Alignments for a candidate for argC in Teredinibacter turnerae T7901

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Teredinibacter turnerae T7901

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_012779335.1 TERTU_RS13580 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:E4PLW0
         (388 letters)



>NCBI__GCF_000023025.1:WP_012779335.1
          Length = 346

 Score =  439 bits (1130), Expect = e-128
 Identities = 219/349 (62%), Positives = 268/349 (76%), Gaps = 7/349 (2%)

Query: 44  VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYD-LAFSE 102
           +IKVGIVGGTGYTGVELLR+LAVHP+V V+ ITSR+EAG  V E++P LRGHYD L FSE
Sbjct: 1   MIKVGIVGGTGYTGVELLRLLAVHPKVEVTLITSRAEAGKCVTELFPTLRGHYDDLYFSE 60

Query: 103 PDVNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHES 162
           P+ + LGACDLVFFATPHGVA  M+ E+++AGVR +DLSADFR++D++VW  WYG  H  
Sbjct: 61  PESHALGACDLVFFATPHGVAQAMMKEVLAAGVRAIDLSADFRIRDIEVWEKWYGQQHGC 120

Query: 163 PEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSG 222
           PE   +AVYGLPE+ R++I++AQLVA PGCYPT++QLGF PLL   L+DP+ LIA + SG
Sbjct: 121 PELVAQAVYGLPEIHREQIKDAQLVACPGCYPTSIQLGFYPLLANDLIDPRSLIASSASG 180

Query: 223 ASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVG---VTFVPHLIP 279
            SGAG+Q K+ +L  E+GESFK Y A GHRHLPEI QGL      D     +TFVPHL+P
Sbjct: 181 VSGAGKQAKVDLLMAEMGESFKTYAAGGHRHLPEIEQGLRDMQTPDAAEPELTFVPHLLP 240

Query: 280 MIRGIEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMAL 339
           MIRGI +TL+A L    D   LQALFE  + +EPFVDV+P G  PETRSV+ +N CR+A+
Sbjct: 241 MIRGIHSTLFARLIENVD---LQALFEDFYANEPFVDVLPQGVLPETRSVKSSNICRLAV 297

Query: 340 HRQEQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
              +    V+V+SVIDNL KGA+GQ +QNMNIMFG  ETMGL APALLP
Sbjct: 298 LEPQSRGTVVVASVIDNLTKGASGQGIQNMNIMFGFDETMGLAAPALLP 346


Lambda     K      H
   0.321    0.137    0.412 

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: 439
Number of extensions: 12
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: 388
Length of database: 346
Length adjustment: 30
Effective length of query: 358
Effective length of database: 316
Effective search space:   113128
Effective search space used:   113128
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: 49 (23.5 bits)

Align candidate WP_012779335.1 TERTU_RS13580 (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.18486.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-129  417.5   0.0   2.6e-129  417.3   0.0    1.0  1  lcl|NCBI__GCF_000023025.1:WP_012779335.1  TERTU_RS13580 N-acetyl-gamma-glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023025.1:WP_012779335.1  TERTU_RS13580 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.3   0.0  2.6e-129  2.6e-129       1     345 []       2     346 .]       2     346 .] 0.96

  Alignments for each domain:
  == domain 1  score: 417.3 bits;  conditional E-value: 2.6e-129
                                 TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvd.lkleeleeeeileea 68 
                                               ikv+ivG++GYtG+eLlrlla Hp+vevt ++s+ eagk ++e++p+l+g++d l ++e  e+++l ++
  lcl|NCBI__GCF_000023025.1:WP_012779335.1   2 IKVGIVGGTGYTGVELLRLLAVHPKVEVTLITSRAEAGKCVTELFPTLRGHYDdLYFSEP-ESHALGAC 69 
                                               69***************************6666666*****************6666655.555778** PP

                                 TIGR01850  69 dvvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnree 137
                                               d+vf+A+phgv++++++e+l++gv+ idlSadfR++d ev+ekwYg++h  +el+++avYGlpE++re+
  lcl|NCBI__GCF_000023025.1:WP_012779335.1  70 DLVFFATPHGVAQAMMKEVLAAGVRAIDLSADFRIRDIEVWEKWYGQQHGCPELVAQAVYGLPEIHREQ 138
                                               ********************************************************************* PP

                                 TIGR01850 138 ikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt 206
                                               ik+a+l+a+PGCy+T+++L+ +Pll+++li+p+s+i  + sGvSgAG++a+ + l+ae+ e++k Y++ 
  lcl|NCBI__GCF_000023025.1:WP_012779335.1 139 IKDAQLVACPGCYPTSIQLGFYPLLANDLIDPRSLIASSASGVSGAGKQAKVDLLMAEMGESFKTYAAG 207
                                               ********************************************************************* PP

                                 TIGR01850 207 kHrHtpEieqelsklaek...kvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfv 272
                                               +HrH pEieq l+++++    + +++f+phl+pm+rGi++t+ a+l +++   +l++l+e++Y++epfv
  lcl|NCBI__GCF_000023025.1:WP_012779335.1 208 GHRHLPEIEQGLRDMQTPdaaEPELTFVPHLLPMIRGIHSTLFARLIENV---DLQALFEDFYANEPFV 273
                                               *************99876666778*********************99865...9*************** PP

                                 TIGR01850 273 rvlkegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLekl 341
                                               +vl++g lP+t++v  sn ++++v   ++ ++vvv s+iDNL+KGa+gq +qn+N+m+gfdet gL   
  lcl|NCBI__GCF_000023025.1:WP_012779335.1 274 DVLPQGVLPETRSVKSSNICRLAVLEPQSRGTVVVASVIDNLTKGASGQGIQNMNIMFGFDETMGLAAP 342
                                               ******************************************************************999 PP

                                 TIGR01850 342 pllp 345
                                               +llp
  lcl|NCBI__GCF_000023025.1:WP_012779335.1 343 ALLP 346
                                               8877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (346 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.27
//
[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