Alignments for a candidate for argG in Xenophilus azovorans DSM 13620

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Xenophilus azovorans DSM 13620

Align argininosuccinate synthase (characterized)
to candidate WP_038213032.1 Q392_RS23010 argininosuccinate synthase

Query= CharProtDB::CH_024687
         (447 letters)



>NCBI__GCF_000745855.1:WP_038213032.1
          Length = 446

 Score =  702 bits (1812), Expect = 0.0
 Identities = 347/446 (77%), Positives = 387/446 (86%), Gaps = 1/446 (0%)

Query: 1   MTTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRA 60
           M+TIL+ LP GQ++GIAFSGGLDTSAALLWM++KGA PYAYTANLGQPDE DYD IPR+A
Sbjct: 1   MSTILQSLPTGQKVGIAFSGGLDTSAALLWMKKKGAQPYAYTANLGQPDEPDYDEIPRKA 60

Query: 61  MEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKE 120
           + YGAE ARL+DCR+QLVAEGIAA+Q  AFH +TGG+TYFNTTPLGRAVTGTMLVAAMKE
Sbjct: 61  LAYGAEKARLVDCRQQLVAEGIAALQANAFHVSTGGVTYFNTTPLGRAVTGTMLVAAMKE 120

Query: 121 DGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACG 180
           D VNIWGDGST+KGNDIERFYRYGLLTN  L+IYKPWLD  FIDELGGR EMSEF+IA G
Sbjct: 121 DDVNIWGDGSTFKGNDIERFYRYGLLTNPGLKIYKPWLDQTFIDELGGRKEMSEFLIANG 180

Query: 181 FDYKMSVEKAYSTDSNMLGATHEAKDLEYLNSSVKIVNPIMGVKFWDESVKIPAEEVTVR 240
           FDYKMSVEKAYSTDSNMLGATHEAKDLE+LNS ++IVNPIMGV FW   V++  EEV VR
Sbjct: 181 FDYKMSVEKAYSTDSNMLGATHEAKDLEHLNSGIRIVNPIMGVAFWKPEVEVKPEEVRVR 240

Query: 241 FEQGHPVALNGKTFSDDVEMMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL 300
           FE+G PVALNGK F D V +M EANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL
Sbjct: 241 FEEGRPVALNGKRFDDLVALMEEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL 300

Query: 301 HIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLRDSLQRWVASQITGEV 360
           HIAYERL+TGIHNEDTIEQY  +G +LGRLLYQGRWFD QA+MLR++ QRWVA  ITGEV
Sbjct: 301 HIAYERLVTGIHNEDTIEQYRINGLRLGRLLYQGRWFDPQAIMLRETAQRWVARAITGEV 360

Query: 361 TLELRRGNDYSILNTVSENLTYKPERLTMEK-GDSVFSPDDRIGQLTMRNLDITDTREKL 419
           TLELRRGNDYS+L+T S NLTY PERL+MEK  D+ FSP DRIGQLTMRNLDI DTR KL
Sbjct: 361 TLELRRGNDYSLLDTESPNLTYAPERLSMEKVEDAPFSPADRIGQLTMRNLDIVDTRAKL 420

Query: 420 FGYAKTGLLSSSAASGVPQVENLENK 445
             Y + GLL+    + +PQ+++   K
Sbjct: 421 ATYVQAGLLAKPEGTELPQIKDASRK 446


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: 663
Number of extensions: 16
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: 446
Length adjustment: 33
Effective length of query: 414
Effective length of database: 413
Effective search space:   170982
Effective search space used:   170982
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_038213032.1 Q392_RS23010 (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.937283.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-163  530.1   0.0   2.4e-163  529.9   0.0    1.0  1  NCBI__GCF_000745855.1:WP_038213032.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745855.1:WP_038213032.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  529.9   0.0  2.4e-163  2.4e-163       1     393 [.      13     420 ..      13     421 .. 0.99

  Alignments for each domain:
  == domain 1  score: 529.9 bits;  conditional E-value: 2.4e-163
                             TIGR00032   1 kvvlaysGGlDtsvalklleekgaeviavtvdvGqp.eedldaieekalklGaekayviDareefvkdylfaa 72 
                                           kv++a+sGGlDts+al+++++kga+++a+t+++Gqp e d+d+i++kal++Gaeka+++D+r+++v++ ++aa
  NCBI__GCF_000745855.1:WP_038213032.1  13 KVGIAFSGGLDTSAALLWMKKKGAQPYAYTANLGQPdEPDYDEIPRKALAYGAEKARLVDCRQQLVAE-GIAA 84 
                                           89**********************************999*****************************.**** PP

                             TIGR00032  73 iqanavyegk....YllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPv 141
                                           +qana++ ++    Y+++t+L+R++++++lv+++k+++++++++G+t+KGnD++RF++++ll+np lk+++P+
  NCBI__GCF_000745855.1:WP_038213032.1  85 LQANAFHVSTggvtYFNTTPLGRAVTGTMLVAAMKEDDVNIWGDGSTFKGNDIERFYRYGLLTNPGLKIYKPW 157
                                           ********999999*********************************************************** PP

                             TIGR00032 142 releli.....ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdp.steppediyelvkdpiekt 208
                                           ++  +i     R+e++e+++++G+++++++ekays+D+n+lg+++Ea++LE++ s  ++++++++v++++ ++
  NCBI__GCF_000745855.1:WP_038213032.1 158 LDQTFIdelggRKEMSEFLIANGFDYKMSVEKAYSTDSNMLGATHEAKDLEHLnSGIRIVNPIMGVAFWKPEV 230
                                           *****************************************************899***************** PP

                             TIGR00032 209 edepevveieFekGvPvalngesle.pvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikA 280
                                           e +pe+v ++Fe+G Pvalng++++  v l+++an+i+g+hG+G++D++E+Rii++KsR+iYEap+++lL++A
  NCBI__GCF_000745855.1:WP_038213032.1 231 EVKPEEVRVRFEEGRPVALNGKRFDdLVALMEEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALLHIA 303
                                           *************************99********************************************** PP

                             TIGR00032 281 hkdLetlvltkdvlefkeiveekyseliYkGlwfdplaeal.dalikktqervtGtvrvklfkGnaivigrk. 351
                                           +++L+t+++++d++e+++i++ ++++l+Y+G+wfdp+a +l +++++++++++tG+v+++l++Gn+++++ + 
  NCBI__GCF_000745855.1:WP_038213032.1 304 YERLVTGIHNEDTIEQYRINGLRLGRLLYQGRWFDPQAIMLrETAQRWVARAITGEVTLELRRGNDYSLLDTe 376
                                           *****************************************99***************************999 PP

                             TIGR00032 352 seyslYdeelvsfek..dkefdqkdaiGfikirglqikvyrekl 393
                                           s++++Y +e++s+ek  d+ f++ d+iG++++r+l+i ++r kl
  NCBI__GCF_000745855.1:WP_038213032.1 377 SPNLTYAPERLSMEKveDAPFSPADRIGQLTMRNLDIVDTRAKL 420
                                           **************99999*******************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (446 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 29.49
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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