Alignments for a candidate for argC in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Pedobacter sp. GW460-11-11-14-LB5

Align N-succinylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate CA265_RS18540 CA265_RS18540 N-acetyl-gamma-glutamyl-phosphate reductase

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



>FitnessBrowser__Pedo557:CA265_RS18540
          Length = 326

 Score =  646 bits (1667), Expect = 0.0
 Identities = 326/326 (100%), Positives = 326/326 (100%)

Query: 1   MKIKAGIIGGAGYTGGEMLRILVNHPNVEIAFVNSTSNAGNLISDVHTDLIGDTDLKFVS 60
           MKIKAGIIGGAGYTGGEMLRILVNHPNVEIAFVNSTSNAGNLISDVHTDLIGDTDLKFVS
Sbjct: 1   MKIKAGIIGGAGYTGGEMLRILVNHPNVEIAFVNSTSNAGNLISDVHTDLIGDTDLKFVS 60

Query: 61  DIPQDIDVLFLCVGHGDAKKFLTANPIKDNIKIIDLSQDFRLHANASFSTKDFVYGLPEL 120
           DIPQDIDVLFLCVGHGDAKKFLTANPIKDNIKIIDLSQDFRLHANASFSTKDFVYGLPEL
Sbjct: 61  DIPQDIDVLFLCVGHGDAKKFLTANPIKDNIKIIDLSQDFRLHANASFSTKDFVYGLPEL 120

Query: 121 NRDKIKAAKNIANPGCFATCIQLGLLPLAAKGLIQNEVHINATTGSTGAGQSLSTTSHFS 180
           NRDKIKAAKNIANPGCFATCIQLGLLPLAAKGLIQNEVHINATTGSTGAGQSLSTTSHFS
Sbjct: 121 NRDKIKAAKNIANPGCFATCIQLGLLPLAAKGLIQNEVHINATTGSTGAGQSLSTTSHFS 180

Query: 181 WRNNNLSIYKAFEHQHLNEISESLLQLQPSISEALNFIPQRGAFTRGILAAMYLESDLSL 240
           WRNNNLSIYKAFEHQHLNEISESLLQLQPSISEALNFIPQRGAFTRGILAAMYLESDLSL
Sbjct: 181 WRNNNLSIYKAFEHQHLNEISESLLQLQPSISEALNFIPQRGAFTRGILAAMYLESDLSL 240

Query: 241 EEAQNIYEAYYSAHPFTHVSRKNIDLKQVVNTNKALVHLEKHGGKLFIISIIDNLLKGAS 300
           EEAQNIYEAYYSAHPFTHVSRKNIDLKQVVNTNKALVHLEKHGGKLFIISIIDNLLKGAS
Sbjct: 241 EEAQNIYEAYYSAHPFTHVSRKNIDLKQVVNTNKALVHLEKHGGKLFIISIIDNLLKGAS 300

Query: 301 GQAVQNMNLMFGLDETAGLKLKAAYF 326
           GQAVQNMNLMFGLDETAGLKLKAAYF
Sbjct: 301 GQAVQNMNLMFGLDETAGLKLKAAYF 326


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: 535
Number of extensions: 8
Number of successful extensions: 1
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: 326
Length adjustment: 28
Effective length of query: 298
Effective length of database: 298
Effective search space:    88804
Effective search space used:    88804
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: 48 (23.1 bits)

Align candidate CA265_RS18540 CA265_RS18540 (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.1042709.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
    2.8e-94  302.1   0.0    3.8e-94  301.7   0.0    1.1  1  FitnessBrowser__Pedo557:CA265_RS18540  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Pedo557:CA265_RS18540  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.7   0.0   3.8e-94   3.8e-94       1     342 [.       3     323 ..       3     325 .. 0.91

  Alignments for each domain:
  == domain 1  score: 301.7 bits;  conditional E-value: 3.8e-94
                              TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvf 72 
                                            ik++i+G+ GYtG+e+lr+l +Hp+ve++ + s+++ag+ +s+vh  l g +dlk+ +    +i +++dv+f
  FitnessBrowser__Pedo557:CA265_RS18540   3 IKAGIIGGAGYTGGEMLRILVNHPNVEIAFVNSTSNAGNLISDVHTDLIGDTDLKFVS----DIPQDIDVLF 70 
                                            689**************************7778888***************9999885....45679***** PP

                              TIGR01850  73 lAlphgvsaelvpel.lekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkakl 143
                                            l++ hg ++++ ++  ++ ++k+idlS dfRl+ ++ +             ++++vYGlpElnr++ik ak 
  FitnessBrowser__Pedo557:CA265_RS18540  71 LCVGHGDAKKFLTANpIKDNIKIIDLSQDFRLHANASF------------STKDFVYGLPELNRDKIKAAKN 130
                                            **********9765427788*************77533............3468****************** PP

                              TIGR01850 144 ianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEie 215
                                            ianPGC+aT+++L+l Pl++++li+++ + ++a +G++gAG++ s++s+f+ +n+nl++Yk+++H+H +Ei+
  FitnessBrowser__Pedo557:CA265_RS18540 131 IANPGCFATCIQLGLLPLAAKGLIQNE-VHINATTGSTGAGQSLSTTSHFSWRNNNLSIYKAFEHQHLNEIS 201
                                            ************************985.******************************************** PP

                              TIGR01850 216 qelsklaek.kvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkav 286
                                            ++l +l+ + +  ++f+p+   +trGila++y++   +l+ ee +++ye++Y+ +pf +v + ++  ++k+v
  FitnessBrowser__Pedo557:CA265_RS18540 202 ESLLQLQPSiSEALNFIPQRGAFTRGILAAMYLES--DLSLEEAQNIYEAYYSAHPFTHVSR-KN-IDLKQV 269
                                            ****999995555*****************99765..5678999*****************8.44.49**** PP

                              TIGR01850 287 lgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklp 342
                                            + +n + + ++ +   +++ ++s iDNL+KGa+gqAvqn+Nlm+g+det+gL+ ++
  FitnessBrowser__Pedo557:CA265_RS18540 270 VNTNKALVHLEKHG--GKLFIISIIDNLLKGASGQAVQNMNLMFGLDETAGLKLKA 323
                                            ****9998776555..9***********************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (326 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 13.79
//
[ok]

This GapMind analysis is from Jul 25 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 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