Alignments for a candidate for aroA in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Synechococcus elongatus PCC 7942

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate Synpcc7942_0232 Synpcc7942_0232 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q31RQ5
         (448 letters)



>FitnessBrowser__SynE:Synpcc7942_0232
          Length = 448

 Score =  853 bits (2203), Expect = 0.0
 Identities = 448/448 (100%), Positives = 448/448 (100%)

Query: 1   MAQPFVLLPTEDSHQTLRIQPPSTGIGLRGRIRVPGDKSISHRALMLGAIASGETTIEGL 60
           MAQPFVLLPTEDSHQTLRIQPPSTGIGLRGRIRVPGDKSISHRALMLGAIASGETTIEGL
Sbjct: 1   MAQPFVLLPTEDSHQTLRIQPPSTGIGLRGRIRVPGDKSISHRALMLGAIASGETTIEGL 60

Query: 61  LLGEDPLSTAACFRAMGAEISELNSELVRVKGIGLQNLQEPLDVLNAGNSGTTIRLMMGL 120
           LLGEDPLSTAACFRAMGAEISELNSELVRVKGIGLQNLQEPLDVLNAGNSGTTIRLMMGL
Sbjct: 61  LLGEDPLSTAACFRAMGAEISELNSELVRVKGIGLQNLQEPLDVLNAGNSGTTIRLMMGL 120

Query: 121 LAGQRDRFFCVTGDESLRSRPMARVIQPLSQMGAEIRGRQGNTRAPLAISGRSLQPIRYV 180
           LAGQRDRFFCVTGDESLRSRPMARVIQPLSQMGAEIRGRQGNTRAPLAISGRSLQPIRYV
Sbjct: 121 LAGQRDRFFCVTGDESLRSRPMARVIQPLSQMGAEIRGRQGNTRAPLAISGRSLQPIRYV 180

Query: 181 SPIASAQVKSSILLAGLTCEGQTTVVEPALSRDHSERMFRAFGAKLTVNPEEISVTVEGP 240
           SPIASAQVKSSILLAGLTCEGQTTVVEPALSRDHSERMFRAFGAKLTVNPEEISVTVEGP
Sbjct: 181 SPIASAQVKSSILLAGLTCEGQTTVVEPALSRDHSERMFRAFGAKLTVNPEEISVTVEGP 240

Query: 241 AELTGQPVVVPGDISSAAFWLVAAAIVPDSDLLIENVGVNPTRTGILEALQQMEAQITLE 300
           AELTGQPVVVPGDISSAAFWLVAAAIVPDSDLLIENVGVNPTRTGILEALQQMEAQITLE
Sbjct: 241 AELTGQPVVVPGDISSAAFWLVAAAIVPDSDLLIENVGVNPTRTGILEALQQMEAQITLE 300

Query: 301 NERIVAGEPVADLRVRSSNLQAIEIGGSLIPRLIDEVPILAVAAAFAKGTTIIRDAEELR 360
           NERIVAGEPVADLRVRSSNLQAIEIGGSLIPRLIDEVPILAVAAAFAKGTTIIRDAEELR
Sbjct: 301 NERIVAGEPVADLRVRSSNLQAIEIGGSLIPRLIDEVPILAVAAAFAKGTTIIRDAEELR 360

Query: 361 VKESDRIAVMASELGRMGATISERPDGLEITGGAALTGATVDSYTDHRIAMSLAIAALQA 420
           VKESDRIAVMASELGRMGATISERPDGLEITGGAALTGATVDSYTDHRIAMSLAIAALQA
Sbjct: 361 VKESDRIAVMASELGRMGATISERPDGLEITGGAALTGATVDSYTDHRIAMSLAIAALQA 420

Query: 421 KGQTQIQQAEAAAVSYPDFVPTLQQLLG 448
           KGQTQIQQAEAAAVSYPDFVPTLQQLLG
Sbjct: 421 KGQTQIQQAEAAAVSYPDFVPTLQQLLG 448


Lambda     K      H
   0.317    0.133    0.366 

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: 942
Number of extensions: 35
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: 448
Length of database: 448
Length adjustment: 33
Effective length of query: 415
Effective length of database: 415
Effective search space:   172225
Effective search space used:   172225
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 Synpcc7942_0232 Synpcc7942_0232 (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.30000.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-131  425.5   1.0   1.1e-131  425.4   1.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_0232  Synpcc7942_0232 3-phosphoshikima


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_0232  Synpcc7942_0232 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.4   1.0  1.1e-131  1.1e-131       1     413 [.      30     447 ..      30     448 .] 0.95

  Alignments for each domain:
  == domain 1  score: 425.4 bits;  conditional E-value: 1.1e-131
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 
                                               g+i++pg+KSishRal+l+a+a+get++++lL +eD l+t  ++r++Ga+++e   e + ++g+g   l
  lcl|FitnessBrowser__SynE:Synpcc7942_0232  30 GRIRVPGDKSISHRALMLGAIASGETTIEGLLLGEDPLSTAACFRAMGAEISELnSELVRVKGIGLqnL 98 
                                               79**************************************************55499999***998778 PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalas.gevvltgdeslkkRPierlveaLrelgaeieskeeegslPl 134
                                               +ep ++l++gnsGtt+Rl++g+la ++   + +tgdesl+ RP+ r++++L+++gaei+ ++++ ++Pl
  lcl|FitnessBrowser__SynE:Synpcc7942_0232  99 QEPLDVLNAGNSGTTIRLMMGLLAGQRdRFFCVTGDESLRSRPMARVIQPLSQMGAEIRGRQGNTRAPL 167
                                               9999**********************99999************************************** PP

                                 TIGR01356 135 aisgplkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               aisg +  +i ++s+ aS+Q+ks++lla+   l+ ++ ++v e+ +sr++ e++   ++++  +v+ e+
  lcl|FitnessBrowser__SynE:Synpcc7942_0232 168 AISGRSLQPIRYVSPIASAQVKSSILLAG---LTCEGQTTVVEPALSRDHSERMFRAFGAK-LTVNPEE 232
                                               ****7666*********************...66777888888**********99998877.6666666 PP

                                 TIGR01356 204 erkivvkggqk.ykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270
                                                 +++v+g ++ ++q+ v v+gD+SsAaf+l+aaai +  ++ +en+g n+t+++  i++ L++m a++
  lcl|FitnessBrowser__SynE:Synpcc7942_0232 233 I-SVTVEGPAElTGQP-VVVPGDISSAAFWLVAAAIVPDsDLLIENVGVNPTRTG--ILEALQQMEAQI 297
                                               5.99999999956666.*********************99***************..889********* PP

                                 TIGR01356 271 eveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsd 330
                                               ++e++r        d++v+ +s+l+++++    +++liDe+p+lav+aafA+g+t i+++eelRvkEsd
  lcl|FitnessBrowser__SynE:Synpcc7942_0232 298 TLENERivagepvaDLRVR-SSNLQAIEIgGSLIPRLIDEVPILAVAAAFAKGTTIIRDAEELRVKESD 365
                                               *******************.799******99************************************** PP

                                 TIGR01356 331 RiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecva 399
                                               Ria++a+eL ++G+++ e++dgl+i+G+ + l ga+vd+y DHRiam+la+++l+a+g+++i++ae++a
  lcl|FitnessBrowser__SynE:Synpcc7942_0232 366 RIAVMASELGRMGATISERPDGLEITGG-AALTGATVDSYTDHRIAMSLAIAALQAKGQTQIQQAEAAA 433
                                               ****************************.6*************************************** PP

                                 TIGR01356 400 ksfPeFfevleqlg 413
                                               +s+P+F+  l+ql 
  lcl|FitnessBrowser__SynE:Synpcc7942_0232 434 VSYPDFVPTLQQLL 447
                                               **********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (448 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: 9.91
//
[ok]

This GapMind analysis is from Apr 09 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