:    83485
Effective search space used:    83485
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)

Align candidate WP_011317314.1 AVA_RS02170 (N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01851 (argC: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01851.hmm
# target sequence database:        /tmp/gapView.23760.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01851  [M=310]
Accession:   TIGR01851
Description: argC_other: N-acetyl-gamma-glutamyl-phosphate reductase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-174  564.8   0.0   2.8e-174  564.6   0.0    1.0  1  lcl|NCBI__GCF_000204075.1:WP_011317314.1  AVA_RS02170 N-acetyl-gamma-gluta


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011317314.1  AVA_RS02170 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  564.6   0.0  2.8e-174  2.8e-174       1     310 []       3     316 ..       3     316 .. 0.99

  Alignments for each domain:
  == domain 1  score: 564.6 bits;  conditional E-value: 2.8e-174
                                 TIGR01851   1 kpkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslv 69 
                                               kpk+fidGeaGttGlqi++rl+erdd+el+si+++krkdaderaklln++dvailclpddaareavslv
  lcl|NCBI__GCF_000204075.1:WP_011317314.1   3 KPKIFIDGEAGTTGLQIYSRLNERDDIELVSIAASKRKDADERAKLLNSVDVAILCLPDDAAREAVSLV 71 
                                               79******************************************************************* PP

                                 TIGR01851  70 dnpntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfP 138
                                               +++++kildastayrta++wvyGfpel+++qrekiana++v+nPGcy+tg++a++rPl+++GilP++fP
  lcl|NCBI__GCF_000204075.1:WP_011317314.1  72 HSSQVKILDASTAYRTAQGWVYGFPELNPGQREKIANAQFVSNPGCYPTGFLACVRPLIAQGILPSSFP 140
                                               ********************************************************************* PP

                                 TIGR01851 139 vtinavsGysGGGkaliakye...eesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGd 204
                                               +tinavsGysGGGk+li+ky+   e++++++++++f iygl+++hkh++em++hsglas+P+f+PavGd
  lcl|NCBI__GCF_000204075.1:WP_011317314.1 141 ITINAVSGYSGGGKSLIQKYDsfhEQQKGATSDYPFGIYGLQFGHKHVKEMHQHSGLASPPLFIPAVGD 209
                                               ********************999899******************************************* PP

                                 TIGR01851 205 faqGllveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaelldd.tildaqglngtnrlel 272
                                               f+qG+lv+ipl+l++ld+++s+e+ih+a+a+yy+Gekfv+va+++d++ll+d t+lda+++ngtn++++
  lcl|NCBI__GCF_000204075.1:WP_011317314.1 210 FEQGMLVQIPLPLWTLDNPPSGEEIHQAIAQYYQGEKFVQVASFKDPSLLRDgTFLDATAVNGTNIVQV 278
                                               ****************************************************99*************** PP

                                 TIGR01851 273 fvfgsddgerallvarldnlGkGasGaavqnlnialGl 310
                                               fvf++d++++allvarldnlGkGasGaavqnlni+lGl
  lcl|NCBI__GCF_000204075.1:WP_011317314.1 279 FVFANDNTKEALLVARLDNLGKGASGAAVQNLNIMLGL 316
                                               *************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (322 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.02
//
[ok]

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis