Alignments for a candidate for argG in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Halomonas desiderata SP1

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_086510012.1 BZY95_RS11225 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>NCBI__GCF_002151265.1:WP_086510012.1
          Length = 406

 Score =  516 bits (1330), Expect = e-151
 Identities = 248/394 (62%), Positives = 311/394 (78%), Gaps = 4/394 (1%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61
           K+VLAYSGGLDTS+I+KWL+ETY  EV+ FTADIGQGEEVE AR KA   G  +    DL
Sbjct: 6   KVVLAYSGGLDTSVIVKWLQETYNCEVVTFTADIGQGEEVEPARAKAQALGVKEIYIEDL 65

Query: 62  KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121
           +EEFVRD+V+PM RA  +YEG YLLGTSIARPLIAK L+ IA E GA+AI+HGATGKGND
Sbjct: 66  REEFVRDYVYPMFRANTIYEGEYLLGTSIARPLIAKRLIEIANETGADAISHGATGKGND 125

Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEK---PYSMDANL 178
           QVRFE+ AYALKP +KVIAPWREW    R++++AY E H IPV  ++ K   PYSMDANL
Sbjct: 126 QVRFEMGAYALKPGVKVIAPWREWDLTSREKLMAYCEQHDIPVDFSKSKKKSPYSMDANL 185

Query: 179 LHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAAL 238
           LHISYEGG+LEDPWAE  + M+R +  PE APD P YVE+ + +GD VA++G+ + P  +
Sbjct: 186 LHISYEGGILEDPWAEAEEDMWRWSVSPEAAPDEPTYVELTYDKGDVVAIDGKPMKPHEV 245

Query: 239 LQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQR 298
           L+RLN++GG +G+GR+DIVENR+VGMKSRG YETPGGTI+  A RA+ES+TLDRE  H +
Sbjct: 246 LERLNKLGGDNGIGRLDIVENRYVGMKSRGCYETPGGTIMLRAHRAIESITLDREEAHLK 305

Query: 299 DMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLY 358
           D L PKYA+++Y G+W++PER  LQA  D   ++V GV R+KLYKGN  VVGRK+ +SL+
Sbjct: 306 DELMPKYAKVIYNGYWWSPERRMLQAAIDETQKNVCGVVRMKLYKGNATVVGRKSEQSLF 365

Query: 359 RQDLVSF-DEAGGYDQKDAEGFIKIQALRLRVRA 391
            + + +F D+AG Y+QKDAEGFIK+ ALRLR+ A
Sbjct: 366 DESIATFEDDAGAYNQKDAEGFIKLNALRLRIAA 399


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: 524
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: 400
Length of database: 406
Length adjustment: 31
Effective length of query: 369
Effective length of database: 375
Effective search space:   138375
Effective search space used:   138375
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_086510012.1 BZY95_RS11225 (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.12120.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     8e-146  472.3   0.0   9.2e-146  472.1   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086510012.1  BZY95_RS11225 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086510012.1  BZY95_RS11225 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.1   0.0  9.2e-146  9.2e-146       1     389 [.       6     398 ..       6     403 .. 0.97

  Alignments for each domain:
  == domain 1  score: 472.1 bits;  conditional E-value: 9.2e-146
                                 TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdy 68 
                                               kvvlaysGGlDtsv++k+l+e  ++ev+++t+d+Gq+ e+++ ++ ka +lG+++ y+ D reefv+dy
  lcl|NCBI__GCF_002151265.1:WP_086510012.1   6 KVVLAYSGGLDTSVIVKWLQETyNCEVVTFTADIGQG-EEVEPARAKAQALGVKEIYIEDLREEFVRDY 73 
                                               8*********************99************9.9****************************** PP

                                 TIGR00032  69 lfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137
                                               + +  +an++yeg+Yll+t++aRpliak+l+e+a++ ga+a++hG+tgKGnDqvRFe+  ++l+p +kv
  lcl|NCBI__GCF_002151265.1:WP_086510012.1  74 VYPMFRANTIYEGEYLLGTSIARPLIAKRLIEIANETGADAISHGATGKGNDQVRFEMGAYALKPGVKV 142
                                               ********************************************************************* PP

                                 TIGR00032 138 iaPvreleli.ReeeieyaaekGievpve...kekaysiDenllgrsiEageLEdpsteppediyelvk 202
                                               iaP+re++l+ Re++++y +++ i+v  +   k+++ys+D nll++s+E+g+LEdp++e  ed++++ +
  lcl|NCBI__GCF_002151265.1:WP_086510012.1 143 IAPWREWDLTsREKLMAYCEQHDIPVDFSkskKKSPYSMDANLLHISYEGGILEDPWAEAEEDMWRWSV 211
                                               *********99**************96651115679********************************* PP

                                 TIGR00032 203 dpiektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEa 271
                                               +p++++ dep +ve++++kG  va++g+ ++p e+++++n+++g +G+Gr+DivE+R++g+KsR++YE+
  lcl|NCBI__GCF_002151265.1:WP_086510012.1 212 SPEAAP-DEPTYVELTYDKGDVVAIDGKPMKPHEVLERLNKLGGDNGIGRLDIVENRYVGMKSRGCYET 279
                                               888887.************************************************************** PP

                                 TIGR00032 272 palllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvkl 340
                                               p+ +++++Ah+++e+ +l+++++++k+    ky+++iY+G+w++p++ +l+a+i++tq++v G+vr+kl
  lcl|NCBI__GCF_002151265.1:WP_086510012.1 280 PGGTIMLRAHRAIESITLDREEAHLKDELMPKYAKVIYNGYWWSPERRMLQAAIDETQKNVCGVVRMKL 348
                                               ********************************************************************* PP

                                 TIGR00032 341 fkGnaivigrkseyslYdeelvsfek.dkefdqkdaiGfikirglqikvy 389
                                               +kGna+v+grkse+sl+de +++fe    +++qkda+Gfik+++l+ ++ 
  lcl|NCBI__GCF_002151265.1:WP_086510012.1 349 YKGNATVVGRKSEQSLFDESIATFEDdAGAYNQKDAEGFIKLNALRLRIA 398
                                               *************************9445799*************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (406 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.21
//
[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