Aligments for a candidate for argG in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Aligments for a candidate for argG in Herbaspirillum seropedicae SmR1

Align argininosuccinate synthase (characterized)
to candidate HSERO_RS07180 HSERO_RS07180 argininosuccinate synthase

Query= CharProtDB::CH_024687
         (447 letters)



>FitnessBrowser__HerbieS:HSERO_RS07180
          Length = 444

 Score =  707 bits (1825), Expect = 0.0
 Identities = 346/437 (79%), Positives = 385/437 (88%)

Query: 1   MTTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRA 60
           M+ IL+ +PV Q++GIAFSGGLDTSAAL WMRQKGA+PYAYTANLGQPDE DYDAIP++A
Sbjct: 1   MSNILQSVPVNQKVGIAFSGGLDTSAALTWMRQKGAIPYAYTANLGQPDEPDYDAIPKKA 60

Query: 61  MEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKE 120
           M+YGA+ ARLIDCR+QL  EGIAA+Q GAFH +T G+TYFNTTPLGRAVTGTMLV+AM+E
Sbjct: 61  MQYGAQQARLIDCREQLANEGIAALQSGAFHISTAGITYFNTTPLGRAVTGTMLVSAMRE 120

Query: 121 DGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACG 180
           D V+IWGDGSTYKGNDIERFYRYGLL N  L+IYKPWLD+ FIDELGGR EMSEFMI  G
Sbjct: 121 DNVDIWGDGSTYKGNDIERFYRYGLLVNPNLKIYKPWLDSTFIDELGGRKEMSEFMIKSG 180

Query: 181 FDYKMSVEKAYSTDSNMLGATHEAKDLEYLNSSVKIVNPIMGVKFWDESVKIPAEEVTVR 240
           FDYKMSVEKAYSTDSNMLGATHEAKDLE+LNS +KIV PIMGV FW + V++ AE VTVR
Sbjct: 181 FDYKMSVEKAYSTDSNMLGATHEAKDLEFLNSGIKIVQPIMGVAFWRDDVEVKAETVTVR 240

Query: 241 FEQGHPVALNGKTFSDDVEMMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL 300
           FE+G PVALNGKTF+   E++LEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPG+ALL
Sbjct: 241 FEEGRPVALNGKTFASMTELILEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGLALL 300

Query: 301 HIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLRDSLQRWVASQITGEV 360
            IAYERL+TGIHNEDTIEQY  +GR+LGRLLYQGRWFDSQA+MLR++ QRWVA  ITGEV
Sbjct: 301 FIAYERLVTGIHNEDTIEQYRDNGRKLGRLLYQGRWFDSQAIMLRETAQRWVARAITGEV 360

Query: 361 TLELRRGNDYSILNTVSENLTYKPERLTMEKGDSVFSPDDRIGQLTMRNLDITDTREKLF 420
           T+ELRRGNDYSILNT S NLTY PERLTMEKG+  FS  DRIGQLTMRNLDI DTR+KL 
Sbjct: 361 TVELRRGNDYSILNTESPNLTYHPERLTMEKGEGSFSAIDRIGQLTMRNLDIADTRQKLA 420

Query: 421 GYAKTGLLSSSAASGVP 437
            Y  TGLL SS A  +P
Sbjct: 421 IYQNTGLLESSTAVSLP 437


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: 661
Number of extensions: 13
Number of successful extensions: 1
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: 444
Length adjustment: 32
Effective length of query: 415
Effective length of database: 412
Effective search space:   170980
Effective search space used:   170980
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 HSERO_RS07180 HSERO_RS07180 (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.27345.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.7e-161  523.8   0.0     2e-161  523.6   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS07180  HSERO_RS07180 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS07180  HSERO_RS07180 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  523.6   0.0    2e-161    2e-161       1     393 [.      13     419 ..      13     420 .. 0.99

  Alignments for each domain:
  == domain 1  score: 523.6 bits;  conditional E-value: 2e-161
                                  TIGR00032   1 kvvlaysGGlDtsvalklleekgaeviavtvdvGqp.eedldaieekalklGaekayviDareefvkd 67 
                                                kv++a+sGGlDts+al+++++kga ++a+t+++Gqp e d+dai++ka+++Ga++a++iD+re+++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS07180  13 KVGIAFSGGLDTSAALTWMRQKGAIPYAYTANLGQPdEPDYDAIPKKAMQYGAQQARLIDCREQLANE 80 
                                                89**********************************999***************************** PP

                                  TIGR00032  68 ylfaaiqanavyegk....YllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilll 131
                                                 ++aa+q +a++ ++    Y+++t+L+R++++++lv ++++++++++++G+t+KGnD++RF++++ll 
  lcl|FitnessBrowser__HerbieS:HSERO_RS07180  81 -GIAALQSGAFHISTagitYFNTTPLGRAVTGTMLVSAMREDNVDIWGDGSTYKGNDIERFYRYGLLV 147
                                                .*************99999************************************************* PP

                                  TIGR00032 132 npdlkviaPvreleli.....ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdp.step 193
                                                np+lk+++P+++  +i     R+e++e++++ G+++++++ekays+D+n+lg+++Ea++LE + s  +
  lcl|FitnessBrowser__HerbieS:HSERO_RS07180 148 NPNLKIYKPWLDSTFIdelggRKEMSEFMIKSGFDYKMSVEKAYSTDSNMLGATHEAKDLEFLnSGIK 215
                                                ***************************************************************899** PP

                                  TIGR00032 194 pediyelvkdpiektedepevveieFekGvPvalngesle.pvelilkaneiagkhGvGriDivEdRi 260
                                                +++++++v+++ +++e ++e+v+++Fe+G Pvalng+++    elil+an+i+g+hG+G++D++E+Ri
  lcl|FitnessBrowser__HerbieS:HSERO_RS07180 216 IVQPIMGVAFWRDDVEVKAETVTVRFEEGRPVALNGKTFAsMTELILEANRIGGRHGLGMSDQIENRI 283
                                                ***************************************9899************************* PP

                                  TIGR00032 261 iglKsReiYEapalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaeal.dalikk 327
                                                i++KsR+iYEap+l+lL +A+++L+t+++++d++e+++ +++k+++l+Y+G+wfd++a +l ++++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS07180 284 IEAKSRGIYEAPGLALLFIAYERLVTGIHNEDTIEQYRDNGRKLGRLLYQGRWFDSQAIMLrETAQRW 351
                                                *************************************************************99***** PP

                                  TIGR00032 328 tqervtGtvrvklfkGnaivigrk.seyslYdeelvsfek.dkefdqkdaiGfikirglqikvyrekl 393
                                                +++++tG+v+v+l++Gn+++i+++ s++++Y++e++++ek + +f+  d+iG++++r+l+i+++r+kl
  lcl|FitnessBrowser__HerbieS:HSERO_RS07180 352 VARAITGEVTVELRRGNDYSILNTeSPNLTYHPERLTMEKgEGSFSAIDRIGQLTMRNLDIADTRQKL 419
                                                ************************9***************999*********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (444 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: 00:00:00.01
# Mc/sec: 12.19
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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