Alignments for a candidate for aroA in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Malonomonas rubra DSM 5091

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_072905141.1 BUB13_RS02365 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::K9RIB8
         (448 letters)



>NCBI__GCF_900142125.1:WP_072905141.1
          Length = 432

 Score =  471 bits (1212), Expect = e-137
 Identities = 247/433 (57%), Positives = 315/433 (72%), Gaps = 5/433 (1%)

Query: 16  HKLVVRRGSSGLSLSGSIRVPGDKSISHRALMLGALAEGETRIEGLLLGEDPRSTAKCFQ 75
           HK   R  +   S+ G I VPGDKSISHR++M  +LA+GE+R+ GLL GED  ST K FQ
Sbjct: 2   HKYETRTIAPVTSVKGEIVVPGDKSISHRSIMFASLAKGESRVVGLLRGEDCMSTLKIFQ 61

Query: 76  AMGALVSDLNTELVRVKGIGLGNLLEPVDVLDAGNSGTTLRLMLGILASHAGRFFSI-TG 134
           AMG  V +   + + ++G G+  LLEP DVLD GNSGTT+RLM GILA+    F+S+ TG
Sbjct: 62  AMGVEVEERGEDELIIQGRGIDGLLEPDDVLDCGNSGTTMRLMSGILAAQP--FYSVMTG 119

Query: 135 DSSLRSRPMSRVVKPLEQMGAQIWGRDNNSKAPLAVRGENLKPIHYHSPIASAQVKSCVL 194
           D  LR RPM RV+ PL +MGA+I GRD N KAPL + G  LKP  YHSP++SAQVKS +L
Sbjct: 120 DQYLRKRPMGRVIDPLREMGAKILGRDGNKKAPLTIDGGGLKPAEYHSPVSSAQVKSALL 179

Query: 195 LAGLSVEGKTTVTEPALSRDHSERMLQAFGAKLDIDTQTNSVSVNGPVKLYGQSVVVPGD 254
           LAG+ +EG TTV EP LSRDHSERML  FGA  ++++      V GPV L G+ V VPGD
Sbjct: 180 LAGMQIEGTTTVYEPHLSRDHSERMLCYFGA--EVESFDGGARVTGPVVLEGREVFVPGD 237

Query: 255 ISSAAFWLVAGAIVSDSELLIENVGVNPTRTGVLEALEMMGAEIARENEREVAGEPVADL 314
           ISSAAF+LVAG IV DSELL++NVGVNPTR+G+++ L+ MG  I   N+RE++GEPVADL
Sbjct: 238 ISSAAFFLVAGLIVPDSELLLKNVGVNPTRSGIIDILQQMGGSIELLNQRELSGEPVADL 297

Query: 315 RVRSSKLKGCTIEGDIIPRLIDEIPILAVAAVFAEGTTVIKDAAELRVKESDRITVMANQ 374
            V+SS+LKG  I G+++PR IDE P+++VAA FAEG T I+DA ELRVKE+DRI  M + 
Sbjct: 298 LVKSSQLKGIEIGGELVPRAIDEFPVVSVAAAFAEGVTTIRDAKELRVKETDRIAAMCDT 357

Query: 375 LNSMGARITELDDGMEITGGTPLTGAELDSFTDHRIAMSLAIAALNASGTTTINRAEAAS 434
           L  +GA+I  L+DGM +TGG  L+G  ++SF DHRIAMS+A+AAL ASG  TI      S
Sbjct: 358 LGKIGAQIEPLEDGMRVTGGKSLSGGTVNSFGDHRIAMSMAVAALRASGEVTIEDTGCTS 417

Query: 435 VSYPDFFETIKRI 447
            S+P+F+E ++ I
Sbjct: 418 TSFPNFWELLENI 430


Lambda     K      H
   0.316    0.132    0.363 

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: 562
Number of extensions: 23
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: 448
Length of database: 432
Length adjustment: 32
Effective length of query: 416
Effective length of database: 400
Effective search space:   166400
Effective search space used:   166400
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_072905141.1 BUB13_RS02365 (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.13335.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-141  455.8   0.0   7.1e-141  455.7   0.0    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072905141.1  BUB13_RS02365 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072905141.1  BUB13_RS02365 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.7   0.0  7.1e-141  7.1e-141       1     412 [.      17     430 ..      17     432 .] 0.96

  Alignments for each domain:
  == domain 1  score: 455.7 bits;  conditional E-value: 7.1e-141
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 
                                               gei +pg+KSishR++++a+La+ge++v +lL++eD+ +tl++++++G++vee  ++el+i+g g   l
  lcl|NCBI__GCF_900142125.1:WP_072905141.1  17 GEIVVPGDKSISHRSIMFASLAKGESRVVGLLRGEDCMSTLKIFQAMGVEVEERgEDELIIQGRGIdgL 85 
                                               7999************************************************55599******98888* PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                                ep+++ld+gnsGtt+Rl++g+la++++ +v+tgd+ l+kRP++r++++Lre+ga+i  +++++++Pl+
  lcl|NCBI__GCF_900142125.1:WP_072905141.1  86 LEPDDVLDCGNSGTTMRLMSGILAAQPFYSVMTGDQYLRKRPMGRVIDPLREMGAKILGRDGNKKAPLT 154
                                               ********************************************************************* PP

                                 TIGR01356 136 isgplkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede 204
                                               i+g+   +  + s+  S+Q+ksallla+    q +++++v e+ +sr++ e++L  ++++   ve  d+
  lcl|NCBI__GCF_900142125.1:WP_072905141.1 155 IDGGGLKPAEYHSPVSSAQVKSALLLAG---MQIEGTTTVYEPHLSRDHSERMLCYFGAE---VESFDG 217
                                               ***97779********************...55678888888*************99988...999887 PP

                                 TIGR01356 205 rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadvev 272
                                                  +v+g    + +ev v+gD+SsAaffl+a++i +  e+ ++n+g n+t+ +  ii++L++mG+++e+
  lcl|NCBI__GCF_900142125.1:WP_072905141.1 218 -GARVTGPVVLEGREVFVPGDISSAAFFLVAGLIVPDsELLLKNVGVNPTRSG--IIDILQQMGGSIEL 283
                                               .99999998877778**********************9***************..888*********** PP

                                 TIGR01356 273 eeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRi 332
                                                +qr        d+ v+ +s+lkg+++  + v+++iDe+p+++v+aafAeg+t+i++++elRvkE+dRi
  lcl|NCBI__GCF_900142125.1:WP_072905141.1 284 LNQRelsgepvaDLLVK-SSQLKGIEIgGELVPRAIDEFPVVSVAAAFAEGVTTIRDAKELRVKETDRI 351
                                               ************9***9.789******99**************************************** PP

                                 TIGR01356 333 aaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaks 401
                                               aa+++ L k+G+++e+ledg+ ++G+ k+l+g++v++++DHRiam++av++l+a+gev+ied++c+++s
  lcl|NCBI__GCF_900142125.1:WP_072905141.1 352 AAMCDTLGKIGAQIEPLEDGMRVTGG-KSLSGGTVNSFGDHRIAMSMAVAALRASGEVTIEDTGCTSTS 419
                                               **************************.7***************************************** PP

                                 TIGR01356 402 fPeFfevleql 412
                                               fP+F+e+le++
  lcl|NCBI__GCF_900142125.1:WP_072905141.1 420 FPNFWELLENI 430
                                               ********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (432 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.33
//
[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