Alignments for a candidate for aroA in Methylovulum miyakonense HT12

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Methylovulum miyakonense HT12

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_019866298.1 METMI_RS0110750 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>NCBI__GCF_000384075.1:WP_019866298.1
          Length = 440

 Score =  436 bits (1122), Expect = e-127
 Identities = 231/424 (54%), Positives = 296/424 (69%), Gaps = 4/424 (0%)

Query: 7   PSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGASIQVI 66
           P   L GE  VPGDKS+SHR+++L ++A+G T V GFL   D LA + A + MG  I+  
Sbjct: 11  PGGKLHGETRVPGDKSMSHRSIMLGSLADGVTHVTGFLEAEDALATLQAFRDMGVEIEG- 69

Query: 67  EDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQRRPMK 126
                + + GVG  GL+ P   L  GNSGT++RLLSGLLAGQPFN VLTGD SL  RPMK
Sbjct: 70  PTNGCVTIHGVGKHGLKEPKNELYLGNSGTSMRLLSGLLAGQPFNCVLTGDKSLSGRPMK 129

Query: 127 RIIDPLTLMGAKIDSTGN-VPPLKIYGNP-RLTGIHYQLPMASAQVKSCLLLAGLYARGK 184
           R+ DPL  MGA I +T N   PL I G   +L  I Y +P+ASAQVKSCLLLAG+YA+G+
Sbjct: 130 RVTDPLATMGADIKTTENGTAPLHITGKAGQLQAIDYTMPIASAQVKSCLLLAGMYAQGE 189

Query: 185 TCITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAFFIVAA 244
           T +TEPAP+RDHTER+L  F Y ++++  +  +S  G LKA DI +P DISSAAFF+V A
Sbjct: 190 TRVTEPAPTRDHTERMLAGFSYPVKREGSTAVISSEGSLKAMDIDVPSDISSAAFFLVGA 249

Query: 245 TITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHARLKGID 304
           +I PGS + L  VG+NPTR GVI++L++MGA+IEV    E   EP AD+ V ++ LKGID
Sbjct: 250 SIAPGSDVTLKHVGINPTRTGVIDILRLMGANIEVLDPREVGGEPVADLHVVYSPLKGID 309

Query: 305 IPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGIAAESL 364
           IP   VPL IDEFPVL +AAA A+G+T L  A ELRVKE+DRI  M DGLQ LG+ A+  
Sbjct: 310 IPEHLVPLAIDEFPVLFVAAACAEGQTRLSGAEELRVKESDRIQVMADGLQILGVDAQPT 369

Query: 365 PDGVIIQGG-TLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFVELAN 423
           PDG++I GG  + GG V S+ DHRIAM+F++AG  A  P+ + +C NV TSFP F +L  
Sbjct: 370 PDGMVINGGRPIGGGVVTSHGDHRIAMSFSIAGLRANAPITVLDCANVNTSFPEFKDLVK 429

Query: 424 EVGM 427
           ++G+
Sbjct: 430 DLGL 433


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: 614
Number of extensions: 36
Number of successful extensions: 4
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: 438
Length of database: 440
Length adjustment: 32
Effective length of query: 406
Effective length of database: 408
Effective search space:   165648
Effective search space used:   165648
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_019866298.1 METMI_RS0110750 (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.31381.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     6e-130  419.7   0.0   6.8e-130  419.5   0.0    1.0  1  lcl|NCBI__GCF_000384075.1:WP_019866298.1  METMI_RS0110750 3-phosphoshikima


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000384075.1:WP_019866298.1  METMI_RS0110750 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.5   0.0  6.8e-130  6.8e-130       1     413 [.      17     432 ..      17     434 .. 0.96

  Alignments for each domain:
  == domain 1  score: 419.5 bits;  conditional E-value: 6.8e-130
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..l 66 
                                               ge ++pg+KS+shR+++l++La+g t vt++L++eD latl+a+r++G+++e  +++ ++i+gvg+  l
  lcl|NCBI__GCF_000384075.1:WP_019866298.1  17 GETRVPGDKSMSHRSIMLGSLADGVTHVTGFLEAEDALATLQAFRDMGVEIEgPTNGCVTIHGVGKhgL 85 
                                               6889************************************************767*********9999* PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                               kep++el+lgnsGt++Rll+g+la +++++vltgd+sl+ RP++r++++L  +ga+i+ +e +g++Pl+
  lcl|NCBI__GCF_000384075.1:WP_019866298.1  86 KEPKNELYLGNSGTSMRLLSGLLAGQPFNCVLTGDKSLSGRPMKRVTDPLATMGADIKTTE-NGTAPLH 153
                                               **********************************************************988.69***** PP

                                 TIGR01356 136 isgp.lkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveee 202
                                               i+g+  ++ +i +  + aS+Q+ks+llla+     a++++ v+e+  +r+++e++L+ ++     v++e
  lcl|NCBI__GCF_000384075.1:WP_019866298.1 154 ITGKaGQLqAIDYTMPIASAQVKSCLLLAGM---YAQGETRVTEPAPTRDHTERMLAGFSYP---VKRE 216
                                               ****86667*********************4...5678999999**************9988...9999 PP

                                 TIGR01356 203 derkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270
                                                + + v+  +++ k  +++v++D+SsAaffl+ a i+++ +vt++++g+n+t+++  +i++L+ mGa++
  lcl|NCBI__GCF_000384075.1:WP_019866298.1 217 GS-TAVISSEGSLKAMDIDVPSDISSAAFFLVGASIAPGsDVTLKHVGINPTRTG--VIDILRLMGANI 282
                                               88.78888888888888**********************9***************..788********* PP

                                 TIGR01356 271 eveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsd 330
                                               ev + r        d+ v   s lkg+++ ++ v+ +iDe+p+l v+aa+Aeg+tr+ ++eelRvkEsd
  lcl|NCBI__GCF_000384075.1:WP_019866298.1 283 EVLDPRevggepvaDLHVV-YSPLKGIDIpEHLVPLAIDEFPVLFVAAACAEGQTRLSGAEELRVKESD 350
                                               ***99999***99999999.689******99************************************** PP

                                 TIGR01356 331 RiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecva 399
                                               Ri+++a+ L+ lGv++++++dg++i+G+ + + g+vv +++DHRiam+++++gl+a++++++ d + v+
  lcl|NCBI__GCF_000384075.1:WP_019866298.1 351 RIQVMADGLQILGVDAQPTPDGMVINGG-RPIGGGVVTSHGDHRIAMSFSIAGLRANAPITVLDCANVN 418
                                               ****************************.7*************************************** PP

                                 TIGR01356 400 ksfPeFfevleqlg 413
                                               +sfPeF ++++ lg
  lcl|NCBI__GCF_000384075.1:WP_019866298.1 419 TSFPEFKDLVKDLG 432
                                               ********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (440 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.46
//
[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