Alignments for a candidate for aroA in Methylococcus capsulatus Bath

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Methylococcus capsulatus Bath

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_050738184.1 MCA_RS06960 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>NCBI__GCF_000008325.1:WP_050738184.1
          Length = 437

 Score =  471 bits (1212), Expect = e-137
 Identities = 242/425 (56%), Positives = 305/425 (71%), Gaps = 2/425 (0%)

Query: 7   PSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGASIQVI 66
           P   + G+I VPGDKSISHR+V+L ++AEG T+V GFL   D LA ++A + MG  I+  
Sbjct: 12  PGGRMQGDIRVPGDKSISHRSVMLGSLAEGVTEVSGFLQAEDCLATMAAFRAMGVEIEG- 70

Query: 67  EDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQRRPMK 126
             E  L + GVG+ GL+ P   LD GNSGT++RLLSGLLAGQ F+T LTGD+SL RRPM+
Sbjct: 71  PTEGRLRIHGVGLHGLKPPAAPLDLGNSGTSMRLLSGLLAGQAFDTTLTGDASLVRRPMR 130

Query: 127 RIIDPLTLMGAKIDST-GNVPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGLYARGKT 185
           R+ +PL  MGA+ID+T     PL+I G  RL GI Y +P+ASAQVKSCLLLAGLYA GKT
Sbjct: 131 RVTEPLRAMGARIDTTEAGTAPLRIAGGSRLKGIDYAMPVASAQVKSCLLLAGLYAEGKT 190

Query: 186 CITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAFFIVAAT 245
           C+TEPAP+RDHTER+L  F Y + +D   +C+  GGKL A  I +P DISSAAFF++ A 
Sbjct: 191 CVTEPAPTRDHTERMLAGFGYPVARDGNRVCIQSGGKLSATRIDVPADISSAAFFMIGAA 250

Query: 246 ITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHARLKGIDI 305
           I+PGS + L  VG+NPTR GVI +L+ MGADIE+    E   EP AD+ +R+  L+GI I
Sbjct: 251 ISPGSDVFLRHVGINPTRTGVIEILREMGADIEILAPREVGGEPVADLRIRYRELRGIRI 310

Query: 306 PPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGIAAESLP 365
           P   VPL IDEFP L IAAA A G+TVL  A ELRVKE+DRI AM DGL  LGI A   P
Sbjct: 311 PEHTVPLAIDEFPALFIAAACATGETVLTGAEELRVKESDRIQAMADGLTTLGIDARPTP 370

Query: 366 DGVIIQGGTLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFVELANEV 425
           DG++I+GG+  GG V+S  DHRIAM+F++A   A  P+ I +C NV TSFPNFVELA  +
Sbjct: 371 DGMVIRGGSFRGGAVDSRGDHRIAMSFSIAALRAPIPIEIHDCANVATSFPNFVELARTL 430

Query: 426 GMNVK 430
           G++++
Sbjct: 431 GLDIE 435


Lambda     K      H
   0.318    0.137    0.392 

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: 644
Number of extensions: 35
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 438
Length of database: 437
Length adjustment: 32
Effective length of query: 406
Effective length of database: 405
Effective search space:   164430
Effective search space used:   164430
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: 51 (24.3 bits)

Align candidate WP_050738184.1 MCA_RS06960 (3-phosphoshikimate 1-carboxyvinyltransferase)
to HMM TIGR01356 (aroA: 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19))

# 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/TIGR01356.hmm
# target sequence database:        /tmp/gapView.25702.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01356  [M=415]
Accession:   TIGR01356
Description: aroA: 3-phosphoshikimate 1-carboxyvinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-130  421.4   0.0     2e-130  421.3   0.0    1.0  1  lcl|NCBI__GCF_000008325.1:WP_050738184.1  MCA_RS06960 3-phosphoshikimate 1


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008325.1:WP_050738184.1  MCA_RS06960 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.3   0.0    2e-130    2e-130       1     413 [.      18     431 ..      18     433 .. 0.96

  Alignments for each domain:
  == domain 1  score: 421.3 bits;  conditional E-value: 2e-130
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..l 66 
                                               g+i++pg+KSishR+++l++Laeg t+v ++L++eD+lat+ a+r++G+++e  ++++l i+gvg   l
  lcl|NCBI__GCF_000008325.1:WP_050738184.1  18 GDIRVPGDKSISHRSVMLGSLAEGVTEVSGFLQAEDCLATMAAFRAMGVEIEgPTEGRLRIHGVGLhgL 86 
                                               79**************************************************7669********98889 PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                               k p a ldlgnsGt++Rll+g+la ++++++ltgd sl +RP++r++e+Lr++ga+i+ +e +g++Pl+
  lcl|NCBI__GCF_000008325.1:WP_050738184.1  87 KPPAAPLDLGNSGTSMRLLSGLLAGQAFDTTLTGDASLVRRPMRRVTEPLRAMGARIDTTE-AGTAPLR 154
                                               **********************************************************988.69***** PP

                                 TIGR01356 136 isgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               i g++++ gi +  + aS+Q+ks+llla+   l a++ + v+e+  +r+++e++L+ ++     v ++ 
  lcl|NCBI__GCF_000008325.1:WP_050738184.1 155 IAGGSRLkGIDYAMPVASAQVKSCLLLAG---LYAEGKTCVTEPAPTRDHTERMLAGFGYP---VARDG 217
                                               ****9999*********************...7778999***************9988866...99987 PP

                                 TIGR01356 204 erkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadve 271
                                               + ++ ++ g+k   ++++v++D+SsAaff++ aai+++ +v ++++g+n+t+++  +i++L+emGad+e
  lcl|NCBI__GCF_000008325.1:WP_050738184.1 218 N-RVCIQSGGKLSATRIDVPADISSAAFFMIGAAISPGsDVFLRHVGINPTRTG--VIEILREMGADIE 283
                                               6.9******9988888**********************9***************..888********** PP

                                 TIGR01356 272 veeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdR 331
                                               + + r        d++++  ++l+g+++ ++ v+ +iDe+p+l ++aa+A get+++++eelRvkEsdR
  lcl|NCBI__GCF_000008325.1:WP_050738184.1 284 ILAPRevggepvaDLRIR-YRELRGIRIpEHTVPLAIDEFPALFIAAACATGETVLTGAEELRVKESDR 351
                                               **9999************.689******99*************************************** PP

                                 TIGR01356 332 iaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvak 400
                                               i+a+a+ L++lG+++++++dg++i+G+  +++g+ vd+ +DHRiam++++++l+a  ++ei+d + va+
  lcl|NCBI__GCF_000008325.1:WP_050738184.1 352 IQAMADGLTTLGIDARPTPDGMVIRGG--SFRGGAVDSRGDHRIAMSFSIAALRAPIPIEIHDCANVAT 418
                                               ***************************..6*************************************** PP

                                 TIGR01356 401 sfPeFfevleqlg 413
                                               sfP+F+e++++lg
  lcl|NCBI__GCF_000008325.1:WP_050738184.1 419 SFPNFVELARTLG 431
                                               *******999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (437 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: 7.80
//
[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