Alignments for a candidate for argG in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Desulfovibrio vulgaris Hildenborough

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate 206530 DVU1095 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>MicrobesOnline__882:206530
          Length = 396

 Score =  511 bits (1317), Expect = e-149
 Identities = 243/387 (62%), Positives = 302/387 (78%), Gaps = 1/387 (0%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61
           K+VLAYSGGLDTS+ILKWL  TY  EV+  TAD+GQ E+++   +KA+RTGAS+A   DL
Sbjct: 6   KVVLAYSGGLDTSVILKWLAVTYNCEVVTLTADLGQEEDLDGVDDKAMRTGASRAYVEDL 65

Query: 62  KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121
           +EEF RDF+FPMMRAGAVYEG YLLGTSIARPLIAK LV IA  EGA+A+AHGATGKGND
Sbjct: 66  QEEFARDFIFPMMRAGAVYEGRYLLGTSIARPLIAKRLVEIARAEGAQAVAHGATGKGND 125

Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLHI 181
           QVRFEL   AL PD++VIAPWREW  + R ++ A+AE HGIP+  +  K YSMD N+LH 
Sbjct: 126 QVRFELAVNALAPDLRVIAPWREWDLRSRTQLNAFAEEHGIPIS-SSAKQYSMDRNMLHC 184

Query: 182 SYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQR 241
           S+EGG LEDPW EP    + M    E+APD  EY+ ++F  G+PVAVNGERLSPAAL+++
Sbjct: 185 SFEGGELEDPWNEPGPNSYVMAVPMEQAPDEAEYISIDFEHGNPVAVNGERLSPAALVKK 244

Query: 242 LNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDML 301
           LN IGGRHG+GR+D+VENRFVG+KSRGVYETPGGT+++ A R +E + +DRE +H RD +
Sbjct: 245 LNSIGGRHGIGRLDMVENRFVGIKSRGVYETPGGTLIHIAHRDLEGICIDRETMHLRDAM 304

Query: 302 SPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQD 361
            P+YA  +Y GFW+APEREA+QA  D   + VTG  RLKLYKGN + VGR++P +LY  D
Sbjct: 305 LPRYAAAIYNGFWFAPEREAMQAMIDVSQQRVTGTVRLKLYKGNAWPVGRQSPNTLYCHD 364

Query: 362 LVSFDEAGGYDQKDAEGFIKIQALRLR 388
           L +F++   YD KDA GFIK+Q LR+R
Sbjct: 365 LATFEDCATYDHKDAAGFIKLQGLRIR 391


Lambda     K      H
   0.319    0.137    0.402 

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: 469
Number of extensions: 15
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: 400
Length of database: 396
Length adjustment: 31
Effective length of query: 369
Effective length of database: 365
Effective search space:   134685
Effective search space used:   134685
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: 50 (23.9 bits)

Align candidate 206530 DVU1095 (argininosuccinate synthase)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))

# 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/TIGR00032.hmm
# target sequence database:        /tmp/gapView.11189.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00032  [M=394]
Accession:   TIGR00032
Description: argG: argininosuccinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.1e-154  499.0   0.0   6.9e-154  498.8   0.0    1.0  1  lcl|MicrobesOnline__882:206530  DVU1095 argininosuccinate syntha


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206530  DVU1095 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  498.8   0.0  6.9e-154  6.9e-154       1     390 [.       6     394 ..       6     396 .] 0.99

  Alignments for each domain:
  == domain 1  score: 498.8 bits;  conditional E-value: 6.9e-154
                       TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfaaiqanav 78 
                                     kvvlaysGGlDtsv+lk+l    ++ev+++t+d+Gq eedld ++ ka++ Ga +ayv D +eef++d++f+ ++a+av
  lcl|MicrobesOnline__882:206530   6 KVVLAYSGGLDTSVILKWLAVTyNCEVVTLTADLGQ-EEDLDGVDDKAMRTGASRAYVEDLQEEFARDFIFPMMRAGAV 83 
                                     8*******************9999************.8***************************************** PP

                       TIGR00032  79 yegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvreleli.Reeeieyaa 156
                                     yeg+Yll+t++aRpliak+lve+a+ ega+avahG+tgKGnDqvRFel + +l+pdl+viaP+re++l  R+++ ++a+
  lcl|MicrobesOnline__882:206530  84 YEGRYLLGTSIARPLIAKRLVEIARAEGAQAVAHGATGKGNDQVRFELAVNALAPDLRVIAPWREWDLRsRTQLNAFAE 162
                                     ********************************************************************88********* PP

                       TIGR00032 157 ekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevveieFekGvPvalngeslepv 235
                                     e+Gi++ ++ +k+ys+D+n+l+ s E+geLEdp+ ep  + y + + p+e+ +de+e++ i+Fe+G Pva+nge+l+p 
  lcl|MicrobesOnline__882:206530 163 EHGIPISSS-AKQYSMDRNMLHCSFEGGELEDPWNEPGPNSYVMAV-PMEQAPDEAEYISIDFEHGNPVAVNGERLSPA 239
                                     ******998.6*******************************9999.******************************** PP

                       TIGR00032 236 elilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwf 314
                                      l++k+n i+g+hG+Gr+D+vE+R +g+KsR++YE+p+ +l+++Ah+dLe    +++++++++++  +y+  iY+G+wf
  lcl|MicrobesOnline__882:206530 240 ALVKKLNSIGGRHGIGRLDMVENRFVGIKSRGVYETPGGTLIHIAHRDLEGICIDRETMHLRDAMLPRYAAAIYNGFWF 318
                                     ******************************************************************************* PP

                       TIGR00032 315 dplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqikvyr 390
                                      p++ea++a+i+ +q+rvtGtvr+kl+kGna  +gr+s+++lY ++l++fe  +++d+kda+Gfik++gl+i+ y+
  lcl|MicrobesOnline__882:206530 319 APEREAMQAMIDVSQQRVTGTVRLKLYKGNAWPVGRQSPNTLYCHDLATFEDCATYDHKDAAGFIKLQGLRIRGYK 394
                                     ***********************************************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (396 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: 9.25
//
[ok]

This GapMind analysis is from Apr 09 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