Alignments for a candidate for aroA in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Kyrpidia tusciae DSM 2912

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_013075704.1 BTUS_RS08515 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::F5A7Q0
         (429 letters)



>NCBI__GCF_000092905.1:WP_013075704.1
          Length = 433

 Score =  444 bits (1142), Expect = e-129
 Identities = 226/424 (53%), Positives = 297/424 (70%)

Query: 4   RTIQPVNNGLNGNITIPGDKSISHRAVMFGSIAEGKTTIKGFLSGADCLSTISCFKEMGV 63
           + I  +   L G + +PGDKSISHRAVMF S+A+G + ++GFL GADCLST++C + +GV
Sbjct: 2   KLIVEMAGALKGQVRVPGDKSISHRAVMFTSLADGVSRVEGFLFGADCLSTVACMRALGV 61

Query: 64  EITQNGDEVTVVGKGLEGLQEPKAVLDVGNSGTTIRLMSGILANTPFFSCVQGDESIAKR 123
            +      V V G G+ GLQEP  VLDVGNSGTTIRL+ G+L+   F SC+ GD SI +R
Sbjct: 62  PVDIEDGTVIVHGVGMHGLQEPDDVLDVGNSGTTIRLLLGLLSGQTFHSCLTGDASIRRR 121

Query: 124 PMKRVTNPLKQMGANIDGREEGTFTPLTIRGGDLKAIEYISPVASAQVKSAILLAGLRAE 183
           PM RV  PL  MGA IDGR +G   PL++RG DL +I+Y  PVASAQVKSAILLAGL A 
Sbjct: 122 PMGRVAKPLLSMGARIDGRRDGDLAPLSVRGADLHSIKYQMPVASAQVKSAILLAGLFAS 181

Query: 184 GVTAVTEPHISRDHTERMLEAFGVKVTREGKTVKLSGGQKLTATNIQVPGDVSSAAFFLV 243
           GVT V EP  SRDHTERML+A G  +++     ++    +L A ++++PGD+SSAAF LV
Sbjct: 182 GVTGVREPSPSRDHTERMLKALGAPISKRSGYTEIGRPARLRAMDMRIPGDLSSAAFLLV 241

Query: 244 AGAIIPNSKLVLQNVGMNPTRTGIIDVLEKMGATFTVDLINEGASEPAANITIETSSLKG 303
           A  I+P S+L+L++VG+NPTRTGI+DVL  MGA F ++     A EP A +   +  L G
Sbjct: 242 ATLIVPGSELILEDVGVNPTRTGILDVLGAMGAQFEIEEGEPQAGEPTARLAARSGPLVG 301

Query: 304 IEIGGDIIPRLIDEIPVIALAATQAEGITVIKDAHELKVKETNRIDTVVAELTKLGARIE 363
             +GG +IPRLIDEIP++A+AA  AEG T I+DA EL+VKET+RI TV  EL K G ++ 
Sbjct: 302 ATVGGSLIPRLIDEIPILAVAAAAAEGTTEIRDARELRVKETDRIRTVAEELRKFGVQVA 361

Query: 364 ATDDGMIIYGKSALKGNTVNSYGDHRIGMMLAIAGCLAEGKTIIEDAEAVGVSYPTFFDE 423
             +DG++I G   LKG    S+GDHRI M +A+AG +AEG+T++E  EA  VS+P F D 
Sbjct: 362 ELEDGLMIEGGRVLKGAHCRSHGDHRIAMAMAVAGLVAEGETVVEGWEAADVSFPGFVDL 421

Query: 424 LQKL 427
           L++L
Sbjct: 422 LREL 425


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: 585
Number of extensions: 28
Number of successful extensions: 5
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: 433
Length adjustment: 32
Effective length of query: 397
Effective length of database: 401
Effective search space:   159197
Effective search space used:   159197
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_013075704.1 BTUS_RS08515 (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.1453.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-126  408.7   0.0   1.5e-126  408.5   0.0    1.0  1  lcl|NCBI__GCF_000092905.1:WP_013075704.1  BTUS_RS08515 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013075704.1  BTUS_RS08515 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.5   0.0  1.5e-126  1.5e-126       1     414 [.      13     427 ..      13     428 .. 0.96

  Alignments for each domain:
  == domain 1  score: 408.5 bits;  conditional E-value: 1.5e-126
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg..lk 67 
                                               g++++pg+KSishRa+++ +La+g ++v+++L ++D+l+t+ ++r+lG+ v  e+++++++gvg+  l+
  lcl|NCBI__GCF_000092905.1:WP_013075704.1  13 GQVRVPGDKSISHRAVMFTSLADGVSRVEGFLFGADCLSTVACMRALGVPVDIEDGTVIVHGVGMhgLQ 81 
                                               78**************************************************8899*******9999** PP

                                 TIGR01356  68 epeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlai 136
                                               ep+++ld+gnsGtt+Rll+g+l+ + +++ ltgd s+++RP++r+ ++L ++ga+i+ +++ + +Pl++
  lcl|NCBI__GCF_000092905.1:WP_013075704.1  82 EPDDVLDVGNSGTTIRLLLGLLSGQTFHSCLTGDASIRRRPMGRVAKPLLSMGARIDGRRDGDLAPLSV 150
                                               ********************************************************************* PP

                                 TIGR01356 137 sgplkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeeder 205
                                               +g     i +  + aS+Q+ksa+lla+   l a++++ v e+  sr+++e++Lk l++    +++  + 
  lcl|NCBI__GCF_000092905.1:WP_013075704.1 151 RGADLHSIKYQMPVASAQVKSAILLAG---LFASGVTGVREPSPSRDHTERMLKALGAP---ISKRSG- 212
                                               **65559********************...7789**********************998...888877. PP

                                 TIGR01356 206 kivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveve 273
                                                  + + +  +  +++++gD+SsAaf+l+a +i ++ e+ +e++g n+t+++  i++vL +mGa+ e+e
  lcl|NCBI__GCF_000092905.1:WP_013075704.1 213 YTEIGRPARLRAMDMRIPGDLSSAAFLLVATLIVPGsELILEDVGVNPTRTG--ILDVLGAMGAQFEIE 279
                                               67777777777778*********************99***************..888************ PP

                                 TIGR01356 274 eqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRia 333
                                               e +         +  + +  l g +v    +++liDe+p+lav+aa Aeg+t+i++++elRvkE+dRi+
  lcl|NCBI__GCF_000092905.1:WP_013075704.1 280 EGEpqageptaRLAAR-SGPLVGATVgGSLIPRLIDEIPILAVAAAAAEGTTEIRDARELRVKETDRIR 347
                                               ********98777777.67899999999***************************************** PP

                                 TIGR01356 334 aiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksf 402
                                                +aeeL+k+Gv+v eledgl+ieG+ + lkga+ ++++DHRiama+av+gl+aege+ +e+ e++++sf
  lcl|NCBI__GCF_000092905.1:WP_013075704.1 348 TVAEELRKFGVQVAELEDGLMIEGG-RVLKGAHCRSHGDHRIAMAMAVAGLVAEGETVVEGWEAADVSF 415
                                               *************************.7****************************************** PP

                                 TIGR01356 403 PeFfevleqlga 414
                                               P F+++l++lga
  lcl|NCBI__GCF_000092905.1:WP_013075704.1 416 PGFVDLLRELGA 427
                                               *********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (433 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: 00:00:00.01
# Mc/sec: 11.66
//
[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