Alignments for a candidate for argG in Nocardiopsis lucentensis DSM 44048

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Nocardiopsis lucentensis DSM 44048

Align argininosuccinate synthase (characterized)
to candidate WP_017601759.1 D471_RS0128425 argininosuccinate synthase

Query= CharProtDB::CH_024687
         (447 letters)



>NCBI__GCF_000341125.1:WP_017601759.1
          Length = 483

 Score =  605 bits (1559), Expect = e-177
 Identities = 295/433 (68%), Positives = 351/433 (81%), Gaps = 1/433 (0%)

Query: 1   MTTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRA 60
           M+ +L  LPVG+R+GIAFSGGLDTS A+ WMR+KGAVP AYTA++GQ DE D  ++P RA
Sbjct: 1   MSKVLTSLPVGERVGIAFSGGLDTSVAVAWMREKGAVPCAYTADIGQYDEPDIASVPGRA 60

Query: 61  MEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKE 120
            +YGAE ARL+D R  LV EG+AA+ CGAFH  +GG  YFNTTPLGRAVTGT+LV AM E
Sbjct: 61  ADYGAEVARLVDGRAALVEEGLAALACGAFHIRSGGRVYFNTTPLGRAVTGTLLVRAMLE 120

Query: 121 DGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACG 180
           DGV IWGDGST+KGNDIERFYRYGLL N  L+IYKPWLD DF++ELGGR EMSE++   G
Sbjct: 121 DGVQIWGDGSTFKGNDIERFYRYGLLANPALRIYKPWLDADFVNELGGRKEMSEWLTERG 180

Query: 181 FDYKMSVEKAYSTDSNMLGATHEAKDLEYLNSSVKIVNPIMGVKFWDESVKIPAEEVTVR 240
             Y+ S EKAYSTD+N+ GATHEAK LE+L++ V+IV+PIMGV+FWD  V+IPAE+VT+ 
Sbjct: 181 LPYRDSTEKAYSTDANIWGATHEAKSLEHLDTGVEIVDPIMGVRFWDPEVEIPAEDVTIG 240

Query: 241 FEQGHPVALNGKTFSDDVEMMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL 300
           FEQG PV++NGK F   V+++LEAN +GGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL
Sbjct: 241 FEQGRPVSINGKGFPSAVDLVLEANAVGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL 300

Query: 301 HIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLRDSLQRWVASQITGEV 360
           H AYERL+  IHNEDTI  YH  GR+LGRL+Y+GRW + QALMLR+SLQRWV + ITGEV
Sbjct: 301 HAAYERLVNAIHNEDTIAAYHNEGRRLGRLMYEGRWLEPQALMLRESLQRWVGTAITGEV 360

Query: 361 TLELRRGNDYSILNTVSENLTYKPERLTMEK-GDSVFSPDDRIGQLTMRNLDITDTREKL 419
           TL LRRG DYSIL+T     +Y P++L+ME+  DS F P DRIGQLTMRNLDI D+R KL
Sbjct: 361 TLRLRRGEDYSILDTNGPAFSYHPDKLSMERTEDSAFGPVDRIGQLTMRNLDIADSRAKL 420

Query: 420 FGYAKTGLLSSSA 432
             YA  G++   A
Sbjct: 421 EEYASIGMVGEGA 433


Lambda     K      H
   0.317    0.135    0.397 

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: 669
Number of extensions: 28
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: 447
Length of database: 483
Length adjustment: 33
Effective length of query: 414
Effective length of database: 450
Effective search space:   186300
Effective search space used:   186300
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: 51 (24.3 bits)

Align candidate WP_017601759.1 D471_RS0128425 (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.17448.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-142  461.1   0.0   2.3e-142  460.9   0.0    1.0  1  lcl|NCBI__GCF_000341125.1:WP_017601759.1  D471_RS0128425 argininosuccinate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000341125.1:WP_017601759.1  D471_RS0128425 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.9   0.0  2.3e-142  2.3e-142       1     393 [.      13     420 ..      13     421 .. 0.98

  Alignments for each domain:
  == domain 1  score: 460.9 bits;  conditional E-value: 2.3e-142
                                 TIGR00032   1 kvvlaysGGlDtsvalklleekgaeviavtvdvGqp.eedldaieekalklGaekayviDareefvkdy 68 
                                               +v++a+sGGlDtsva+++++ekga++ a+t+d+Gq  e d+++++ +a  +Gae a+++D+r+ +v++ 
  lcl|NCBI__GCF_000341125.1:WP_017601759.1  13 RVGIAFSGGLDTSVAVAWMREKGAVPCAYTADIGQYdEPDIASVPGRAADYGAEVARLVDGRAALVEE- 80 
                                               69*********************************9899*****************************. PP

                                 TIGR00032  69 lfaaiqanavyegk....YllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnp 133
                                               ++aa+ ++a++       Y+++t+L+R+++++ lv ++ ++g++++++G+t+KGnD++RF++++ll np
  lcl|NCBI__GCF_000341125.1:WP_017601759.1  81 GLAALACGAFHIRSggrvYFNTTPLGRAVTGTLLVRAMLEDGVQIWGDGSTFKGNDIERFYRYGLLANP 149
                                               ***********9988899*************************************************** PP

                                 TIGR00032 134 dlkviaPvreleli.....ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdp.stepped 196
                                                l++++P+++ +++     R+e++e+++e+G++++ ++ekays+D n++g+++Ea++LE++ + + ++d
  lcl|NCBI__GCF_000341125.1:WP_017601759.1 150 ALRIYKPWLDADFVnelggRKEMSEWLTERGLPYRDSTEKAYSTDANIWGATHEAKSLEHLdTGVEIVD 218
                                               *************************************************************8889**** PP

                                 TIGR00032 197 iyelvkdpiektedepevveieFekGvPvalngesle.pvelilkaneiagkhGvGriDivEdRiiglK 264
                                               ++++v++++ ++e+ +e+v+i+Fe+G Pv++ng+ +  +v+l+l+an ++g+hG+G++D++E+Rii++K
  lcl|NCBI__GCF_000341125.1:WP_017601759.1 219 PIMGVRFWDPEVEIPAEDVTIGFEQGRPVSINGKGFPsAVDLVLEANAVGGRHGLGMSDQIENRIIEAK 287
                                               ************************************99******************************* PP

                                 TIGR00032 265 sReiYEapalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaeal.dalikktqerv 332
                                               sR+iYEap+++lL+ A+++L++ ++++d++  ++  ++++++l+Y+G+w++p+a +l ++l++++  ++
  lcl|NCBI__GCF_000341125.1:WP_017601759.1 288 SRGIYEAPGMALLHAAYERLVNAIHNEDTIAAYHNEGRRLGRLMYEGRWLEPQALMLrESLQRWVGTAI 356
                                               *********************************************************99********** PP

                                 TIGR00032 333 tGtvrvklfkGnaivigrk.seyslYdeelvsfek..dkefdqkdaiGfikirglqikvyrekl 393
                                               tG+v+++l++G++++i+ +  +   Y+++++s+e+  d++f + d+iG++++r+l+i++ r kl
  lcl|NCBI__GCF_000341125.1:WP_017601759.1 357 TGEVTLRLRRGEDYSILDTnGPAFSYHPDKLSMERteDSAFGPVDRIGQLTMRNLDIADSRAKL 420
                                               *****************998999***********988999*****************9998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (483 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 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