Alignments for a candidate for aroA in Desulfacinum hydrothermale DSM 13146

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Desulfacinum hydrothermale DSM 13146

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_084057310.1 B9A12_RS07660 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::B2IYE4
         (426 letters)



>NCBI__GCF_900176285.1:WP_084057310.1
          Length = 439

 Score =  311 bits (798), Expect = 2e-89
 Identities = 171/423 (40%), Positives = 255/423 (60%), Gaps = 3/423 (0%)

Query: 2   DTIEIPALNRPVDATVEIPGSKSLTNRALLVAALAQGDSILENALFSEDSEYFAKCLEQL 61
           + + IP + R V   V +PGSKS+T+RA ++AAL+ G+S++ NAL +ED+   A  L  L
Sbjct: 16  EEVAIPTVER-VTGRVPLPGSKSVTHRAFILAALSGGESVVLNALDAEDTRVTASALRDL 74

Query: 62  GIPITLNPHLAQIQLAGRGGEIPAKQADLFVGLSGTTARFISALVALGNGEYRLDGVPRM 121
           G  +       +I+        P+   +  VG SGT+ R ++ L A G G +  DG  R+
Sbjct: 75  GARVEWRGSTVRIRPPHELWRSPSSPIN--VGNSGTSLRLLAGLAAAGKGTFVFDGTARL 132

Query: 122 RERPMGDMLTVLETGGATVNFEGNSGFMPYTVYSQGFAGGNFCLKANQTSQQLSALLMIA 181
           RERP+G +   LET GA V F    G+ P  + S G  GG  C+ A+Q+SQ LS++L+ +
Sbjct: 133 RERPVGALTVALETLGAVVRFPLKRGYPPVVIESDGLCGGRVCVDASQSSQYLSSILLAS 192

Query: 182 PYAQQDTIFEVEGTLVSLSYIKMTCRLMADFGVEVIQIGDNQFQIKAGQRYQAQHYTVEP 241
             A        E  + S  Y+++T ++MA  G++  + G  +  + A Q  +  HY VE 
Sbjct: 193 TKASGPVAVSWEENVSSFPYVEITLQMMAQAGLDFRKAGPTEVVVNAPQVVKPFHYRVEG 252

Query: 242 DASNASYFFAAAAVTGGRVRVKHLTKQSCQGDILWLNVLEQMGCQIKDSDDYTEVTGPKQ 301
           D S+ASYF+AAAA+TGG V    +++ + QGD  +L++L  MGC++  +++   V GP+ 
Sbjct: 253 DCSSASYFWAAAALTGGSVLTYPVSQAALQGDCAFLDILSAMGCRVDWTEEGVCVQGPRT 312

Query: 302 LQGIDIDMNDISDLVQTLAAIAPFASSPITIRNVEHIRYKETDRIKAVVTELRRLGVQVE 361
           L+ +D DMN + D+V TLA +A  A     IRNV H+R KE+DR++AV  EL +LGVQVE
Sbjct: 313 LRSVDADMNRMPDMVPTLAVLAACAEGASRIRNVAHLRIKESDRLRAVAVELSKLGVQVE 372

Query: 362 EFPDRLKIEPGPITPAEIETYHDHRMAMAFAVTGLKVPGIVIKDPGCTAKTFPDYFTRFF 421
           E  D L I+  P   A IETY DHR+AMAFAV GL+VPG+VI+      K+FP+++  FF
Sbjct: 373 EGSDGLVIQGPPRRGATIETYEDHRIAMAFAVLGLRVPGVVIRGAATVRKSFPEFWDTFF 432

Query: 422 QML 424
            ++
Sbjct: 433 GLI 435


Lambda     K      H
   0.320    0.136    0.393 

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: 413
Number of extensions: 11
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: 426
Length of database: 439
Length adjustment: 32
Effective length of query: 394
Effective length of database: 407
Effective search space:   160358
Effective search space used:   160358
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_084057310.1 B9A12_RS07660 (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.6427.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-132  427.2   0.0   3.7e-132  427.0   0.0    1.0  1  lcl|NCBI__GCF_900176285.1:WP_084057310.1  B9A12_RS07660 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176285.1:WP_084057310.1  B9A12_RS07660 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.0   0.0  3.7e-132  3.7e-132       1     411 [.      28     433 ..      28     437 .. 0.97

  Alignments for each domain:
  == domain 1  score: 427.0 bits;  conditional E-value: 3.7e-132
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg.lke 68 
                                               g++ +pgsKS++hRa++laaL+ ge+vv n L++eDt++t +alr+lGa+ve  + ++ i++ +   + 
  lcl|NCBI__GCF_900176285.1:WP_084057310.1  28 GRVPLPGSKSVTHRAFILAALSGGESVVLNALDAEDTRVTASALRDLGARVEWRGSTVRIRPPHElWRS 96 
                                               68899***********************************************8899******9987899 PP

                                 TIGR01356  69 peaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlais 137
                                               p++ +++gnsGt++Rll g++a+ +g++v++g  +l++RP++ l+ aL+ lga ++   ++g++P++i+
  lcl|NCBI__GCF_900176285.1:WP_084057310.1  97 PSSPINVGNSGTSLRLLAGLAAAGKGTFVFDGTARLRERPVGALTVALETLGAVVRFPLKRGYPPVVIE 165
                                               99******************************************************************* PP

                                 TIGR01356 138 gp.lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeeder 205
                                               ++ l gg v +++s SsQy+s++lla  +a+ +v ++ ++ +++s py+eitL++++++g ++++   +
  lcl|NCBI__GCF_900176285.1:WP_084057310.1 166 SDgLCGGRVCVDASQSSQYLSSILLASTKASGPVAVSWEE-NVSSFPYVEITLQMMAQAGLDFRKAGPT 233
                                               *98888*********************9999899888887.************************999* PP

                                 TIGR01356 206 kivvkggqkykqkevevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadvevee 274
                                               ++vv+  q  k+ +++vegD SsA++f aaaa+tg+ v    + ++ +qgd a++++L++mG++v+++e
  lcl|NCBI__GCF_900176285.1:WP_084057310.1 234 EVVVNAPQVVKPFHYRVEGDCSSASYFWAAAALTGGSVLTYPVSQAALQGDCAFLDILSAMGCRVDWTE 302
                                               *******999999******************************************************** PP

                                 TIGR01356 275 qrdvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklG 343
                                               +  v v+g++ l+ v+  +d+++++D +ptlavlaa+Aeg +ri+n+++lR+kEsdR++a+a eL+klG
  lcl|NCBI__GCF_900176285.1:WP_084057310.1 303 E-GVCVQGPRTLRSVD--ADMNRMPDMVPTLAVLAACAEGASRIRNVAHLRIKESDRLRAVAVELSKLG 368
                                               *.7**********999..*************************************************** PP

                                 TIGR01356 344 veveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleq 411
                                               v+vee++dgl+i+G     +ga+++ty+DHRiama+avlgl++  +v i +a++v+ksfPeF++    
  lcl|NCBI__GCF_900176285.1:WP_084057310.1 369 VQVEEGSDGLVIQGPP--RRGATIETYEDHRIAMAFAVLGLRVP-GVVIRGAATVRKSFPEFWDTFFG 433
                                               ***************5..899**********************9.******************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (439 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: 8.19
//
[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