Alignments for a candidate for argC in Pontibacter ramchanderi LP43

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Pontibacter ramchanderi LP43

Align N-succinylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_101442816.1 BD749_RS02635 N-acetyl-gamma-glutamyl-phosphate reductase

Query= reanno::Pedo557:CA265_RS18540
         (326 letters)



>NCBI__GCF_002846395.1:WP_101442816.1
          Length = 333

 Score =  405 bits (1042), Expect = e-118
 Identities = 200/331 (60%), Positives = 246/331 (74%), Gaps = 5/331 (1%)

Query: 1   MKIKAGIIGGAGYTGGEMLRILVNHPNVEIAFVNSTSNAGNLISDVHTDLIGDTDLKFVS 60
           MKIKAGI+GGAGY GGE+LR+L+ HPNVE+AFV S S AG  +   H DL+G+TD+ F +
Sbjct: 3   MKIKAGIVGGAGYAGGELLRLLLLHPNVELAFVQSRSQAGKPVHTAHPDLLGETDISFSA 62

Query: 61  DIPQDIDVLFLCVGHGDAKKFLTANPIKDNIKIIDLSQDFRLHANA-----SFSTKDFVY 115
           D    ++VLFLC GHG+A +FL  N +    KIIDLSQDFR +            + FVY
Sbjct: 63  DAAIPVEVLFLCAGHGEAARFLAENEVPAETKIIDLSQDFRWNEKTICDVVEAGERSFVY 122

Query: 116 GLPELNRDKIKAAKNIANPGCFATCIQLGLLPLAAKGLIQNEVHINATTGSTGAGQSLST 175
           GLPEL R++I+ AK+IANPGCFAT IQL LLPLA + ++Q++VH++  TGSTGAGQSLS 
Sbjct: 123 GLPELQREQIRQAKHIANPGCFATGIQLALLPLAKQNMLQSDVHVSGITGSTGAGQSLSA 182

Query: 176 TSHFSWRNNNLSIYKAFEHQHLNEISESLLQLQPSISEALNFIPQRGAFTRGILAAMYLE 235
           TSHFSWR  N+S YK  EHQHL EI+ SLL LQP     ++FIP RG F RGI    YL+
Sbjct: 183 TSHFSWRTENISTYKVMEHQHLREINRSLLYLQPEDQSNIHFIPYRGPFARGIFITAYLQ 242

Query: 236 SDLSLEEAQNIYEAYYSAHPFTHVSRKNIDLKQVVNTNKALVHLEKHGGKLFIISIIDNL 295
           + +SLEEAQ +Y  YY+ HPFT V+ +N DLKQVVNTNK ++HL+KHG  L I S+IDNL
Sbjct: 243 TAISLEEAQALYGNYYAGHPFTIVTDQNPDLKQVVNTNKCVLHLQKHGNMLVITSLIDNL 302

Query: 296 LKGASGQAVQNMNLMFGLDETAGLKLKAAYF 326
           LKGA+GQAVQNMNL+FGL+ET GLKLKA  F
Sbjct: 303 LKGAAGQAVQNMNLVFGLEETTGLKLKATSF 333


Lambda     K      H
   0.319    0.135    0.387 

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: 346
Number of extensions: 11
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: 326
Length of database: 333
Length adjustment: 28
Effective length of query: 298
Effective length of database: 305
Effective search space:    90890
Effective search space used:    90890
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_101442816.1 BD749_RS02635 (N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01850 (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/TIGR01850.hmm
# target sequence database:        /tmp/gapView.1763538.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01850  [M=345]
Accession:   TIGR01850
Description: argC: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.2e-96  308.1   0.0      5e-96  307.8   0.0    1.0  1  NCBI__GCF_002846395.1:WP_101442816.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101442816.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.8   0.0     5e-96     5e-96       1     341 [.       5     329 ..       5     332 .. 0.91

  Alignments for each domain:
  == domain 1  score: 307.8 bits;  conditional E-value: 5e-96
                             TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvfl 73 
                                           ik++ivG+ GY+G+eLlrll  Hp+ve++ + s+++agk+++++hp l g++d ++++ ++      ++v+fl
  NCBI__GCF_002846395.1:WP_101442816.1   5 IKAGIVGGAGYAGGELLRLLLLHPNVELAFVQSRSQAGKPVHTAHPDLLGETDISFSADAA----IPVEVLFL 73 
                                           689**************************7777777****************999996433....379***** PP

                             TIGR01850  74 Alphgvsaelvpel.lekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklia 145
                                           +  hg +a++ +e  + +++k+idlS dfR +++++        ++     +++vYGlpEl+re+i++ak ia
  NCBI__GCF_002846395.1:WP_101442816.1  74 CAGHGEAARFLAENeVPAETKIIDLSQDFRWNEKTI----CDVVEA---GERSFVYGLPELQREQIRQAKHIA 139
                                           ******9998766515699*************9853....333333...3578******************** PP

                             TIGR01850 146 nPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqel 218
                                           nPGC+aT+++Lal Pl+k+++++++ + v +++G++gAG++ s++s+f+ ++en++ Ykv +H+H +Ei+++l
  NCBI__GCF_002846395.1:WP_101442816.1 140 NPGCFATGIQLALLPLAKQNMLQSD-VHVSGITGSTGAGQSLSATSHFSWRTENISTYKVMEHQHLREINRSL 211
                                           **********************985.*********************************************** PP

                             TIGR01850 219 sklaek.kvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsn 290
                                             l+ + + +++f+p   p+ rGi+ t+y++++   + ee ++ly ++Y+++pf  v +  + P++k+v+ +n
  NCBI__GCF_002846395.1:WP_101442816.1 212 LYLQPEdQSNIHFIPYRGPFARGIFITAYLQTAI--SLEEAQALYGNYYAGHPFTIVTD--QNPDLKQVVNTN 280
                                           *999884556******************998876..668999************99987..89********** PP

                             TIGR01850 291 fvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLekl 341
                                            + + ++ +   + +v++s iDNL+KGaagqAvqn+Nl +g++et+gL+ +
  NCBI__GCF_002846395.1:WP_101442816.1 281 KCVLHLQKHG--NMLVITSLIDNLLKGAAGQAVQNMNLVFGLEETTGLKLK 329
                                           **98876655..9***********************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (333 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 19.79
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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