GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argC in Desulfovibrio vulgaris Hildenborough

Align Probable N-acetyl-gamma-glutamyl-phosphate reductase, chloroplastic; AGPR; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase; EC 1.2.1.38 (characterized)
to candidate 209429 DVU0492 N-acetyl-gamma-glutamyl-phosphate reductase

Query= SwissProt::Q93Z70
         (401 letters)



>lcl|MicrobesOnline__882:209429 DVU0492
           N-acetyl-gamma-glutamyl-phosphate reductase
          Length = 354

 Score =  276 bits (706), Expect = 7e-79
 Identities = 148/353 (41%), Positives = 216/353 (61%), Gaps = 12/353 (3%)

Query: 59  IRIGLLGASGYTGAEIVRLLANHPHFQVTLMTADRKAGQSMESVFPHLRAQKLP----TL 114
           IR GL+G +GYTG E+ RLLA HP  ++ L T+  +AG+ ++ ++P L    LP    T+
Sbjct: 4   IRAGLVGVTGYTGMELARLLAGHPAMRLVLATSRAEAGRRLDDIYPFLIG--LPGGDITI 61

Query: 115 VSVK-DADFSTVDAVFCCLPHGTTQEIIKEL-PTALKIVDLSADFRLRNIAEYEEWYGQP 172
           V+   D   ++ D  F  +PHG   E+   L    L++VDLSADFRLR++  YE WY   
Sbjct: 62  VAPDPDVIAASCDIAFLAVPHGAAMEMAASLRERGLRVVDLSADFRLRDVTVYESWYRTD 121

Query: 173 HKAVELQKEVVYGLTEILREDIKKARLVANPGCYPTTIQLPLVPLLKANLIKHENIIIDA 232
           H    L  E VYGL E+  +D+ +A LVANPGCYPT++ L L   L  +++  ++I+IDA
Sbjct: 122 HTRKGLLPEAVYGLPELYGKDVAQAGLVANPGCYPTSVILGLAAALDTDIVHRDDIVIDA 181

Query: 233 KSGVSGAGRGAKEANLYSEIAEGISSYGVTRHRHVPEIEQGLSDVAQSKVTVSFTPHLMP 292
           KSG SGAGR A   +L+ E+ +   +Y + +HRH PEIEQ LS +A   +TVSF  HL+P
Sbjct: 182 KSGASGAGRKAAVGSLFCEVHDSFKAYNLGKHRHTPEIEQELSVIAGEALTVSFNTHLLP 241

Query: 293 MIRGMQSTIYVEMAPGVRTEDLHQQLKTSYEDEE----FVKVLDEGVVPRTHNVRGSNYC 348
           + RG+ ST+Y+ M   +  + +H      +   +    +V++L +G +P T +V+G+ +C
Sbjct: 242 IDRGILSTMYLRMKKPLDLDTVHAMYADYWAAHQTRGGWVRLLPKGRLPETRHVKGTMFC 301

Query: 349 HMSVFPDRIPGRAIIISVIDNLVKGASGQALQNLNIMLGYPETTGLLHQPLFP 401
            + +  D   GR I++S IDNL +GASGQA+ N NIMLG P   GL   PL P
Sbjct: 302 DIGLVVDPRTGRLIVVSAIDNLCRGASGQAVANANIMLGLPVDAGLRLAPLMP 354


Lambda     K      H
   0.318    0.134    0.386 

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: 389
Number of extensions: 19
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: 401
Length of database: 354
Length adjustment: 30
Effective length of query: 371
Effective length of database: 324
Effective search space:   120204
Effective search space used:   120204
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 209429 DVU0492 (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.11453.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.7e-121  390.9   0.0     3e-121  390.8   0.0    1.0  1  lcl|MicrobesOnline__882:209429  DVU0492 N-acetyl-gamma-glutamyl-


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:209429  DVU0492 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.8   0.0    3e-121    3e-121       1     345 []       4     354 .]       4     354 .] 0.96

  Alignments for each domain:
  == domain 1  score: 390.8 bits;  conditional E-value: 3e-121
                       TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssre.agkklsevhphlkglvd..lkleeleeeeileeadvvflAlp 76 
                                     i++++vG +GYtG+eL rlla Hp+++++ l++sr+ ag++l++++p l gl     ++ + + + i++++d+ flA+p
  lcl|MicrobesOnline__882:209429   4 IRAGLVGVTGYTGMELARLLAGHPAMRLV-LATSRAeAGRRLDDIYPFLIGLPGgdITIVAPDPDVIAASCDIAFLAVP 81 
                                     5789*************************.5555555*************9987446666777799************* PP

                       TIGR01850  77 hgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCyaTaal 155
                                     hg+++e++++l e+g++v+dlSadfRl+d +vYe+wY+++h+++ ll eavYGlpEl+ +++++a l+anPGCy+T+++
  lcl|MicrobesOnline__882:209429  82 HGAAMEMAASLRERGLRVVDLSADFRLRDVTVYESWYRTDHTRKGLLPEAVYGLPELYGKDVAQAGLVANPGCYPTSVI 160
                                     ******************************************************************************* PP

                       TIGR01850 156 LalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaekkvkvsftphl 234
                                     L+la +l+++++++++i++daksG SgAGrka   slf+ev++++k+Y++ kHrHtpEieqels +a++  +vsf +hl
  lcl|MicrobesOnline__882:209429 161 LGLAAALDTDIVHRDDIVIDAKSGASGAGRKAAVGSLFCEVHDSFKAYNLGKHRHTPEIEQELSVIAGEALTVSFNTHL 239
                                     *******************************************************************99********** PP

                       TIGR01850 235 vpmtrGilatiyaklkkelteeelrklyeevYedep....fvrvlkegelPstkavlgsnfvdigvavdeetkrvvvvs 309
                                     +p+ rGil+t+y+++kk+l+ ++++++y+++++ ++    +vr+l++g+lP+t++v g+ f+dig+ vd +t+r++vvs
  lcl|MicrobesOnline__882:209429 240 LPIDRGILSTMYLRMKKPLDLDTVHAMYADYWAAHQtrggWVRLLPKGRLPETRHVKGTMFCDIGLVVDPRTGRLIVVS 318
                                     *******************************9977545559************************************** PP

                       TIGR01850 310 aiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                     aiDNL +Ga+gqAv n N+mlg++ ++gL+  pl+p
  lcl|MicrobesOnline__882:209429 319 AIDNLCRGASGQAVANANIMLGLPVDAGLRLAPLMP 354
                                     ********************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (354 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: 00:00:00.01
# Mc/sec: 6.66
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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