Alignments for a candidate for aroA in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Nitriliruptor alkaliphilus DSM 45188

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_052667428.1 NITAL_RS17225 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::B1XM36
         (446 letters)



>NCBI__GCF_000969705.1:WP_052667428.1
          Length = 445

 Score =  316 bits (809), Expect = 1e-90
 Identities = 182/424 (42%), Positives = 257/424 (60%), Gaps = 7/424 (1%)

Query: 24  LQGKVRIPGDKSISHRALMLGAIAEGETIIEGLLLGEDPRSTAACFAAMGANISELNETE 83
           L G+V +PGDKS+SHRAL+L A A+    + GL    D  +TAA    MGA +    + +
Sbjct: 16  LHGEVAVPGDKSLSHRALLLSAFADRPVRVGGLAPSGDVAATAAALTTMGAQVDLAPQAD 75

Query: 84  VRVQGVGLGNLQEPDNVLDAGNSGTTMRLMMGLLASSPDRFFAVTGDGSLRSRPMSRVVN 143
             + G   G L E  +VLD GNSGT++RL+ G++A   D    +TGD SLRSRP+ R+  
Sbjct: 76  GSLAGSVRGPLGEARDVLDCGNSGTSLRLLAGVVAGI-DGLTVLTGDASLRSRPVDRIAV 134

Query: 144 PLKEMGAQIWGKKGNTLAPLAIQGQQLKGIHYHSPIASAQVKSCVLLAGLLAEGQTTVTE 203
           PL+ MGA++    G    PL ++G  L G  Y SP+ASAQ+KS +LLAGL A+G TTVT 
Sbjct: 135 PLRAMGARLDAAAGGHRPPLVVRGGHLTGTSYLSPVASAQIKSAILLAGLRADGPTTVTS 194

Query: 204 PALSRDHSERMLRAFGANLTID---PETHSVTIDP--HPTLRGQKVVVPGDISSAAFWMV 258
           P  SRDH+ERML  FG  +  +     T  VT+DP    TL   +VVV  D SSAAFW+V
Sbjct: 195 PLPSRDHTERMLAHFGHPVQREVYRDGTEVVTVDPLGDRTLAADEVVVARDPSSAAFWLV 254

Query: 259 AAAIVPDSDLTIENVGINPTRTGIIEAMQMMGADMTLDNAREVAGEPVADLRVQYSPLKG 318
           AAA    + +T   V  NP R G++ A++ +G ++ + +  E AGEP+ADL V  + L G
Sbjct: 255 AAACGAGT-ITATGVCANPLRLGVVAALRRLGVEVAVTDQGETAGEPLADLTVAPTALTG 313

Query: 319 CTIGGEIIPRLIDEIPILAVAACFAAGTTIIKDAEELRVKESDRLAVMAAELTKMGANII 378
            ++ G+++   +DE+P+LA+A   +A    + DA ELRVKESDR+AV+AA L  +G  + 
Sbjct: 314 ASLQGQLVVDALDELPVLALAGACSADGLEVHDAAELRVKESDRIAVLAAALRAVGLEVE 373

Query: 379 EHPDGLEIIGGASLNGAEMDSYTDHRIAMSLAIAALNAKDETRIHRAEAASISYPTFVET 438
           E PDG  + GG       ++++ DHRIAM+ AIAA+       I    A + SYP+F++ 
Sbjct: 374 ERPDGYRVPGGQRPGPGTVEAHGDHRIAMTAAIAAVLGTGPVEIGGFGAVATSYPSFLDD 433

Query: 439 LTNV 442
           L  +
Sbjct: 434 LARL 437


Lambda     K      H
   0.317    0.133    0.376 

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: 569
Number of extensions: 33
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: 446
Length of database: 445
Length adjustment: 32
Effective length of query: 414
Effective length of database: 413
Effective search space:   170982
Effective search space used:   170982
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: 41 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate WP_052667428.1 NITAL_RS17225 (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.22768.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.1e-105  337.1   0.0     8e-105  336.9   0.0    1.0  1  lcl|NCBI__GCF_000969705.1:WP_052667428.1  NITAL_RS17225 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_052667428.1  NITAL_RS17225 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.9   0.0    8e-105    8e-105       1     414 [.      18     439 ..      18     440 .. 0.93

  Alignments for each domain:
  == domain 1  score: 336.9 bits;  conditional E-value: 8e-105
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 
                                               ge+++pg+KS+shRalll+a+a+ +++v +l  s D+ at  al  +Ga+v  + + +    g     l
  lcl|NCBI__GCF_000969705.1:WP_052667428.1  18 GEVAVPGDKSLSHRALLLSAFADRPVRVGGLAPSGDVAATAAALTTMGAQVDLApQADGSLAGSVRgpL 86 
                                               79*************************************************954455555555433357 PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                                e+ ++ld+gnsGt++Rll gv+a ++g +vltgd sl+ RP++r+  +Lr++ga+ +++ + +++Pl+
  lcl|NCBI__GCF_000969705.1:WP_052667428.1  87 GEARDVLDCGNSGTSLRLLAGVVAGIDGLTVLTGDASLRSRPVDRIAVPLRAMGARLDAAAGGHRPPLV 155
                                               8889***************************************************************** PP

                                 TIGR01356 136 isgplkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede 204
                                               ++g+   g+++ls+ aS+Q ksa+lla+   l+a++ ++v+++l sr+++e++L+ +++  v+ e+ ++
  lcl|NCBI__GCF_000969705.1:WP_052667428.1 156 VRGGHLTGTSYLSPVASAQIKSAILLAG---LRADGPTTVTSPLPSRDHTERMLAHFGHP-VQREVYRD 220
                                               ***8777*********************...8899999********************87.66555555 PP

                                 TIGR01356 205 ..rkivvkggqk..ykqkevevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGad 269
                                                 + ++v + +    + +ev v+ D+SsAaf+l+aaa   +++t +++ +n+++ +  +++ L+++G +
  lcl|NCBI__GCF_000969705.1:WP_052667428.1 221 gtEVVTVDPLGDrtLAADEVVVARDPSSAAFWLVAAACGAGTITATGVCANPLRLG--VVAALRRLGVE 287
                                               4467777665443355559*************************************..777******** PP

                                 TIGR01356 270 veveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEs 329
                                               v v++q         d++v  +  l g     + v ++ Delp+la+++a+     ++++++elRvkEs
  lcl|NCBI__GCF_000969705.1:WP_052667428.1 288 VAVTDQGetageplaDLTVA-PTALTGASLqGQLVVDALDELPVLALAGACSADGLEVHDAAELRVKES 355
                                               *****999************.78899999988****************99999999************* PP

                                 TIGR01356 330 dRiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecv 398
                                               dRia++a++L+++G+evee++dg  + G+ ++  +++v+ ++DHRiam  a++++   g+vei + ++v
  lcl|NCBI__GCF_000969705.1:WP_052667428.1 356 DRIAVLAAALRAVGLEVEERPDGYRVPGG-QRPGPGTVEAHGDHRIAMTAAIAAVLGTGPVEIGGFGAV 423
                                               *****************************.6************************************** PP

                                 TIGR01356 399 aksfPeFfevleqlga 414
                                               a+s+P+F+++l++lg 
  lcl|NCBI__GCF_000969705.1:WP_052667428.1 424 ATSYPSFLDDLARLGG 439
                                               ************9985 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.40
//
[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