Alignments for a candidate for argG in Pseudomonas benzenivorans DSM 8628

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Pseudomonas benzenivorans DSM 8628

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_090448166.1 BLS63_RS23185 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>NCBI__GCF_900100495.1:WP_090448166.1
          Length = 405

 Score =  508 bits (1309), Expect = e-149
 Identities = 250/393 (63%), Positives = 303/393 (77%), Gaps = 3/393 (0%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61
           K+VLAYSGGLDTS+ILKWL++TY  EV+ FTAD+GQGEEVE AR KA   G  +    DL
Sbjct: 6   KVVLAYSGGLDTSVILKWLQDTYNCEVVTFTADLGQGEEVEPARAKAKAMGVKEIYIDDL 65

Query: 62  KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121
           +EEFVRDFV+PM RA  +YEG YLLGTSIARPLIAK L+ IA E GA+AI+HGATGKGND
Sbjct: 66  REEFVRDFVYPMFRANTIYEGEYLLGTSIARPLIAKRLIEIANETGADAISHGATGKGND 125

Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEK--PYSMDANLL 179
           QVRFEL AYALKP +KVIAPWREW    R++++ YAE H IP+    +K  PYSMDANLL
Sbjct: 126 QVRFELGAYALKPGVKVIAPWREWDLLSREKLMDYAEKHAIPIERHGKKKSPYSMDANLL 185

Query: 180 HISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALL 239
           HISYEGGVLED W E  + M+R T+ PE APD P Y+E+ +  GD VA++G+ +SPA++L
Sbjct: 186 HISYEGGVLEDTWTEHEEDMWRWTKSPEAAPDKPTYIELSYRGGDIVAIDGKEMSPASVL 245

Query: 240 QRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRD 299
             LN IGG +G+GR+DIVENRFVGMKSRG YETPGGTI+    RA+ES+TLDREV H +D
Sbjct: 246 TELNRIGGENGIGRLDIVENRFVGMKSRGCYETPGGTIMLKGHRAIESITLDREVAHLKD 305

Query: 300 MLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYR 359
            L PKYA L+Y GFW++PER  LQ   D    SV GV RLKLYKGNV V GRK+  SL+ 
Sbjct: 306 ELMPKYASLIYNGFWWSPERLMLQQMIDASQASVNGVVRLKLYKGNVIVTGRKSDDSLFD 365

Query: 360 QDLVSF-DEAGGYDQKDAEGFIKIQALRLRVRA 391
            ++ +F D+AG Y+Q+DA GFIK+ ALR+R+ A
Sbjct: 366 ANIATFEDDAGAYNQQDAAGFIKLNALRMRIAA 398


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: 498
Number of extensions: 22
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: 400
Length of database: 405
Length adjustment: 31
Effective length of query: 369
Effective length of database: 374
Effective search space:   138006
Effective search space used:   138006
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 WP_090448166.1 BLS63_RS23185 (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.5240.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-144  468.2   0.0   1.5e-144  468.0   0.0    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090448166.1  BLS63_RS23185 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090448166.1  BLS63_RS23185 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.0   0.0  1.5e-144  1.5e-144       1     391 [.       6     399 ..       6     402 .. 0.97

  Alignments for each domain:
  == domain 1  score: 468.0 bits;  conditional E-value: 1.5e-144
                                 TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdy 68 
                                               kvvlaysGGlDtsv+lk+l++  ++ev+++t+d+Gq+ e+++ ++ ka+++G+++ y+ D reefv+d+
  lcl|NCBI__GCF_900100495.1:WP_090448166.1   6 KVVLAYSGGLDTSVILKWLQDTyNCEVVTFTADLGQG-EEVEPARAKAKAMGVKEIYIDDLREEFVRDF 73 
                                               8*********************99************9.9****************************** PP

                                 TIGR00032  69 lfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137
                                               + +  +an++yeg+Yll+t++aRpliak+l+e+a++ ga+a++hG+tgKGnDqvRFel  ++l+p +kv
  lcl|NCBI__GCF_900100495.1:WP_090448166.1  74 VYPMFRANTIYEGEYLLGTSIARPLIAKRLIEIANETGADAISHGATGKGNDQVRFELGAYALKPGVKV 142
                                               ********************************************************************* PP

                                 TIGR00032 138 iaPvreleli.ReeeieyaaekGievpv..ekekaysiDenllgrsiEageLEdpsteppediyelvkd 203
                                               iaP+re++l  Re++++ya+++ i+++   +k+++ys+D nll++s+E+g LEd +te  ed+++++k+
  lcl|NCBI__GCF_900100495.1:WP_090448166.1 143 IAPWREWDLLsREKLMDYAEKHAIPIERhgKKKSPYSMDANLLHISYEGGVLEDTWTEHEEDMWRWTKS 211
                                               ********987*************99862367889*********************************8 PP

                                 TIGR00032 204 piektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEap 272
                                               p++++ d+p ++e++++ G  va++g++++p  ++ ++n+i+g++G+Gr+DivE+R +g+KsR++YE+p
  lcl|NCBI__GCF_900100495.1:WP_090448166.1 212 PEAAP-DKPTYIELSYRGGDIVAIDGKEMSPASVLTELNRIGGENGIGRLDIVENRFVGMKSRGCYETP 279
                                               88887.*************************************************************** PP

                                 TIGR00032 273 alllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklf 341
                                               + ++++k h+++e+ +l+++v+++k+    ky+ liY+G+w++p++ +l+ +i+ +q +v+G+vr+kl+
  lcl|NCBI__GCF_900100495.1:WP_090448166.1 280 GGTIMLKGHRAIESITLDREVAHLKDELMPKYASLIYNGFWWSPERLMLQQMIDASQASVNGVVRLKLY 348
                                               ********************************************************************* PP

                                 TIGR00032 342 kGnaivigrkseyslYdeelvsfek.dkefdqkdaiGfikirglqikvyre 391
                                               kGn+iv grks++sl+d+++++fe    +++q+da+Gfik+++l++++ ++
  lcl|NCBI__GCF_900100495.1:WP_090448166.1 349 KGNVIVTGRKSDDSLFDANIATFEDdAGAYNQQDAAGFIKLNALRMRIAAN 399
                                               ************************9445799**************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (405 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.22
//
[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