GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argG in Streptacidiphilus oryzae TH49

Align argininosuccinate synthase (characterized)
to candidate WP_037574015.1 BS73_RS18735 argininosuccinate synthase

Query= CharProtDB::CH_024687
         (447 letters)



>NCBI__GCF_000744815.1:WP_037574015.1
          Length = 485

 Score =  597 bits (1539), Expect = e-175
 Identities = 289/434 (66%), Positives = 345/434 (79%), Gaps = 1/434 (0%)

Query: 1   MTTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRA 60
           M+ +L  LPVG+R+GIAFSGGLDTS A+ WMR+KGAVP  +TA+LGQ DE D  ++P RA
Sbjct: 1   MSKVLSSLPVGERVGIAFSGGLDTSVAVAWMREKGAVPCTFTADLGQYDEPDIASVPGRA 60

Query: 61  MEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKE 120
             YGAE +RL+DCR  LV EG+AA+ CGAFH  +GG  YFNTTPLGRAVTGTMLV AM E
Sbjct: 61  GAYGAELSRLVDCRAALVEEGLAALTCGAFHIRSGGRPYFNTTPLGRAVTGTMLVRAMLE 120

Query: 121 DGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACG 180
           D V IWGDGSTYKGNDIERFYRYGLL N  L+IYKPWLD +F+ ELGGR EMSE+++A  
Sbjct: 121 DDVQIWGDGSTYKGNDIERFYRYGLLANPALRIYKPWLDAEFVGELGGRTEMSEWLLARD 180

Query: 181 FDYKMSVEKAYSTDSNMLGATHEAKDLEYLNSSVKIVNPIMGVKFWDESVKIPAEEVTVR 240
             Y+ S EKAYSTD+N+ GATHEAK LE+L++ V++V PIMGV+FWD  V+I AE+VT+ 
Sbjct: 181 LPYRASTEKAYSTDANIWGATHEAKALEHLDNGVELVEPIMGVRFWDPEVEIAAEDVTIA 240

Query: 241 FEQGHPVALNGKTFSDDVEMMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL 300
           F+QG PVA+NGK F   V+++LEAN IGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL
Sbjct: 241 FQQGRPVAINGKEFPSAVDLVLEANAIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL 300

Query: 301 HIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLRDSLQRWVASQITGEV 360
             AYERL+  IHNEDT+  YH  GR+LGRLLY+GRW D QALM+R+SLQRWV S +TGEV
Sbjct: 301 FAAYERLVNAIHNEDTVAAYHNEGRRLGRLLYEGRWLDPQALMIRESLQRWVGSAVTGEV 360

Query: 361 TLELRRGNDYSILNTVSENLTYKPERLTMEK-GDSVFSPDDRIGQLTMRNLDITDTREKL 419
           TL LRRG DYS++NT     +Y P++L+ME+  DS F P DRIGQLTMRNLDI D+R +L
Sbjct: 361 TLRLRRGEDYSVINTTGPAFSYHPDKLSMERTEDSAFGPTDRIGQLTMRNLDIADSRSRL 420

Query: 420 FGYAKTGLLSSSAA 433
             Y   GL+    +
Sbjct: 421 EQYTALGLIGGEGS 434


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: 677
Number of extensions: 22
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: 485
Length adjustment: 33
Effective length of query: 414
Effective length of database: 452
Effective search space:   187128
Effective search space used:   187128
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_037574015.1 BS73_RS18735 (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.970637.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.6e-142  459.6   0.0   6.5e-142  459.4   0.0    1.0  1  NCBI__GCF_000744815.1:WP_037574015.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037574015.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.4   0.0  6.5e-142  6.5e-142       1     392 [.      13     419 ..      13     421 .. 0.98

  Alignments for each domain:
  == domain 1  score: 459.4 bits;  conditional E-value: 6.5e-142
                             TIGR00032   1 kvvlaysGGlDtsvalklleekgaeviavtvdvGqp.eedldaieekalklGaekayviDareefvkdylfaa 72 
                                           +v++a+sGGlDtsva+++++ekga++ ++t+d+Gq  e d+++++ +a ++Gae ++++D+r+ +v++ ++aa
  NCBI__GCF_000744815.1:WP_037574015.1  13 RVGIAFSGGLDTSVAVAWMREKGAVPCTFTADLGQYdEPDIASVPGRAGAYGAELSRLVDCRAALVEE-GLAA 84 
                                           69*********************************9899*****************************.**** PP

                             TIGR00032  73 iqanavyegk....YllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPv 141
                                           + ++a++       Y+++t+L+R++++++lv ++ +++++++++G+t+KGnD++RF++++ll np l++++P+
  NCBI__GCF_000744815.1:WP_037574015.1  85 LTCGAFHIRSggrpYFNTTPLGRAVTGTMLVRAMLEDDVQIWGDGSTYKGNDIERFYRYGLLANPALRIYKPW 157
                                           ********99999************************************************************ PP

                             TIGR00032 142 releli.....ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdp.steppediyelvkdpiekt 208
                                           ++ e++     R+e++e++ ++ +++++++ekays+D n++g+++Ea+ LE++ + +  ++++++v++++ ++
  NCBI__GCF_000744815.1:WP_037574015.1 158 LDAEFVgelggRTEMSEWLLARDLPYRASTEKAYSTDANIWGATHEAKALEHLdNGVELVEPIMGVRFWDPEV 230
                                           *****************************************************889***************** PP

                             TIGR00032 209 edepevveieFekGvPvalngesle.pvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikA 280
                                           e+ +e+v+i+F++G Pva+ng+++  +v+l+l+an i+g+hG+G++D++E+Rii++KsR+iYEap+++lL  A
  NCBI__GCF_000744815.1:WP_037574015.1 231 EIAAEDVTIAFQQGRPVAINGKEFPsAVDLVLEANAIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALLFAA 303
                                           ************************99*********************************************** PP

                             TIGR00032 281 hkdLetlvltkdvlefkeiveekyseliYkGlwfdplaeal.dalikktqervtGtvrvklfkGnaivigrk. 351
                                           +++L++ ++++d++  ++  ++++++l+Y+G+w+dp+a ++ ++l++++ ++vtG+v+++l++G+++++ ++ 
  NCBI__GCF_000744815.1:WP_037574015.1 304 YERLVNAIHNEDTVAAYHNEGRRLGRLLYEGRWLDPQALMIrESLQRWVGSAVTGEVTLRLRRGEDYSVINTt 376
                                           *****************************************99************************999998 PP

                             TIGR00032 352 seyslYdeelvsfek..dkefdqkdaiGfikirglqikvyrek 392
                                            +   Y+++++s+e+  d++f ++d+iG++++r+l+i++ r++
  NCBI__GCF_000744815.1:WP_037574015.1 377 GPAFSYHPDKLSMERteDSAFGPTDRIGQLTMRNLDIADSRSR 419
                                           99************988999*****************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (485 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 30.93
//
[ok]

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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