Alignments for a candidate for aroA in Methylomicrobium alcaliphilum 20Z

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Methylomicrobium alcaliphilum 20Z

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_014148949.1 MEALZ_RS12205 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>NCBI__GCF_000968535.2:WP_014148949.1
          Length = 439

 Score =  454 bits (1167), Expect = e-132
 Identities = 237/430 (55%), Positives = 309/430 (71%), Gaps = 3/430 (0%)

Query: 7   PSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGASIQVI 66
           P   L+G+  VPGDKSISHR+++L ++A+G T V GFL   D LA + A + MG  I+  
Sbjct: 11  PGGSLNGQARVPGDKSISHRSIMLGSLADGVTHVKGFLEAEDALATLQAFKDMGVVIEGP 70

Query: 67  EDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQRRPMK 126
           ++   L + GVG  GL+AP + L  GNSGT++RLLSGLLAGQ F+++LTGD SL  RPMK
Sbjct: 71  KNGE-LTIHGVGKHGLKAPQKPLYLGNSGTSMRLLSGLLAGQAFDSILTGDKSLSGRPMK 129

Query: 127 RIIDPLTLMGAKIDSTGN-VPPLKIYGNP-RLTGIHYQLPMASAQVKSCLLLAGLYARGK 184
           R+ DPL  MGA I++T     PL I G   +L GI YQ+PMASAQVKSCLLLAG+YA G 
Sbjct: 130 RVTDPLAQMGAVIETTEKGTAPLHIKGQDGKLKGIDYQMPMASAQVKSCLLLAGMYAEGA 189

Query: 185 TCITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAFFIVAA 244
           T +TEPAP+RDHTER+L  F Y ++K+   + ++  G+L A DI +P DISSAAFF+V A
Sbjct: 190 TRVTEPAPTRDHTERMLSGFSYPVEKEGAKVTITAEGRLTAADIDVPSDISSAAFFLVGA 249

Query: 245 TITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHARLKGID 304
           +I PGS I L  VG+NPTR GVI++L++MGA+IE+ +      EP AD+ V+ A LKGID
Sbjct: 250 SIAPGSDIVLNHVGINPTRTGVIDILRLMGANIEILNERIVGGEPVADLHVKSAPLKGID 309

Query: 305 IPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGIAAESL 364
           IP + VPL IDEFPVL +AAA A+G+T L  A ELRVKE+DRI  M DGLQ LG+ A+S 
Sbjct: 310 IPEELVPLAIDEFPVLFVAAACAEGQTRLTGAEELRVKESDRIQVMADGLQILGVDAQST 369

Query: 365 PDGVIIQGGTLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFVELANE 424
           PDG+IIQGG +  G V S+ DHRIAMAF++AG  A G + I +C+NV TSFP F+E+A  
Sbjct: 370 PDGMIIQGGKIGSGSVESHGDHRIAMAFSIAGLRADGKIVINDCENVNTSFPEFIEIAPA 429

Query: 425 VGMNVKGVRG 434
           +G+ ++  +G
Sbjct: 430 LGLKLQSEQG 439


Lambda     K      H
   0.318    0.137    0.392 

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: 622
Number of extensions: 30
Number of successful extensions: 3
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: 438
Length of database: 439
Length adjustment: 32
Effective length of query: 406
Effective length of database: 407
Effective search space:   165242
Effective search space used:   165242
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_014148949.1 MEALZ_RS12205 (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.32331.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.4e-132  426.7   0.0     5e-132  426.5   0.0    1.0  1  lcl|NCBI__GCF_000968535.2:WP_014148949.1  MEALZ_RS12205 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000968535.2:WP_014148949.1  MEALZ_RS12205 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.5   0.0    5e-132    5e-132       1     413 [.      17     431 ..      17     433 .. 0.96

  Alignments for each domain:
  == domain 1  score: 426.5 bits;  conditional E-value: 5e-132
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..l 66 
                                               g+ ++pg+KSishR+++l++La+g t v+++L++eD latl+a++++G+ +e  +++el+i+gvg+  l
  lcl|NCBI__GCF_000968535.2:WP_014148949.1  17 GQARVPGDKSISHRSIMLGSLADGVTHVKGFLEAEDALATLQAFKDMGVVIEgPKNGELTIHGVGKhgL 85 
                                               6789************************************************777*********9999* PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                               k p++ l+lgnsGt++Rll+g+la ++++++ltgd+sl+ RP++r++++L ++ga ie +e +g++Pl+
  lcl|NCBI__GCF_000968535.2:WP_014148949.1  86 KAPQKPLYLGNSGTSMRLLSGLLAGQAFDSILTGDKSLSGRPMKRVTDPLAQMGAVIETTE-KGTAPLH 153
                                               **********************************************************988.59***** PP

                                 TIGR01356 136 isgp.lkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveee 202
                                               i+g+  k+ gi +  ++aS+Q+ks+llla+     a++++ v+e+  +r+++e++L  ++     ve+e
  lcl|NCBI__GCF_000968535.2:WP_014148949.1 154 IKGQdGKLkGIDYQMPMASAQVKSCLLLAGM---YAEGATRVTEPAPTRDHTERMLSGFSYP---VEKE 216
                                               ****96667*********************5...5669999999*************99988...9999 PP

                                 TIGR01356 203 derkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270
                                                  k++++ ++  +  +++v++D+SsAaffl+ a i+++ +++++++g+n+t+++  +i++L+ mGa++
  lcl|NCBI__GCF_000968535.2:WP_014148949.1 217 GA-KVTITAEGRLTAADIDVPSDISSAAFFLVGASIAPGsDIVLNHVGINPTRTG--VIDILRLMGANI 282
                                               87.99999999977778**********************9***************..788********* PP

                                 TIGR01356 271 eveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsd 330
                                               e+ ++r        d+ v+ +  lkg+++ ++ v+ +iDe+p+l v+aa+Aeg+tr++++eelRvkEsd
  lcl|NCBI__GCF_000968535.2:WP_014148949.1 283 EILNERivggepvaDLHVK-SAPLKGIDIpEELVPLAIDEFPVLFVAAACAEGQTRLTGAEELRVKESD 350
                                               *******************.578******99************************************** PP

                                 TIGR01356 331 RiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecva 399
                                               Ri+++a+ L+ lGv++++++dg++i+G+  ++ +++v++++DHRiama++++gl+a+g++ i+d e v+
  lcl|NCBI__GCF_000968535.2:WP_014148949.1 351 RIQVMADGLQILGVDAQSTPDGMIIQGG--KIGSGSVESHGDHRIAMAFSIAGLRADGKIVINDCENVN 417
                                               ****************************..6************************************** PP

                                 TIGR01356 400 ksfPeFfevleqlg 413
                                               +sfPeF+e + +lg
  lcl|NCBI__GCF_000968535.2:WP_014148949.1 418 TSFPEFIEIAPALG 431
                                               *******9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (439 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: 12.49
//
[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