Alignments for a candidate for argC in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Herbaspirillum seropedicae SmR1

Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; EC 1.2.1.38; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase (uncharacterized)
to candidate HSERO_RS14025 HSERO_RS14025 N-acetyl-gamma-glutamyl-phosphate reductase

Query= curated2:B1K264
         (313 letters)



>FitnessBrowser__HerbieS:HSERO_RS14025
          Length = 309

 Score =  410 bits (1053), Expect = e-119
 Identities = 208/306 (67%), Positives = 240/306 (78%), Gaps = 1/306 (0%)

Query: 2   SFPTVFIDGDQGTTGLQIHARLRDRTDVRLLTLPAAERKDAARRADALNACDIAILCLPD 61
           + P +FIDGDQGTTGLQIH RLR R D+R+LTLPAAERKDA RRA+A+N+ DIA+LCLPD
Sbjct: 3   TLPLIFIDGDQGTTGLQIHERLRARQDLRVLTLPAAERKDAQRRAEAINSADIALLCLPD 62

Query: 62  AAAREAVGFIRNPAVRVIDASSAHRTQPDWVYGFPEMADGHAHDIAHAKRVTNPGCYPTG 121
           AAAREAV  I NP VRVIDASSAHRT PDWVYGFPEMA G A  IA A RV+NPGCYPTG
Sbjct: 63  AAAREAVAMISNPRVRVIDASSAHRTSPDWVYGFPEMAAGQAEAIATALRVSNPGCYPTG 122

Query: 122 AIGLLRPLLQAGLLPRDYPVSIHAVSGYSGGGRAAVDAFESGDAAARALPLQVYGLALEH 181
           AI LLRPL+QAGL+P DYP++IHAVSGYSGGGRA V+ +E G  AA A P   YGL L+H
Sbjct: 123 AIALLRPLVQAGLVPADYPLNIHAVSGYSGGGRAQVEQYE-GAEAAHAAPFVTYGLGLQH 181

Query: 182 KHVPEIRQHAGLAHRPFFVPAYGAYRQGIVLTIPIELRLLPAGVTGERLHACLAHHYADA 241
           KH PE++ HAGL+ RP FVP+YGA+RQGIVLTI ++ RLLPA  + ERL A L  HY  A
Sbjct: 182 KHPPEMQLHAGLSQRPLFVPSYGAFRQGIVLTIALQSRLLPAQASLERLRATLQAHYDGA 241

Query: 242 RHVDVMPLADAAAATHLDPQALNGTNDLRLGVLVNADGGQVLLSAVFDNLGKGASGAAVQ 301
            +V V+  A + + T LDP   N +N + LGV  +A  G +LL AVFDNLGKGASGAAVQ
Sbjct: 242 HYVTVLDAAQSESTTQLDPTRHNHSNQMSLGVFGHAGHGHILLCAVFDNLGKGASGAAVQ 301

Query: 302 NLDLML 307
           NLDLML
Sbjct: 302 NLDLML 307


Lambda     K      H
   0.322    0.138    0.417 

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: 348
Number of extensions: 15
Number of successful extensions: 2
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: 313
Length of database: 309
Length adjustment: 27
Effective length of query: 286
Effective length of database: 282
Effective search space:    80652
Effective search space used:    80652
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate HSERO_RS14025 HSERO_RS14025 (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.3001.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.6e-123  397.2   0.0     3e-123  397.0   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS14025  HSERO_RS14025 N-acetyl-gamma-glu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS14025  HSERO_RS14025 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.0   0.0    3e-123    3e-123       2     308 ..       5     307 ..       4     309 .] 0.98

  Alignments for each domain:
  == domain 1  score: 397.0 bits;  conditional E-value: 3e-123
                                  TIGR01851   2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslv 69 
                                                p +fidG++GttGlqi+erl  r+dl++l++ +  rkda+ ra+ +n+ad+a+lclpd aareav+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS14025   5 PLIFIDGDQGTTGLQIHERLRARQDLRVLTLPAAERKDAQRRAEAINSADIALLCLPDAAAREAVAMI 72 
                                                569***************************************************************** PP

                                  TIGR01851  70 dnpntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadf 137
                                                +np+++++das+a+rt++dwvyGfpe+aa+q e ia a rv+nPGcy+tgaiallrPlv+aG++Pad+
  lcl|FitnessBrowser__HerbieS:HSERO_RS14025  73 SNPRVRVIDASSAHRTSPDWVYGFPEMAAGQAEAIATALRVSNPGCYPTGAIALLRPLVQAGLVPADY 140
                                                ******************************************************************** PP

                                  TIGR01851 138 PvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdf 205
                                                P++i+avsGysGGG+a +++ye   a++++ a+f++ygl l+hkh pem+ h+gl ++P+f+P+ G f
  lcl|FitnessBrowser__HerbieS:HSERO_RS14025 141 PLNIHAVSGYSGGGRAQVEQYE--GAEAAHAAPFVTYGLGLQHKHPPEMQLHAGLSQRPLFVPSYGAF 206
                                                **********************..45555579************************************ PP

                                  TIGR01851 206 aqGllveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelf 273
                                                 qG++++i+l+   l +++s e + ++l+ +y+G ++v v +++++e  + t ld++  n +n+++l 
  lcl|FitnessBrowser__HerbieS:HSERO_RS14025 207 RQGIVLTIALQSRLLPAQASLERLRATLQAHYDGAHYVTVLDAAQSE--STTQLDPTRHNHSNQMSLG 272
                                                *******************************************9999..459**************** PP

                                  TIGR01851 274 vfgsddgerallvarldnlGkGasGaavqnlnial 308
                                                vfg +  +++ll+a +dnlGkGasGaavqnl+++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS14025 273 VFGHAGHGHILLCAVFDNLGKGASGAAVQNLDLML 307
                                                **********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (309 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: 6.49
//
[ok]

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:

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, or view the source code, or see 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