Alignments for a candidate for aroA in Sulfurimonas denitrificans DSM 1251

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Sulfurimonas denitrificans DSM 1251

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_011372501.1 SUDEN_RS04580 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::F5A7Q0
         (429 letters)



>NCBI__GCF_000012965.1:WP_011372501.1
          Length = 428

 Score =  319 bits (818), Expect = 9e-92
 Identities = 176/412 (42%), Positives = 253/412 (61%), Gaps = 9/412 (2%)

Query: 19  IPGDKSISHRAVMFGSIAEGKTTIKGFLSGADCLSTISCFKEMGVEITQNGDEVTVVGKG 78
           I  DKSISHR  MF  +A+G + I  FL   D ++++   K +G  I  +G+ + +    
Sbjct: 19  IASDKSISHRCAMFAMLADGTSQITNFLRAEDTMNSLKIVKNLGATIDDDGETIKISS-- 76

Query: 79  LEGLQEPKAVLDVGNSGTTIRLMSGILANTPFFSCVQGDESIAKRPMKRVTNPLKQMGAN 138
            +G++E   VLD GNSGT +RL  G+L++      + GDE + +RPMKR+T PL+ +GA 
Sbjct: 77  -DGIKESSEVLDCGNSGTGMRLFCGLLSSADGHFVLSGDEYLRRRPMKRITAPLRDIGAK 135

Query: 139 IDGREEGTFTPLTIRGGDLKAIEYISPVASAQVKSAILLAGLRAEGVTAVTEPHISRDHT 198
           +DGRE G   PL+IRG  LKA  Y S +ASAQVKSA++LA LRA+G  + +EP +SRDHT
Sbjct: 136 LDGRENGDLAPLSIRGASLKAFNYESKIASAQVKSAMILAALRADGECSFSEPELSRDHT 195

Query: 199 ERMLEAFGVKVTREGKTVKLSGGQK-LTATNIQVPGDVSSAAFFLVAGAIIPNSKLVLQN 257
           ERML+  G ++  EG   K+   +K L+   I+VP D SSA FF VA AI PNS +VL+ 
Sbjct: 196 ERMLKGMGAEIEVEGLITKIKPMKKLLSPLKIRVPADPSSAFFFAVAAAITPNSNVVLEG 255

Query: 258 VGMNPTRTGIIDVLEKMGATFTVDLINEGASEPAANITIETSSLKGIEIGGDIIPRLIDE 317
           V +NPTR      LE+MGA    +   E   EP  NI ++ + LK I +  D I  LIDE
Sbjct: 256 VTLNPTRIEAFKALERMGADIRYE-ATENIYEPIGNIHVKYAPLKAITV-EDNISWLIDE 313

Query: 318 IPVIALAATQAEGITVIKDAHELKVKETNRIDTVVAELTKLGARIEATDDGMIIYGKSAL 377
           +P +++A   A+G++++K+A EL+VKE++RI TVV  L   G  ++   DG  + G   L
Sbjct: 314 LPALSIAFACADGVSIVKNAQELRVKESDRISTVVNGLKACGIEVDEVHDGYSVKG-GVL 372

Query: 378 KGNTVNSYGDHRIGMMLAIAGCLAEGKTIIEDAEAVGVSYPTFFDELQKLAK 429
           K   ++S+GDHRI M   IAG     +  ++D   +  S+P FF+ L+K+ K
Sbjct: 373 KEAKIDSHGDHRIAMSFIIAGVTCGMR--VDDIACINTSFPNFFELLKKITK 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: 486
Number of extensions: 24
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: 428
Length adjustment: 32
Effective length of query: 397
Effective length of database: 396
Effective search space:   157212
Effective search space used:   157212
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_011372501.1 SUDEN_RS04580 (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.5403.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-126  406.6   0.1   6.5e-126  406.4   0.1    1.0  1  lcl|NCBI__GCF_000012965.1:WP_011372501.1  SUDEN_RS04580 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012965.1:WP_011372501.1  SUDEN_RS04580 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.4   0.1  6.5e-126  6.5e-126       4     414 ..      18     422 ..      16     423 .. 0.96

  Alignments for each domain:
  == domain 1  score: 406.4 bits;  conditional E-value: 6.5e-126
                                 TIGR01356   4 kipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgglkepeae 72 
                                               +i+++KSishR  ++a La+g++++tn+L++eDt ++l+++++lGa++ +++e+++i   g +ke++++
  lcl|NCBI__GCF_000012965.1:WP_011372501.1  18 EIASDKSISHRCAMFAMLADGTSQITNFLRAEDTMNSLKIVKNLGATIDDDGETIKISSDG-IKESSEV 85 
                                               5789**********************************************9********87.8****** PP

                                 TIGR01356  73 ldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgplk 141
                                               ld+gnsGt +Rl  g+l+ a+g++vl+gde l++RP++r++ +Lr +ga+ + +e+ + +Pl+i+g + 
  lcl|NCBI__GCF_000012965.1:WP_011372501.1  86 LDCGNSGTGMRLFCGLLSSADGHFVLSGDEYLRRRPMKRITAPLRDIGAKLDGRENGDLAPLSIRGASL 154
                                               ******************************************************************766 PP

                                 TIGR01356 142 ggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvk 210
                                                +  + s+ aS+Q+ksa++laa   l+a+++    e+++sr+++e++Lk ++++   +e+e     ++k
  lcl|NCBI__GCF_000012965.1:WP_011372501.1 155 KAFNYESKIASAQVKSAMILAA---LRADGECSFSEPELSRDHTERMLKGMGAE---IEVEGL-ITKIK 216
                                               6*********************...77778888888****************88...777766.88999 PP

                                 TIGR01356 211 ggqkykqk.evevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr. 276
                                               + +k  ++ +++v++D+SsA+ff++aaait++ +v++e+++ n+t+ +  ++  Le+mGad+++e+++ 
  lcl|NCBI__GCF_000012965.1:WP_011372501.1 217 PMKKLLSPlKIRVPADPSSAFFFAVAAAITPNsNVVLEGVTLNPTRIE--AFKALERMGADIRYEATEn 283
                                               999955555***************************************..677**************** PP

                                 TIGR01356 277 ......dvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeL 339
                                                     ++ v+    lk+++v+ +++ liDelp+l+++ a+A+g++ +kn++elRvkEsdRi+ +++ L
  lcl|NCBI__GCF_000012965.1:WP_011372501.1 284 iyepigNIHVK-YAPLKAITVEDNISWLIDELPALSIAFACADGVSIVKNAQELRVKESDRISTVVNGL 351
                                               ***********.568****************************************************** PP

                                 TIGR01356 340 eklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfev 408
                                               ++ G+ev+e +dg +++G+   lk+a++d+++DHRiam++ ++g+ +   ++++d +c+++sfP+Ffe+
  lcl|NCBI__GCF_000012965.1:WP_011372501.1 352 KACGIEVDEVHDGYSVKGG--VLKEAKIDSHGDHRIAMSFIIAGVTCG--MRVDDIACINTSFPNFFEL 416
                                               *******************..6*************************6..******************* PP

                                 TIGR01356 409 leqlga 414
                                               l+++++
  lcl|NCBI__GCF_000012965.1:WP_011372501.1 417 LKKITK 422
                                               **9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (428 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.27
//
[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