Alignments for a candidate for aroA in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Escherichia coli BW25113

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate 15032 b0908 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI)

Query= BRENDA::P0A6D3
         (427 letters)



>FitnessBrowser__Keio:15032
          Length = 427

 Score =  846 bits (2185), Expect = 0.0
 Identities = 427/427 (100%), Positives = 427/427 (100%)

Query: 1   MESLTLQPIARVDGTINLPGSKSVSNRALLLAALAHGKTVLTNLLDSDDVRHMLNALTAL 60
           MESLTLQPIARVDGTINLPGSKSVSNRALLLAALAHGKTVLTNLLDSDDVRHMLNALTAL
Sbjct: 1   MESLTLQPIARVDGTINLPGSKSVSNRALLLAALAHGKTVLTNLLDSDDVRHMLNALTAL 60

Query: 61  GVSYTLSADRTRCEIIGNGGPLHAEGALELFLGNAGTAMRPLAAALCLGSNDIVLTGEPR 120
           GVSYTLSADRTRCEIIGNGGPLHAEGALELFLGNAGTAMRPLAAALCLGSNDIVLTGEPR
Sbjct: 61  GVSYTLSADRTRCEIIGNGGPLHAEGALELFLGNAGTAMRPLAAALCLGSNDIVLTGEPR 120

Query: 121 MKERPIGHLVDALRLGGAKITYLEQENYPPLRLQGGFTGGNVDVDGSVSSQFLTALLMTA 180
           MKERPIGHLVDALRLGGAKITYLEQENYPPLRLQGGFTGGNVDVDGSVSSQFLTALLMTA
Sbjct: 121 MKERPIGHLVDALRLGGAKITYLEQENYPPLRLQGGFTGGNVDVDGSVSSQFLTALLMTA 180

Query: 181 PLAPEDTVIRIKGDLVSKPYIDITLNLMKTFGVEIENQHYQQFVVKGGQSYQSPGTYLVE 240
           PLAPEDTVIRIKGDLVSKPYIDITLNLMKTFGVEIENQHYQQFVVKGGQSYQSPGTYLVE
Sbjct: 181 PLAPEDTVIRIKGDLVSKPYIDITLNLMKTFGVEIENQHYQQFVVKGGQSYQSPGTYLVE 240

Query: 241 GDASSASYFLAAAAIKGGTVKVTGIGRNSMQGDIRFADVLEKMGATICWGDDYISCTRGE 300
           GDASSASYFLAAAAIKGGTVKVTGIGRNSMQGDIRFADVLEKMGATICWGDDYISCTRGE
Sbjct: 241 GDASSASYFLAAAAIKGGTVKVTGIGRNSMQGDIRFADVLEKMGATICWGDDYISCTRGE 300

Query: 301 LNAIDMDMNHIPDAAMTIATAALFAKGTTTLRNIYNWRVKETDRLFAMATELRKVGAEVE 360
           LNAIDMDMNHIPDAAMTIATAALFAKGTTTLRNIYNWRVKETDRLFAMATELRKVGAEVE
Sbjct: 301 LNAIDMDMNHIPDAAMTIATAALFAKGTTTLRNIYNWRVKETDRLFAMATELRKVGAEVE 360

Query: 361 EGHDYIRITPPEKLNFAEIATYNDHRMAMCFSLVALSDTPVTILDPKCTAKTFPDYFEQL 420
           EGHDYIRITPPEKLNFAEIATYNDHRMAMCFSLVALSDTPVTILDPKCTAKTFPDYFEQL
Sbjct: 361 EGHDYIRITPPEKLNFAEIATYNDHRMAMCFSLVALSDTPVTILDPKCTAKTFPDYFEQL 420

Query: 421 ARISQAA 427
           ARISQAA
Sbjct: 421 ARISQAA 427


Lambda     K      H
   0.319    0.135    0.391 

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: 714
Number of extensions: 18
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: 427
Length of database: 427
Length adjustment: 32
Effective length of query: 395
Effective length of database: 395
Effective search space:   156025
Effective search space used:   156025
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 15032 b0908 (3-phosphoshikimate 1-carboxyvinyltransferase (NCBI))
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.1012.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   8.4e-144  465.3   0.0   9.5e-144  465.2   0.0    1.0  1  lcl|FitnessBrowser__Keio:15032  b0908 3-phosphoshikimate 1-carbo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15032  b0908 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.2   0.0  9.5e-144  9.5e-144       1     413 [.      14     424 ..      14     426 .. 0.96

  Alignments for each domain:
  == domain 1  score: 465.2 bits;  conditional E-value: 9.5e-144
                       TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee.keelviegvgg..lkepeaeldl 75 
                                     g i++pgsKS+s+RalllaaLa+g+tv+tnlL+s+D++ +l+al +lG++ + ++ + ++ i g+gg   +e   el l
  lcl|FitnessBrowser__Keio:15032  14 GTINLPGSKSVSNRALLLAALAHGKTVLTNLLDSDDVRHMLNALTALGVSYTlSAdRTRCEIIGNGGplHAEGALELFL 92 
                                     789**********************************************999644588999999999633444499*** PP

                       TIGR01356  76 gnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgplkggivelsgsaSsQ 154
                                     gn+Gt++R+l ++l l s ++vltg++++k+RPi+ lv+aLr  ga+i + e+e+++Pl+++g+ +gg v ++gs+SsQ
  lcl|FitnessBrowser__Keio:15032  93 GNAGTAMRPLAAALCLGSNDIVLTGEPRMKERPIGHLVDALRLGGAKITYLEQENYPPLRLQGGFTGGNVDVDGSVSSQ 171
                                     ******************************************************************************* PP

                       TIGR01356 155 yksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqkykqk.evevegDaSsAaff 232
                                     +++all++apla ++  ++i g +l+s+pyi+itL+l+k fgve+e+++ +++vvkggq+y+++ ++ vegDaSsA++f
  lcl|FitnessBrowser__Keio:15032 172 FLTALLMTAPLAPEDTVIRIKG-DLVSKPYIDITLNLMKTFGVEIENQHYQQFVVKGGQSYQSPgTYLVEGDASSASYF 249
                                     **********999777777777.*************************************88888************** PP

                       TIGR01356 233 laaaaitgeevtvenlgenstqgdkaiiivLeemGadveveeqrdvevegasklkgvkvdidvdsliDelptlavlaaf 311
                                     laaaai+g++v+v+++g ns qgd ++++vLe+mGa++ + ++  ++ + + +l++++  +d+++++D+++t+a++a+f
  lcl|FitnessBrowser__Keio:15032 250 LAAAAIKGGTVKVTGIGRNSMQGDIRFADVLEKMGATICWGDD-YISCT-RGELNAID--MDMNHIPDAAMTIATAALF 324
                                     *******************************************.69999.57899999..******************* PP

                       TIGR01356 312 AegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegev 390
                                     A+g+t+++ni ++RvkE+dR+ a+a+eL+k+G+evee++d++ i++  ++l+ a++ ty+DHR+am++++++l    +v
  lcl|FitnessBrowser__Keio:15032 325 AKGTTTLRNIYNWRVKETDRLFAMATELRKVGAEVEEGHDYIRITPP-EKLNFAEIATYNDHRMAMCFSLVALSDT-PV 401
                                     ***********************************************.6*************************98.** PP

                       TIGR01356 391 eiedaecvaksfPeFfevleqlg 413
                                     +i d++c+ak+fP++fe l+++ 
  lcl|FitnessBrowser__Keio:15032 402 TILDPKCTAKTFPDYFEQLARIS 424
                                     *******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (427 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.29
//
[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