Alignments for a candidate for aroA in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Trichormus variabilis ATCC 29413

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_011319044.1 AVA_RS11430 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q3MAV9
         (426 letters)



>NCBI__GCF_000204075.1:WP_011319044.1
          Length = 426

 Score =  847 bits (2189), Expect = 0.0
 Identities = 426/426 (100%), Positives = 426/426 (100%)

Query: 1   MDTIAIPALNRPVDATVEIPGSKSITNRALLVAALAQGDSTLENALFSEDSEYFAKCVEQ 60
           MDTIAIPALNRPVDATVEIPGSKSITNRALLVAALAQGDSTLENALFSEDSEYFAKCVEQ
Sbjct: 1   MDTIAIPALNRPVDATVEIPGSKSITNRALLVAALAQGDSTLENALFSEDSEYFAKCVEQ 60

Query: 61  LGIPITLNPHLAQIQVSGKGGDIPAKQADLFVGLAGTAARFITALVALGNGEYRLDGVPR 120
           LGIPITLNPHLAQIQVSGKGGDIPAKQADLFVGLAGTAARFITALVALGNGEYRLDGVPR
Sbjct: 61  LGIPITLNPHLAQIQVSGKGGDIPAKQADLFVGLAGTAARFITALVALGNGEYRLDGVPR 120

Query: 121 MRERPMGDLVTVLQNSGIKINFEGNSGFMPYTIYGQQFAGGHFRLKANQTSQQLSALLMI 180
           MRERPMGDLVTVLQNSGIKINFEGNSGFMPYTIYGQQFAGGHFRLKANQTSQQLSALLMI
Sbjct: 121 MRERPMGDLVTVLQNSGIKINFEGNSGFMPYTIYGQQFAGGHFRLKANQTSQQLSALLMI 180

Query: 181 APYAQQDTTIEVEGTLVSQSYVKMTCRLMADFGVDVTQTDDNQFHIKAGQRYQARHYTIE 240
           APYAQQDTTIEVEGTLVSQSYVKMTCRLMADFGVDVTQTDDNQFHIKAGQRYQARHYTIE
Sbjct: 181 APYAQQDTTIEVEGTLVSQSYVKMTCRLMADFGVDVTQTDDNQFHIKAGQRYQARHYTIE 240

Query: 241 PDASNASYFFAAAAVTGGRVRVNHLTKQSCQGDILWLNVLEQMGCQVLEGEDYTEVIGPE 300
           PDASNASYFFAAAAVTGGRVRVNHLTKQSCQGDILWLNVLEQMGCQVLEGEDYTEVIGPE
Sbjct: 241 PDASNASYFFAAAAVTGGRVRVNHLTKQSCQGDILWLNVLEQMGCQVLEGEDYTEVIGPE 300

Query: 301 QLQGIDVDMNDMSDLVQTLGAIAPYANSPVIIRNVEHIRYKETERIRAVVTELRRLGVKV 360
           QLQGIDVDMNDMSDLVQTLGAIAPYANSPVIIRNVEHIRYKETERIRAVVTELRRLGVKV
Sbjct: 301 QLQGIDVDMNDMSDLVQTLGAIAPYANSPVIIRNVEHIRYKETERIRAVVTELRRLGVKV 360

Query: 361 EEFADGMKIEPTPINPAAIETYHDHRMAMAFAVTGLKTPGIVIQDPGCTAKTFPDYFTRF 420
           EEFADGMKIEPTPINPAAIETYHDHRMAMAFAVTGLKTPGIVIQDPGCTAKTFPDYFTRF
Sbjct: 361 EEFADGMKIEPTPINPAAIETYHDHRMAMAFAVTGLKTPGIVIQDPGCTAKTFPDYFTRF 420

Query: 421 FKMIGQ 426
           FKMIGQ
Sbjct: 421 FKMIGQ 426


Lambda     K      H
   0.320    0.136    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: 746
Number of extensions: 15
Number of successful extensions: 1
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: 426
Length of database: 426
Length adjustment: 32
Effective length of query: 394
Effective length of database: 394
Effective search space:   155236
Effective search space used:   155236
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_011319044.1 AVA_RS11430 (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.27738.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-130  420.5   0.0   3.8e-130  420.4   0.0    1.0  1  lcl|NCBI__GCF_000204075.1:WP_011319044.1  AVA_RS11430 3-phosphoshikimate 1


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011319044.1  AVA_RS11430 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.4   0.0  3.8e-130  3.8e-130       2     409 ..      16     420 ..      15     426 .] 0.97

  Alignments for each domain:
  == domain 1  score: 420.4 bits;  conditional E-value: 3.8e-130
                                 TIGR01356   2 eikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee.keelviegvgg.lk 67 
                                                ++ipgsKSi++Rall+aaLa+g+++++n L seD ++  +++++lG+ ++ +    ++ + g+gg + 
  lcl|NCBI__GCF_000204075.1:WP_011319044.1  16 TVEIPGSKSITNRALLVAALAQGDSTLENALFSEDSEYFAKCVEQLGIPITlNPhLAQIQVSGKGGdIP 84 
                                               589********************************************9999644688999999999888 PP

                                 TIGR01356  68 epeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlai 136
                                                ++a l +g +Gt+aR++t+++al +ge+ l+g +++++RP+++lv+ L++ g++i+ + ++g++P +i
  lcl|NCBI__GCF_000204075.1:WP_011319044.1  85 AKQADLFVGLAGTAARFITALVALGNGEYRLDGVPRMRERPMGDLVTVLQNSGIKINFEGNSGFMPYTI 153
                                               889****************************************************************** PP

                                 TIGR01356 137 sgp.lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede 204
                                                g+   gg+ +l+++  sQ +sall+ ap+a+q+ t+e++g  l+s++y+++t  l+++fgv+v+++d+
  lcl|NCBI__GCF_000204075.1:WP_011319044.1 154 YGQqFAGGHFRLKANQTSQQLSALLMIAPYAQQDTTIEVEG-TLVSQSYVKMTCRLMADFGVDVTQTDD 221
                                               ***7777*******************************999.*************************** PP

                                 TIGR01356 205 rkivvkggqkykqkevevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadveve 273
                                               +++++k gq y+ +++++e DaS+A++f aaaa+tg++v+v++l+++s qgd   ++vLe+mG++v   
  lcl|NCBI__GCF_000204075.1:WP_011319044.1 222 NQFHIKAGQRYQARHYTIEPDASNASYFFAAAAVTGGRVRVNHLTKQSCQGDILWLNVLEQMGCQVLEG 290
                                               ****************************************************99999*********999 PP

                                 TIGR01356 274 eqrdvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLekl 342
                                               e+  +ev g+++l+g++  +d+++++D+++tl ++a +A+ +  i+n+e++R+kE++Ri+a+++eL++l
  lcl|NCBI__GCF_000204075.1:WP_011319044.1 291 ED-YTEVIGPEQLQGID--VDMNDMSDLVQTLGAIAPYANSPVIIRNVEHIRYKETERIRAVVTELRRL 356
                                               99.6*************..************************************************** PP

                                 TIGR01356 343 GveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevl 409
                                               Gv+vee++dg++ie++   +++a ++ty+DHR+ama+av gl+   ++ i+d++c+ak+fP++f   
  lcl|NCBI__GCF_000204075.1:WP_011319044.1 357 GVKVEEFADGMKIEPTP--INPAAIETYHDHRMAMAFAVTGLKTP-GIVIQDPGCTAKTFPDYFTRF 420
                                               ****************5..*************************9.9****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (426 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.26
//
[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