Alignments for a candidate for aroA in Desulfovibrio bastinii DSM 16055

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Desulfovibrio bastinii DSM 16055

Align 3-phosphoshikimate 1-carboxyvinyltransferase; EC 2.5.1.19 (characterized, see rationale)
to candidate WP_027177589.1 G496_RS0100780 3-phosphoshikimate 1-carboxyvinyltransferase

Query= uniprot:Q72EV5_DESVH
         (439 letters)



>NCBI__GCF_000429985.1:WP_027177589.1
          Length = 445

 Score =  440 bits (1132), Expect = e-128
 Identities = 224/435 (51%), Positives = 282/435 (64%), Gaps = 4/435 (0%)

Query: 4   VVVTAPPSKSLSHRALIGAALAAGESTVEHVLESRDLTCTADILRAAGAHIERRAPGSYL 63
           + +  P SKSLSHRALI  A++   + V   LES D+  T D L   GA IE     +  
Sbjct: 7   IQIKVPSSKSLSHRALIAGAMSQDTTVVLEPLESNDINRTMDCLTTMGAEIEINGSAT-T 65

Query: 64  VRGVAGTPAGGFEAPVSCDVHESGTTCRLLTAVLAAGMGRFRIHGAPRMHERPIGELTDA 123
           V+G A  P GG   P   ++ +SGTTCRL+TAV AAG G FR+ G PRMH+RPI  LT A
Sbjct: 66  VKGFASGPKGGLSEPAILEMRDSGTTCRLITAVAAAGKGLFRVQGTPRMHQRPISALTAA 125

Query: 124 LASLGVQIAFEARAGFPPLVIDAAGMRGGEVSIGMDESSQYLSGLLLAAPLT-QGMTVNV 182
           + S G+ + F  R G+PP+ I+  G  GG V I +++SSQYLSGLLLAAPL  + M +NV
Sbjct: 126 IRSQGINVTFAGRQGYPPMTIETRGFSGGIVDISLEDSSQYLSGLLLAAPLAREEMVINV 185

Query: 183 AGKSVVSWPYVGLTLQTLEDFGIDFTVETRDAVDAPWGAVDWRSLHEAVPGLVRFRVRPG 242
            G+  VSWPYV LTL+ +E F + F+VE     D  W   DW+ +   VPG +RFRV+P 
Sbjct: 186 IGRKAVSWPYVALTLEVMEGFRVPFSVEILK--DGKWEKADWKKITRVVPGEIRFRVQPS 243

Query: 243 MYRAGSYRVEGDWSGASYFLAAGAVGPRPVRVEGLRVDSLQGDRALLDILTAMGADIRPG 302
            Y    ++VE DWS ASYF AAGAVG +PV ++G+ VDS+QGDRA+LDIL  MGA I   
Sbjct: 244 KYNCEEFKVEADWSSASYFAAAGAVGRKPVMIKGVSVDSMQGDRAILDILKKMGAYIEYD 303

Query: 303 EGHVVVHPAPLHGVEVDMGHCPDLVPTVAAVAAFATGRTVVRNVAHLRIKESDRIAAPVG 362
              + VHP+ LHGVEVDMG CPDLVPTV A AAFA G TV++NVAHLRIKE DR+ A   
Sbjct: 304 NHGITVHPSKLHGVEVDMGLCPDLVPTVCATAAFAEGPTVIKNVAHLRIKECDRLEASAN 363

Query: 363 ELRRAGVNAEERADGLVVQGGALATEPGTLFSAHGDHRMAMSLALLGLGGVDVRLDDPSC 422
           E+ RAG  AE   D + V  G        +FS + DHR+AMS A+ GL G+    +DP C
Sbjct: 364 EVIRAGGKAEVYKDSIKVMPGKFRKGEKIVFSTYDDHRLAMSTAIYGLAGIKAVAEDPGC 423

Query: 423 VSKSFPHFWELWEKV 437
           V+KSFP FW+ W+KV
Sbjct: 424 VAKSFPGFWDEWKKV 438


Lambda     K      H
   0.320    0.137    0.413 

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: 533
Number of extensions: 22
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: 439
Length of database: 445
Length adjustment: 32
Effective length of query: 407
Effective length of database: 413
Effective search space:   168091
Effective search space used:   168091
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_027177589.1 G496_RS0100780 (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.26250.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-116  374.3   0.1   5.3e-115  370.5   0.1    1.9  1  lcl|NCBI__GCF_000429985.1:WP_027177589.1  G496_RS0100780 3-phosphoshikimat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429985.1:WP_027177589.1  G496_RS0100780 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.5   0.1  5.3e-115  5.3e-115       2     413 ..       8     439 ..       7     441 .. 0.91

  Alignments for each domain:
  == domain 1  score: 370.5 bits;  conditional E-value: 5.3e-115
                                 TIGR01356   2 eikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgglkepe 70 
                                               +ik+p+sKS+shRal+++a+++ +tvv ++L+s+D++ t+++l  +Ga++e ++  ++++g++    p+
  lcl|NCBI__GCF_000429985.1:WP_027177589.1   8 QIKVPSSKSLSHRALIAGAMSQDTTVVLEPLESNDINRTMDCLTTMGAEIEINGSATTVKGFAS--GPK 74 
                                               69*************************************************8899******874..444 PP

                                 TIGR01356  71 ......aeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslP 133
                                                     a+l++++sGtt Rl+t+v+a+ +g + ++g +++++RPi  l+ a r+ g+++  + ++g++P
  lcl|NCBI__GCF_000429985.1:WP_027177589.1  75 gglsepAILEMRDSGTTCRLITAVAAAGKGLFRVQGTPRMHQRPISALTAAIRSQGINVTFAGRQGYPP 143
                                               4567778************************************************************** PP

                                 TIGR01356 134 laisgp.lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgvevee 201
                                               ++i+    +ggiv +s + SsQy+s+lllaapla ++  ++++g k +s py+ +tL++++ f v +++
  lcl|NCBI__GCF_000429985.1:WP_027177589.1 144 MTIETRgFSGGIVDISLEDSSQYLSGLLLAAPLAREEMVINVIGRKAVSWPYVALTLEVMEGFRVPFSV 212
                                               *****98899***************************************************99876554 PP

                                 TIGR01356 202 e....de..............r..kivvkggqkykqkevevegDaSsAafflaaaaitgeevtvenlge 250
                                               e     +                 +++v++  ky+++e++ve+D SsA++f+aa+a+  + v ++++  
  lcl|NCBI__GCF_000429985.1:WP_027177589.1 213 EilkdGKwekadwkkitrvvpGeiRFRVQP-SKYNCEEFKVEADWSSASYFAAAGAVGRKPVMIKGVSV 280
                                               322212244344533222222111233443.3599********************************** PP

                                 TIGR01356 251 nstqgdkaiiivLeemGadveveeqrdvevegasklkgvkvdidvdsliDelptlavlaafAegetrik 319
                                               +s qgd+ai+++L++mGa +e++++  ++v+ +skl+gv+  +d+  ++D++pt+ + aafAeg+t+ik
  lcl|NCBI__GCF_000429985.1:WP_027177589.1 281 DSMQGDRAILDILKKMGAYIEYDNH-GITVH-PSKLHGVE--VDMGLCPDLVPTVCATAAFAEGPTVIK 345
                                               *************************.7***9.899*****..*************************** PP

                                 TIGR01356 320 nieelRvkEsdRiaaiaeeLeklGveveeledgllieGkk.kelkgavvdtydDHRiamalavlglaae 387
                                               n+++lR+kE+dR++a a+e  + G ++e+ +d++++ ++k ++ ++ v +tydDHR+am++a+ gla  
  lcl|NCBI__GCF_000429985.1:WP_027177589.1 346 NVAHLRIKECDRLEASANEVIRAGGKAEVYKDSIKVMPGKfRKGEKIVFSTYDDHRLAMSTAIYGLAGI 414
                                               ***************************************9989999*********************98 PP

                                 TIGR01356 388 geveiedaecvaksfPeFfevleqlg 413
                                                +   ed++cvaksfP F++ ++++ 
  lcl|NCBI__GCF_000429985.1:WP_027177589.1 415 -KAVAEDPGCVAKSFPGFWDEWKKVL 439
                                               .8889*****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (445 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: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 2.82
//
[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