Alignments for a candidate for aroA in Heliobacterium modesticaldum Ice1; ATCC 51547

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Heliobacterium modesticaldum Ice1; ATCC 51547

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_049754094.1 HM1_RS08665 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::B1XM36
         (446 letters)



>NCBI__GCF_000019165.1:WP_049754094.1
          Length = 443

 Score =  460 bits (1184), Expect = e-134
 Identities = 248/431 (57%), Positives = 312/431 (72%), Gaps = 6/431 (1%)

Query: 11  QQLVITPPASGLSLQGKVRIPGDKSISHRALMLGAIAEGETIIEGLLLGEDPRSTAACFA 70
           + L I P   GL L+G+  +PGDKSISHRA+M GA+A G T +   L G+D  ST  CF 
Sbjct: 10  KSLAIRP---GLPLRGETEVPGDKSISHRAVMFGALARGVTRVHRFLPGQDCLSTIDCFR 66

Query: 71  AMGANISELNETEVRVQGVGLGNLQEPDNVLDAGNSGTTMRLMMGLLASSPDRFFAVTGD 130
            +G  I + N +EV V G G G L+EP  VLD GNSGTT+RLM G+L+  P  F  VTGD
Sbjct: 67  KLGVRIEQPNPSEVVVYGQGPGGLKEPSEVLDVGNSGTTIRLMTGILSGLPF-FSIVTGD 125

Query: 131 GSLRSRPMSRVVNPLKEMGAQIWGKKGNTLAPLAIQGQQ--LKGIHYHSPIASAQVKSCV 188
            S+R RPM RV  PL EMGA IWG++  T APLAI G    L+ IHY+SP+ASAQVKS V
Sbjct: 126 TSIRRRPMGRVTRPLLEMGASIWGRENATKAPLAINGASMALEAIHYNSPVASAQVKSAV 185

Query: 189 LLAGLLAEGQTTVTEPALSRDHSERMLRAFGANLTIDPETHSVTIDPHPTLRGQKVVVPG 248
           LLAGL AEG T+V EP +SRDH+ERML AFGA +    +  + +++  P LR Q+V VPG
Sbjct: 186 LLAGLFAEGCTSVREPLVSRDHTERMLAAFGAKIGRSEDRLTASVEGFPELRAQEVEVPG 245

Query: 249 DISSAAFWMVAAAIVPDSDLTIENVGINPTRTGIIEAMQMMGADMTLDNAREVAGEPVAD 308
           DISSAAF +VAA+IVP S+L + N+G+NPTR GIIE ++ MG D+ ++NAREVAGE VAD
Sbjct: 246 DISSAAFLLVAASIVPGSELVLYNIGVNPTRDGIIEVLRAMGGDVQVENAREVAGELVAD 305

Query: 309 LRVQYSPLKGCTIGGEIIPRLIDEIPILAVAACFAAGTTIIKDAEELRVKESDRLAVMAA 368
           L V+ + LKG TIGG IIPRLIDE+PI+AVAA FA GTT I+DA E+RVKE+DR+AVM  
Sbjct: 306 LIVRSASLKGTTIGGAIIPRLIDELPIIAVAALFAEGTTEIRDAAEMRVKETDRIAVMIR 365

Query: 369 ELTKMGANIIEHPDGLEIIGGASLNGAEMDSYTDHRIAMSLAIAALNAKDETRIHRAEAA 428
           EL K+GA+I E PDG+ I GGA+L GA  +S+ DHR+AM+LA+A L A+ ET I+ A + 
Sbjct: 366 ELRKLGADIEERPDGMIIRGGAALRGAATESHGDHRVAMALAVAGLLAEGETVINDAGSI 425

Query: 429 SISYPTFVETL 439
            +S+P F E L
Sbjct: 426 DVSFPGFAELL 436


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: 539
Number of extensions: 20
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: 446
Length of database: 443
Length adjustment: 32
Effective length of query: 414
Effective length of database: 411
Effective search space:   170154
Effective search space used:   170154
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_049754094.1 HM1_RS08665 (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.20365.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-134  434.4   0.1   2.3e-134  434.2   0.1    1.0  1  lcl|NCBI__GCF_000019165.1:WP_049754094.1  HM1_RS08665 3-phosphoshikimate 1


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019165.1:WP_049754094.1  HM1_RS08665 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.2   0.1  2.3e-134  2.3e-134       1     413 [.      22     440 ..      22     442 .. 0.95

  Alignments for each domain:
  == domain 1  score: 434.2 bits;  conditional E-value: 2.3e-134
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 
                                               ge ++pg+KSishRa++++aLa+g t+v+++L ++D+l+t++++rklG+++e+    e+v+ g+g   l
  lcl|NCBI__GCF_000019165.1:WP_049754094.1  22 GETEVPGDKSISHRAVMFGALARGVTRVHRFLPGQDCLSTIDCFRKLGVRIEQPnPSEVVVYGQGPggL 90 
                                               6789************************************************7647788887766566* PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                               kep+++ld+gnsGtt+Rl+tg+l+ +++ +++tgd s+++RP++r++ +L e+ga+i  +e++ ++Pla
  lcl|NCBI__GCF_000019165.1:WP_049754094.1  91 KEPSEVLDVGNSGTTIRLMTGILSGLPFFSIVTGDTSIRRRPMGRVTRPLLEMGASIWGRENATKAPLA 159
                                               ********************************************************************* PP

                                 TIGR01356 136 isgp.lkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveee 202
                                               i+g  + + +i++ s+ aS+Q+ksa+lla+   l a++ + v e+l+sr+++e++L+ ++++   + ++
  lcl|NCBI__GCF_000019165.1:WP_049754094.1 160 INGAsMALeAIHYNSPVASAQVKSAVLLAG---LFAEGCTSVREPLVSRDHTERMLAAFGAK---IGRS 222
                                               ****87778*********************...7789******************9998877...7777 PP

                                 TIGR01356 203 de.rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGad 269
                                               ++  + +v+g  + + +evev+gD+SsAaf+l+aa i ++ e+++ n+g n+t+ +  ii+vL++mG+d
  lcl|NCBI__GCF_000019165.1:WP_049754094.1 223 EDrLTASVEGFPELRAQEVEVPGDISSAAFLLVAASIVPGsELVLYNIGVNPTRDG--IIEVLRAMGGD 289
                                               775688999998878888********************999***************..888******** PP

                                 TIGR01356 270 veveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEs 329
                                               v+ve+ r        d++v+ + +lkg+++  + +++liDelp++av+a+fAeg+t+i++++e+RvkE+
  lcl|NCBI__GCF_000019165.1:WP_049754094.1 290 VQVENARevagelvaDLIVR-SASLKGTTIgGAIIPRLIDELPIIAVAALFAEGTTEIRDAAEMRVKET 357
                                               ********************.567******99************************************* PP

                                 TIGR01356 330 dRiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecv 398
                                               dRia++ +eL+klG+++ee++dg++i+G+ + l+ga +++++DHR+amalav+gl aege+ i+da+ +
  lcl|NCBI__GCF_000019165.1:WP_049754094.1 358 DRIAVMIRELRKLGADIEERPDGMIIRGG-AALRGAATESHGDHRVAMALAVAGLLAEGETVINDAGSI 425
                                               *****************************.6************************************** PP

                                 TIGR01356 399 aksfPeFfevleqlg 413
                                               ++sfP F e+le+l 
  lcl|NCBI__GCF_000019165.1:WP_049754094.1 426 DVSFPGFAELLERLR 440
                                               ************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (443 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: 10.28
//
[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