Alignments for a candidate for aroA in Sulfuricurvum kujiense DSM 16994

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Sulfuricurvum kujiense DSM 16994

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_013459745.1 SULKU_RS04475 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::F5A7Q0
         (429 letters)



>NCBI__GCF_000183725.1:WP_013459745.1
          Length = 425

 Score =  323 bits (828), Expect = 6e-93
 Identities = 184/414 (44%), Positives = 250/414 (60%), Gaps = 13/414 (3%)

Query: 19  IPGDKSISHRAVMFGSIAEGKTTIKGFLSGADCLSTISCFKEMGVEITQNGDEVTVVGKG 78
           I  DKSISHR  MF  +AEG++ ++ FL   D L+T+     +G +I  +G+ +T+   G
Sbjct: 19  IAPDKSISHRCAMFAVLAEGESRVENFLRAEDTLNTLKIVGHLGAQIHDDGEVITIRSNG 78

Query: 79  LEGLQEPKAVLDVGNSGTTIRLMSGILANTPFFSCVQGDESIAKRPMKRVTNPLKQMGAN 138
           +   QE   +LD GNSGT +RL  G+L++      + GDE + +RPMKRVT PL+ +GA 
Sbjct: 79  I---QETSEILDCGNSGTGMRLFCGLLSSAEGHFVLTGDEYLKRRPMKRVTQPLRSIGAK 135

Query: 139 IDGREEGTFTPLTIRGGDLKAIEYISPVASAQVKSAILLAGLRAEGVTAVTEPHISRDHT 198
           +DGR  G   PL+IRG  LKA +Y+SP+ASAQVKSA++LA LR++GV    EP +SRDHT
Sbjct: 136 LDGRNNGDLAPLSIRGASLKAFDYVSPIASAQVKSAMMLAALRSDGVCTFREPELSRDHT 195

Query: 199 ERMLEAFGVKVTREGKTVKLSGGQ-KLTATNIQVPGDVSSAAFFLVAGAIIPNSKLVLQN 257
           ERML   G +V   G   K+   +  L   NI+VP D SSA FF VA AI PNS  +++ 
Sbjct: 196 ERMLRGMGARVEINGLETKIWPLEAPLKPLNIRVPADPSSAFFFAVAAAITPNSSTLIEG 255

Query: 258 VGMNPTRTGIIDVLEKMGATFTVDLINEGASEPAANITIETSSLKGIEIGGDIIPRLIDE 317
           V +NPTR     VLE+MGA  T  L N+   EP   I +E + L  + +  + I  LIDE
Sbjct: 256 VTLNPTRIEAFKVLERMGAKITYTL-NDERYEPIGTIRVEHAPLHAVTV-EENIAWLIDE 313

Query: 318 IPVIALAATQAEGITVIKDAHELKVKETNRIDTVVAELTKLGARIEATDDGMIIYGKSAL 377
           +P +++A   AEG ++IK+A EL+VKE++RI TVV  L   G   E   DG  + G   L
Sbjct: 314 LPALSIAMACAEGKSIIKNAEELRVKESDRIKTVVDNLNLCGIETEEYPDGYAVIG-GEL 372

Query: 378 KGNTVNSYGDHRIGMMLAIAG--CLAEGKTIIEDAEAVGVSYPTFFDELQKLAK 429
           K   VNS+GDHRI M   I G  C  E    +ED E +  S+P FF+ L+   K
Sbjct: 373 KSARVNSFGDHRIAMSFLIGGLKCGME----VEDIECINTSFPNFFELLEMCTK 422


Lambda     K      H
   0.315    0.134    0.369 

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: 449
Number of extensions: 25
Number of successful extensions: 6
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: 429
Length of database: 425
Length adjustment: 32
Effective length of query: 397
Effective length of database: 393
Effective search space:   156021
Effective search space used:   156021
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: 42 (22.0 bits)
S2: 51 (24.3 bits)

Align candidate WP_013459745.1 SULKU_RS04475 (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.14964.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.3e-128  413.0   0.0   7.7e-128  412.7   0.0    1.0  1  lcl|NCBI__GCF_000183725.1:WP_013459745.1  SULKU_RS04475 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183725.1:WP_013459745.1  SULKU_RS04475 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.7   0.0  7.7e-128  7.7e-128       5     412 ..      19     420 ..      17     423 .. 0.95

  Alignments for each domain:
  == domain 1  score: 412.7 bits;  conditional E-value: 7.7e-128
                                 TIGR01356   5 ipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgglkepeael 73 
                                               i+++KSishR  ++a Laege++v+n+L++eDtl+tl+++ +lGa++++++e+++i+ +g ++e +++l
  lcl|NCBI__GCF_000183725.1:WP_013459745.1  19 IAPDKSISHRCAMFAVLAEGESRVENFLRAEDTLNTLKIVGHLGAQIHDDGEVITIRSNG-IQETSEIL 86 
                                               78********************************************************98.7******* PP

                                 TIGR01356  74 dlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgplkg 142
                                               d+gnsGt +Rl  g+l+ a+g++vltgde lk+RP++r++++Lr++ga+ + +++ + +Pl+i+g +  
  lcl|NCBI__GCF_000183725.1:WP_013459745.1  87 DCGNSGTGMRLFCGLLSSAEGHFVLTGDEYLKRRPMKRVTQPLRSIGAKLDGRNNGDLAPLSIRGASLK 155
                                               *****************************************************************7666 PP

                                 TIGR01356 143 givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkg 211
                                               +  ++s+ aS+Q+ksa++laa   l+ +++ +  e+++sr+++e++L  +++    ve +  ++ + + 
  lcl|NCBI__GCF_000183725.1:WP_013459745.1 156 AFDYVSPIASAQVKSAMMLAA---LRSDGVCTFREPELSRDHTERMLRGMGAR---VEINGLETKIWPL 218
                                               *********************...78899999999***************988...6666555566666 PP

                                 TIGR01356 212 gqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr... 276
                                               ++  k+ +++v++D+SsA+ff++aaait++  + +e+++ n+t+ +  ++ vLe+mGa+++++ ++   
  lcl|NCBI__GCF_000183725.1:WP_013459745.1 219 EAPLKPLNIRVPADPSSAFFFAVAAAITPNsSTLIEGVTLNPTRIE--AFKVLERMGAKITYTLNDery 285
                                               66688889**********************99**************..677***********998889* PP

                                 TIGR01356 277 ....dvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLek 341
                                                   +++ve+   l++v+v+++++ liDelp+l++++a+Aeg++ ikn+eelRvkEsdRi+ ++++L+ 
  lcl|NCBI__GCF_000183725.1:WP_013459745.1 286 epigTIRVEH-APLHAVTVEENIAWLIDELPALSIAMACAEGKSIIKNAEELRVKESDRIKTVVDNLNL 353
                                               *********5.68******************************************************** PP

                                 TIGR01356 342 lGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevle 410
                                                G+e+ee +dg  + G+  elk+a+v++++DHRiam++ + gl++   +e+ed ec+++sfP+Ffe+le
  lcl|NCBI__GCF_000183725.1:WP_013459745.1 354 CGIETEEYPDGYAVIGG--ELKSARVNSFGDHRIAMSFLIGGLKCG--MEVEDIECINTSFPNFFELLE 418
                                               *****************..7*************************6..*******************99 PP

                                 TIGR01356 411 ql 412
                                                 
  lcl|NCBI__GCF_000183725.1:WP_013459745.1 419 MC 420
                                               76 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (425 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: 10.79
//
[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