Alignments for a candidate for aroA in Desulfuromonas acetexigens

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Desulfuromonas acetexigens

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_092053417.1 BQ4888_RS00685 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::B1XM36
         (446 letters)



>NCBI__GCF_900111775.1:WP_092053417.1
          Length = 430

 Score =  449 bits (1155), Expect = e-131
 Identities = 240/421 (57%), Positives = 298/421 (70%), Gaps = 5/421 (1%)

Query: 23  SLQGKVRIPGDKSISHRALMLGAIAEGETIIEGLLLGEDPRSTAACFAAMGANISELNET 82
           SL+G++ +PGDKSISHR++MLG++A+G T++ G L GED  +T   F AMG  I EL + 
Sbjct: 12  SLRGEISVPGDKSISHRSIMLGSLAQGTTLVRGFLHGEDNHATLKAFRAMGVTIEELADG 71

Query: 83  EVRVQGVGLGNLQEPDNVLDAGNSGTTMRLMMGLLASSPDRFFAV-TGDGSLRSRPMSRV 141
           ++R+ G GL  L EP +VLD GNSGTT+RLM GLL  S   FF+V TGD  LR RPM RV
Sbjct: 72  DLRIDGRGLHGLAEPADVLDCGNSGTTIRLMTGLL--SGQTFFSVLTGDRYLRKRPMKRV 129

Query: 142 VNPLKEMGAQIWGKKGNTLAPLAIQGQQLKGIHYHSPIASAQVKSCVLLAGLLAEGQTTV 201
           + PL  MGAQIWG+ G  LAPLAI G  LKG  Y SPI+SAQVKS +LLAGL A+G TTV
Sbjct: 130 LAPLATMGAQIWGRGGGDLAPLAIHGGALKGTEYDSPISSAQVKSALLLAGLYADGPTTV 189

Query: 202 TEPALSRDHSERMLRAFGANLTIDPETHSVTIDPHPTLRGQKVVVPGDISSAAFWMVAAA 261
            EP LSRDHSERMLR FGA   + P    VT+ P P L G++V VPGDISSAAF+MVAA 
Sbjct: 190 WEPHLSRDHSERMLRYFGAE--VRPFEGGVTVAPQPQLEGREVAVPGDISSAAFFMVAAL 247

Query: 262 IVPDSDLTIENVGINPTRTGIIEAMQMMGADMTLDNAREVAGEPVADLRVQYSPLKGCTI 321
           IVP ++L I NVG+NPTR+GII+ +Q MG  + L N RE++GEPVADL V+ S LKG  I
Sbjct: 248 IVPGAELLIRNVGVNPTRSGIIDILQAMGGSIELLNTRELSGEPVADLLVRGSSLKGIEI 307

Query: 322 GGEIIPRLIDEIPILAVAACFAAGTTIIKDAEELRVKESDRLAVMAAELTKMGANIIEHP 381
           GG ++PR IDE P+++VAA FA GTT I+DA+ELRVKE+DR+A M  ELT +G  +    
Sbjct: 308 GGAVVPRAIDEFPVISVAASFAEGTTTIRDAKELRVKETDRIAAMVEELTTLGGRVEARN 367

Query: 382 DGLEIIGGASLNGAEMDSYTDHRIAMSLAIAALNAKDETRIHRAEAASISYPTFVETLTN 441
           DG+ I G  S NG  + S+ DHRIAMS+A+AAL A+ E  I      + S+P F   L  
Sbjct: 368 DGMVIDGVESFNGGAVKSHGDHRIAMSMAVAALRARAEVSIDDTACTATSFPNFWSLLEK 427

Query: 442 V 442
           V
Sbjct: 428 V 428


Lambda     K      H
   0.317    0.133    0.376 

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: 550
Number of extensions: 23
Number of successful extensions: 3
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: 446
Length of database: 430
Length adjustment: 32
Effective length of query: 414
Effective length of database: 398
Effective search space:   164772
Effective search space used:   164772
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate WP_092053417.1 BQ4888_RS00685 (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.13519.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-134  434.9   0.0   1.6e-134  434.7   0.0    1.0  1  lcl|NCBI__GCF_900111775.1:WP_092053417.1  BQ4888_RS00685 3-phosphoshikimat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900111775.1:WP_092053417.1  BQ4888_RS00685 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.7   0.0  1.6e-134  1.6e-134       1     412 [.      15     428 ..      15     430 .] 0.96

  Alignments for each domain:
  == domain 1  score: 434.7 bits;  conditional E-value: 1.6e-134
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 
                                               gei++pg+KSishR+++l++La+g+t v+++L++eD +atl+a+r++G+++ee  +++l i+g g   l
  lcl|NCBI__GCF_900111775.1:WP_092053417.1  15 GEISVPGDKSISHRSIMLGSLAQGTTLVRGFLHGEDNHATLKAFRAMGVTIEELaDGDLRIDGRGLhgL 83 
                                               89**************************************************5559*******987889 PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                               +ep ++ld+gnsGtt+Rl+tg+l+ + + +vltgd  l+kRP++r++ +L  +ga+i  + + + +Pla
  lcl|NCBI__GCF_900111775.1:WP_092053417.1  84 AEPADVLDCGNSGTTIRLMTGLLSGQTFFSVLTGDRYLRKRPMKRVLAPLATMGAQIWGRGGGDLAPLA 152
                                               ********************************************************************* PP

                                 TIGR01356 136 isgplkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede 204
                                               i+g+   g+ + s+  S+Q+ksallla+   l a++ ++v e+ +sr++ e++L  ++++   v+  ++
  lcl|NCBI__GCF_900111775.1:WP_092053417.1 153 IHGGALKGTEYDSPISSAQVKSALLLAG---LYADGPTTVWEPHLSRDHSERMLRYFGAE---VRPFEG 215
                                               ***8888*********************...66778899999*************99988...777666 PP

                                 TIGR01356 205 rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadvev 272
                                                 ++v ++ + + +ev+v+gD+SsAaff++aa+i ++ e+ ++n+g n+t+ +  ii++L++mG+++e+
  lcl|NCBI__GCF_900111775.1:WP_092053417.1 216 -GVTVAPQPQLEGREVAVPGDISSAAFFMVAALIVPGaELLIRNVGVNPTRSG--IIDILQAMGGSIEL 281
                                               .89999998877778**************************************..888*********** PP

                                 TIGR01356 273 eeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRi 332
                                                ++r        d+ v+g s+lkg+++  + v+++iDe+p+++v+a+fAeg+t+i++++elRvkE+dRi
  lcl|NCBI__GCF_900111775.1:WP_092053417.1 282 LNTRelsgepvaDLLVRG-SSLKGIEIgGAVVPRAIDEFPVISVAASFAEGTTTIRDAKELRVKETDRI 349
                                               *****************6.68******99**************************************** PP

                                 TIGR01356 333 aaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaks 401
                                               aa++eeL++lG +ve ++dg++i G  ++++g+ v++++DHRiam++av++l+a++ev i+d++c+a+s
  lcl|NCBI__GCF_900111775.1:WP_092053417.1 350 AAMVEELTTLGGRVEARNDGMVIDGV-ESFNGGAVKSHGDHRIAMSMAVAALRARAEVSIDDTACTATS 417
                                               **************************.6***************************************** PP

                                 TIGR01356 402 fPeFfevleql 412
                                               fP+F+ +le++
  lcl|NCBI__GCF_900111775.1:WP_092053417.1 418 FPNFWSLLEKV 428
                                               ********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (430 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.35
//
[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