Alignments for a candidate for aroA in Desulfobacter vibrioformis DSM 8776

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Desulfobacter vibrioformis DSM 8776

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_035240987.1 Q366_RS16540 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q9KRB0
         (426 letters)



>NCBI__GCF_000745975.1:WP_035240987.1
          Length = 420

 Score =  269 bits (687), Expect = 1e-76
 Identities = 161/412 (39%), Positives = 231/412 (56%), Gaps = 8/412 (1%)

Query: 16  VNLPGSKSVSNRALLLAALASGTTRLTNLLDSDDIRHMLNALTKLGVNYRLSADKTTCEV 75
           V +PGSKS+S+R L+ +ALA G + + N+LDS DI     AL  +G       +      
Sbjct: 14  VRIPGSKSISHRMLICSALAHGISEIYNVLDSQDISLTRKALECMGAQIESKTNSALVVT 73

Query: 76  EGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPRMKERPIGHLVDALRQ 135
              G+     +P+ L  GN+GT+MR LA    LG   Y LTG+ RM++RP+G L+DAL +
Sbjct: 74  GFGGRPRPWAEPIHL--GNSGTSMRLLAGIAALGTTPYTLTGDERMRQRPMGELLDALGR 131

Query: 136 AGAQIEYLEQENFPPLRIQGTGLQAGTVTIDGSISSQFLTAFLMSAPLAQGKVTIKIVGE 195
                     E  PP+ IQG     G   +D S SSQ+L+A LM+       + I + G 
Sbjct: 132 IRIHAGSQNNEGTPPVVIQGGDRAGGRTLLDCSRSSQYLSALLMAGAFFDQGLVIDLTGP 191

Query: 196 LVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPGQFLVEGDASSASYFLAAAA 255
            VS+PYID+TL +M+QFGV         + +P GQ+Y   G+  VE D S+A YF AA A
Sbjct: 192 AVSQPYIDLTLDVMKQFGVNAFRISDTCYEVPGGQTYTC-GKKSVEPDLSNAGYFWAAGA 250

Query: 256 IKGGEVKVTGIGKNSIQGDIQFADALEKMGAQIEWGDDYVIARR---GELNAVDLDFNHI 312
           + G ++ V  IG  S+QGD++ A   EKMG  +   D  V+  +   G L+ VD+D +  
Sbjct: 251 VTGADIGVDNIGTASLQGDLKQAYIFEKMGCTVN-RDGLVLRVKGGPGPLHGVDVDMSDT 309

Query: 313 PDAAMTIATTALFAKGTTAIRNVYNWRVKETDRLAAMATELRKVGATVEEGEDFIVITPP 372
           PDA   +A TA FA GTT I N+ + RVKE DR+ A+ ++L K+G    +G DF+ IT  
Sbjct: 310 PDAVPAVAVTAAFATGTTRITNIGHLRVKECDRIDAVCSQLTKMGIKAVQGPDFMEITGG 369

Query: 373 TKLIHAAIDTYDDHRMAMCFSLVALSDTPVTINDPKCTSKTFPDYFDKFAQL 424
           T    A I+T++DHR+AM F++  L    + I +P C  K+FP ++  F  L
Sbjct: 370 TP-HGAVIETFNDHRIAMAFAVAGLRVDGIKIENPVCVEKSFPTFWQLFNAL 420



 Score = 28.5 bits (62), Expect = 4e-04
 Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 5/53 (9%)

Query: 15  EVNLPGSKSVSNRALLLAALASGTTRLTNL-----LDSDDIRHMLNALTKLGV 62
           +V++  +        + AA A+GTTR+TN+      + D I  + + LTK+G+
Sbjct: 303 DVDMSDTPDAVPAVAVTAAFATGTTRITNIGHLRVKECDRIDAVCSQLTKMGI 355


Lambda     K      H
   0.318    0.135    0.384 

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: 423
Number of extensions: 25
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 426
Length of database: 420
Length adjustment: 32
Effective length of query: 394
Effective length of database: 388
Effective search space:   152872
Effective search space used:   152872
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: 50 (23.9 bits)

Align candidate WP_035240987.1 Q366_RS16540 (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.19169.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.6e-136  438.8   0.0   1.1e-135  438.6   0.0    1.0  1  lcl|NCBI__GCF_000745975.1:WP_035240987.1  Q366_RS16540 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745975.1:WP_035240987.1  Q366_RS16540 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.6   0.0  1.1e-135  1.1e-135       3     411 ..      14     419 ..      12     420 .] 0.96

  Alignments for each domain:
  == domain 1  score: 438.6 bits;  conditional E-value: 1.1e-135
                                 TIGR01356   3 ikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgglkepe 70 
                                               ++ipgsKSishR+l+ +aLa+g ++++n+L+s+D+  t +al+ +Ga++e++ +  lv++g+gg  +p 
  lcl|NCBI__GCF_000745975.1:WP_035240987.1  14 VRIPGSKSISHRMLICSALAHGISEIYNVLDSQDISLTRKALECMGAQIESKtNSALVVTGFGGRPRPW 82 
                                               89************************************************555999*******955554 PP

                                 TIGR01356  71 .aeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisg 138
                                                + ++lgnsGt++Rll g++al  ++++ltgde++++RP+++l++aL ++ ++  s+++eg++P++i+g
  lcl|NCBI__GCF_000745975.1:WP_035240987.1  83 aEPIHLGNSGTSMRLLAGIAALGTTPYTLTGDERMRQRPMGELLDALGRIRIHAGSQNNEGTPPVVIQG 151
                                               69*******************999********************************************* PP

                                 TIGR01356 139 p.lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederk 206
                                               +   gg + l++s SsQy+sall+a++  +q+  + ++g + +s+pyi++tL+++k+fgv++ +  ++ 
  lcl|NCBI__GCF_000745975.1:WP_035240987.1 152 GdRAGGRTLLDCSRSSQYLSALLMAGAFFDQGLVIDLTG-PAVSQPYIDLTLDVMKQFGVNAFRISDTC 219
                                               *6666**********************999999888888.*********************9988888* PP

                                 TIGR01356 207 ivvkggqkykqkevevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadveveeq 275
                                               + v+ggq+y++ + +ve D+S+A +f aa+a+tg ++ v n+g++s+qgd + ++++e+mG++v+++  
  lcl|NCBI__GCF_000745975.1:WP_035240987.1 220 YEVPGGQTYTCGKKSVEPDLSNAGYFWAAGAVTGADIGVDNIGTASLQGDLKQAYIFEKMGCTVNRDGL 288
                                               ********************************************************************* PP

                                 TIGR01356 276 rdveveg.asklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklG 343
                                                 ++v+g +  l+gv+  +d+++++D++p++av aafA g+tri+ni +lRvkE+dRi a++++L+k+G
  lcl|NCBI__GCF_000745975.1:WP_035240987.1 289 -VLRVKGgPGPLHGVD--VDMSDTPDAVPAVAVTAAFATGTTRITNIGHLRVKECDRIDAVCSQLTKMG 354
                                               .7****9888999999..*************************************************** PP

                                 TIGR01356 344 veveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleq 411
                                               +++ +++d+++i+G+  + +gav++t++DHRiama+av+gl+++ +++ie++ cv+ksfP F+++ ++
  lcl|NCBI__GCF_000745975.1:WP_035240987.1 355 IKAVQGPDFMEITGG--TPHGAVIETFNDHRIAMAFAVAGLRVD-GIKIENPVCVEKSFPTFWQLFNA 419
                                               ***************..6*************************9.*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (420 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: 00:00:00.01
# Mc/sec: 9.19
//
[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