Alignments for a candidate for argG in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Pseudomonas fluorescens GW456-L13

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate PfGW456L13_1749 Argininosuccinate synthase (EC 6.3.4.5)

Query= SwissProt::P59846
         (400 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1749
          Length = 405

 Score =  503 bits (1295), Expect = e-147
 Identities = 249/393 (63%), Positives = 300/393 (76%), Gaps = 3/393 (0%)

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

Query: 62  KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121
           +EEFVRDFVFPM RA  VYEG YLLGTSIARPLIAK L+ IA E GA+AI+HGATGKGND
Sbjct: 66  REEFVRDFVFPMFRANTVYEGEYLLGTSIARPLIAKRLIEIANETGADAISHGATGKGND 125

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

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

Query: 240 QRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRD 299
             LN IGG HG+GR+DIVENR+VGMKSRG YETPGGTI+  A RA+ES+TLDREV H +D
Sbjct: 246 ATLNRIGGEHGIGRLDIVENRYVGMKSRGCYETPGGTIMLRAHRAIESITLDREVAHLKD 305

Query: 300 MLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYR 359
            L PKYA L+Y G+W++PER  LQ   D    +V GV RLKLYKGNV V GRK+  SL+ 
Sbjct: 306 ELMPKYASLIYTGYWWSPERLMLQQMIDASQVNVNGVVRLKLYKGNVIVTGRKSDDSLFD 365

Query: 360 QDLVSFDEAGG-YDQKDAEGFIKIQALRLRVRA 391
            ++ +F+E GG Y+Q DA GFIK+ ALR+R+ A
Sbjct: 366 ANIATFEEDGGAYNQADAAGFIKLNALRMRIAA 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: 16
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 PfGW456L13_1749 (Argininosuccinate synthase (EC 6.3.4.5))
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.10890.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   7.3e-146  472.4   0.0   8.5e-146  472.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1749  Argininosuccinate synthase (EC 6


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1749  Argininosuccinate synthase (EC 6.3.4.5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.2   0.0  8.5e-146  8.5e-146       1     391 [.       6     399 ..       6     402 .. 0.97

  Alignments for each domain:
  == domain 1  score: 472.2 bits;  conditional E-value: 8.5e-146
                                               TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaek 54 
                                                             kvvlaysGGlDtsv+lk+l++  ++ev+++t+d+Gq+ e+++ ++ ka ++G+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1749   6 KVVLAYSGGLDTSVILKWLQDTyNCEVVTFTADLGQG-EEVEPARAKAQAMGVKE 59 
                                                             8*********************99************9.9**************** PP

                                               TIGR00032  55 ayviDareefvkdylfaaiqanavyegkYllstaLaRpliakklvevakkegaea 109
                                                              y+ D reefv+d++f+  +an+vyeg+Yll+t++aRpliak+l+e+a++ ga+a
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1749  60 IYIDDLREEFVRDFVFPMFRANTVYEGEYLLGTSIARPLIAKRLIEIANETGADA 114
                                                             ******************************************************* PP

                                               TIGR00032 110 vahGctgKGnDqvRFelsilllnpdlkviaPvreleli.ReeeieyaaekGievp 163
                                                             ++hG+tgKGnDqvRFel  ++l+p +kviaP+re++l  Re++++yaa++ i+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1749 115 ISHGATGKGNDQVRFELGAYALKPGVKVIAPWREWDLLsREKLMDYAAKHAIPIE 169
                                                             ************************************987*************998 PP

                                               TIGR00032 164 v..ekekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevve 216
                                                                +k+++ys+D nll++s+E+g LEd +te  ed+++++++p++++ d+p+++e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1749 170 RhgKKKSPYSMDANLLHISYEGGVLEDTWTEHEEDMWRWTVSPENAP-DKPQYLE 223
                                                             62367889*********************************998888.******* PP

                                               TIGR00032 217 ieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEa 271
                                                             +++++G  val+g++++p +++ ++n+i+g+hG+Gr+DivE+R++g+KsR++YE+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1749 224 LTYRNGDIVALDGVEMTPATVLATLNRIGGEHGIGRLDIVENRYVGMKSRGCYET 278
                                                             ******************************************************* PP

                                               TIGR00032 272 palllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalik 326
                                                             p+ +++++Ah+++e+ +l+++v+++k+    ky+ liY+G+w++p++ +l+ +i+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1749 279 PGGTIMLRAHRAIESITLDREVAHLKDELMPKYASLIYTGYWWSPERLMLQQMID 333
                                                             ******************************************************* PP

                                               TIGR00032 327 ktqervtGtvrvklfkGnaivigrkseyslYdeelvsfek.dkefdqkdaiGfik 380
                                                              +q +v+G+vr+kl+kGn+iv grks++sl+d+++++fe+   +++q da+Gfik
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1749 334 ASQVNVNGVVRLKLYKGNVIVTGRKSDDSLFDANIATFEEdGGAYNQADAAGFIK 388
                                                             ***************************************9456899********* PP

                                               TIGR00032 381 irglqikvyre 391
                                                             +++l++++ ++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1749 389 LNALRMRIAAN 399
                                                             *****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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.56
//
[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