GapMind for Amino acid biosynthesis

 

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

Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; EC 1.2.1.38; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase (uncharacterized)
to candidate CA265_RS18540 CA265_RS18540 N-acetyl-gamma-glutamyl-phosphate reductase

Query= curated2:A6KXY5
         (322 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS18540 CA265_RS18540
           N-acetyl-gamma-glutamyl-phosphate reductase
          Length = 326

 Score =  401 bits (1031), Expect = e-116
 Identities = 196/325 (60%), Positives = 246/325 (75%), Gaps = 5/325 (1%)

Query: 2   IKAGIIGGAGYTAGELIRLLINHPDVDIKFINSSSNAGNKITDVHEGLYGETDLVFTDEL 61
           IKAGIIGGAGYT GE++R+L+NHP+V+I F+NS+SNAGN I+DVH  L G+TDL F  ++
Sbjct: 3   IKAGIIGGAGYTGGEMLRILVNHPNVEIAFVNSTSNAGNLISDVHTDLIGDTDLKFVSDI 62

Query: 62  PLDEIDVLFFCTAHGDTKKFMDSHNVPEDLKIIDLSMDYRIKSD----DHDFIYGLPELN 117
           P D IDVLF C  HGD KKF+ ++ + +++KIIDLS D+R+ ++      DF+YGLPELN
Sbjct: 63  PQD-IDVLFLCVGHGDAKKFLTANPIKDNIKIIDLSQDFRLHANASFSTKDFVYGLPELN 121

Query: 118 RRAICHSKHVANPGCFATCIQLGLLPLAKHLLLNEDIMVNAITGSTGAGVKPGATSHFSW 177
           R  I  +K++ANPGCFATCIQLGLLPLA   L+  ++ +NA TGSTGAG     TSHFSW
Sbjct: 122 RDKIKAAKNIANPGCFATCIQLGLLPLAAKGLIQNEVHINATTGSTGAGQSLSTTSHFSW 181

Query: 178 RNNNMSIYKPFSHQHVPEIKQSLKQLQNSFNAEIDFIPYRGDFPRGIFATLVVKCKVELE 237
           RNNN+SIYK F HQH+ EI +SL QLQ S +  ++FIP RG F RGI A + ++  + LE
Sbjct: 182 RNNNLSIYKAFEHQHLNEISESLLQLQPSISEALNFIPQRGAFTRGILAAMYLESDLSLE 241

Query: 238 ELVKMYQDYYAEDSFVHIVDKNIDLKQVVNTNKCLIHLEKHGDKLLVISCIDNLLKGASG 297
           E   +Y+ YY+   F H+  KNIDLKQVVNTNK L+HLEKHG KL +IS IDNLLKGASG
Sbjct: 242 EAQNIYEAYYSAHPFTHVSRKNIDLKQVVNTNKALVHLEKHGGKLFIISIIDNLLKGASG 301

Query: 298 QAVHNMNLMFNLEETVGLRLKPSAF 322
           QAV NMNLMF L+ET GL+LK + F
Sbjct: 302 QAVQNMNLMFGLDETAGLKLKAAYF 326


Lambda     K      H
   0.321    0.139    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: 334
Number of extensions: 9
Number of successful extensions: 3
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: 322
Length of database: 326
Length adjustment: 28
Effective length of query: 294
Effective length of database: 298
Effective search space:    87612
Effective search space used:    87612
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 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.23712.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  lcl|FitnessBrowser__Pedo557:CA265_RS18540  CA265_RS18540 N-acetyl-gamma-glu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS18540  CA265_RS18540 N-acetyl-gamma-glutamyl-phosphate reductase
   #    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 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileea 68 
                                                ik++i+G+ GYtG+e+lr+l +Hp+ve++ + s+++ag+ +s+vh  l g +dlk+ +    +i +++
  lcl|FitnessBrowser__Pedo557:CA265_RS18540   3 IKAGIIGGAGYTGGEMLRILVNHPNVEIAFVNSTSNAGNLISDVHTDLIGDTDLKFVS----DIPQDI 66 
                                                689**************************7778888***************9999885....45679* PP

                                  TIGR01850  69 dvvflAlphgvsaelvpel.lekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnr 135
                                                dv+fl++ hg ++++ ++  ++ ++k+idlS dfRl+ ++ +             ++++vYGlpElnr
  lcl|FitnessBrowser__Pedo557:CA265_RS18540  67 DVLFLCVGHGDAKKFLTANpIKDNIKIIDLSQDFRLHANASF------------STKDFVYGLPELNR 122
                                                **************9765427788*************77533............3468********** PP

                                  TIGR01850 136 eeikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpY 203
                                                ++ik ak ianPGC+aT+++L+l Pl++++li+++ + ++a +G++gAG++ s++s+f+ +n+nl++Y
  lcl|FitnessBrowser__Pedo557:CA265_RS18540 123 DKIKAAKNIANPGCFATCIQLGLLPLAAKGLIQNE-VHINATTGSTGAGQSLSTTSHFSWRNNNLSIY 189
                                                ********************************985.******************************** PP

                                  TIGR01850 204 kvtkHrHtpEieqelsklaek.kvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedep 270
                                                k+++H+H +Ei+++l +l+ + +  ++f+p+   +trGila++y++   +l+ ee +++ye++Y+ +p
  lcl|FitnessBrowser__Pedo557:CA265_RS18540 190 KAFEHQHLNEISESLLQLQPSiSEALNFIPQRGAFTRGILAAMYLES--DLSLEEAQNIYEAYYSAHP 255
                                                ****************999995555*****************99765..5678999************ PP

                                  TIGR01850 271 fvrvlkegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegL 338
                                                f +v + ++  ++k+v+ +n + + ++ +   +++ ++s iDNL+KGa+gqAvqn+Nlm+g+det+gL
  lcl|FitnessBrowser__Pedo557:CA265_RS18540 256 FTHVSR-KN-IDLKQVVNTNKALVHLEKHG--GKLFIISIIDNLLKGASGQAVQNMNLMFGLDETAGL 319
                                                *****8.44.49********9998776555..9*********************************** PP

                                  TIGR01850 339 eklp 342
                                                + ++
  lcl|FitnessBrowser__Pedo557:CA265_RS18540 320 KLKA 323
                                                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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.75
//
[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:

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:

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:

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