Alignments for a candidate for aroA in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Klebsiella michiganensis M5al

Align 3-phosphoshikimate 1-carboxyvinyltransferase; 5-enolpyruvylshikimate-3-phosphate synthase; EPSP synthase; EPSPS; EC 2.5.1.19 (characterized)
to candidate BWI76_RS09760 BWI76_RS09760 3-phosphoshikimate 1-carboxyvinyltransferase

Query= SwissProt::P24497
         (427 letters)



>FitnessBrowser__Koxy:BWI76_RS09760
          Length = 427

 Score =  795 bits (2053), Expect = 0.0
 Identities = 400/427 (93%), Positives = 412/427 (96%)

Query: 1   MESLTLQPIARVDGTVNLPGSKSVSNRALLLAALARGTTVLTNLLDSDDVRHMLNALSAL 60
           MESLTLQPIARVDGT+NLPGSKSVSNRALLLAALARGTTVLTNLLDSDDVRHMLNALSAL
Sbjct: 1   MESLTLQPIARVDGTINLPGSKSVSNRALLLAALARGTTVLTNLLDSDDVRHMLNALSAL 60

Query: 61  GVHYVLSSDRTRCEVTGTGGPLQAGSALELFLGNAGTAMRPLAAALCLGSNDIVLTGEPR 120
           GVHY LSSDRTRCEVTG GGPLQA  ALEL+LGNAGTAMRPLAAALCLG NDIVLTGEPR
Sbjct: 61  GVHYTLSSDRTRCEVTGNGGPLQAAEALELYLGNAGTAMRPLAAALCLGRNDIVLTGEPR 120

Query: 121 MKERPIGHLVDALRQGGAQIDYLEQENYPPLRLRGGFTGGDVEVDGSVSSQFLTALLMAS 180
           MKERPIGHLVDALRQGGAQIDYLEQENYPPLRLRGGF+GG VEVDGSVSSQFLTALLMA+
Sbjct: 121 MKERPIGHLVDALRQGGAQIDYLEQENYPPLRLRGGFSGGQVEVDGSVSSQFLTALLMAA 180

Query: 181 PLAPQDTVIAIKGELVSRPYIDITLHLMKTFGVEVENQAYQRFIVRGNQQYQSPGDYLVE 240
           PLAPQDT I IKG+LVS+PYIDITLHLMKTFGVEVENQ+YQRFIVRGNQ Y +PGDYLVE
Sbjct: 181 PLAPQDTAIVIKGDLVSKPYIDITLHLMKTFGVEVENQSYQRFIVRGNQHYLAPGDYLVE 240

Query: 241 GDASSASYFLAAGAIKGGTVKVTGIGRNSVQGDIRFADVLEKMGATVTWGEDYIACTRGE 300
           GDASSASYFLAAGAIKGGTVKVTGIGRNSVQGDIRFADVLEKMGATVTWG+D+IACT GE
Sbjct: 241 GDASSASYFLAAGAIKGGTVKVTGIGRNSVQGDIRFADVLEKMGATVTWGDDFIACTHGE 300

Query: 301 LNAIDMDMNHIPDAAMTIATAALFARGTTTLRNIYNWRVKETDRLFAMATELRKVGAEVE 360
           LNAIDMDMNHIPDAAMTIATAALFA+GTTTLRNIYNWRVKETDRLFAMATELRKVGAEVE
Sbjct: 301 LNAIDMDMNHIPDAAMTIATAALFAKGTTTLRNIYNWRVKETDRLFAMATELRKVGAEVE 360

Query: 361 EGEDYIRITPPLTLQFAEIGTYNDHRMAMCFSLVALSDTPVTILDPKCTAKTFPDYFGQL 420
           EGEDYIRITPP  LQFAEIGT+NDHRMAMCFSLVALSDTPVTILDPKCTAKTFPDYF QL
Sbjct: 361 EGEDYIRITPPAKLQFAEIGTWNDHRMAMCFSLVALSDTPVTILDPKCTAKTFPDYFEQL 420

Query: 421 ARISTLA 427
           ARIST A
Sbjct: 421 ARISTPA 427


Lambda     K      H
   0.319    0.135    0.389 

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: 760
Number of extensions: 20
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate BWI76_RS09760 BWI76_RS09760 (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.26383.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   4.6e-147  476.1   0.0   5.5e-147  475.8   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS09760  BWI76_RS09760 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS09760  BWI76_RS09760 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.8   0.0  5.5e-147  5.5e-147       1     412 [.      14     423 ..      14     425 .. 0.96

  Alignments for each domain:
  == domain 1  score: 475.8 bits;  conditional E-value: 5.5e-147
                               TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee.keelviegvgg.lke 68 
                                             g i++pgsKS+s+RalllaaLa+g+tv+tnlL+s+D++ +l+al++lG++ + ++ + ++ ++g+gg l+ 
  lcl|FitnessBrowser__Koxy:BWI76_RS09760  14 GTINLPGSKSVSNRALLLAALARGTTVLTNLLDSDDVRHMLNALSALGVHYTlSSdRTRCEVTGNGGpLQA 84 
                                             789**********************************************99975568999******97666 PP

                               TIGR01356  69 pe.aeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisg 138
                                             +e  el+lgn+Gt++R+l ++l l + ++vltg++++k+RPi+ lv+aLr+ ga+i++ e+e+++Pl+++g
  lcl|FitnessBrowser__Koxy:BWI76_RS09760  85 AEaLELYLGNAGTAMRPLAAALCLGRNDIVLTGEPRMKERPIGHLVDALRQGGAQIDYLEQENYPPLRLRG 155
                                             55689****************************************************************** PP

                               TIGR01356 139 plkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivv 209
                                             + +gg ve++gs+SsQ+++all+aapla q+  + i g +l+s+pyi+itL+l+k fgveve++  ++++v
  lcl|FitnessBrowser__Koxy:BWI76_RS09760 156 GFSGGQVEVDGSVSSQFLTALLMAAPLAPQDTAIVIKG-DLVSKPYIDITLHLMKTFGVEVENQSYQRFIV 225
                                             **************************999777666666.**************************9***** PP

                               TIGR01356 210 kggqkykqk.evevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadveveeqrdve 279
                                             +g+q+y  + ++ vegDaSsA++flaa+ai+g++v+v+++g ns qgd ++++vLe+mGa+v++ ++ ++ 
  lcl|FitnessBrowser__Koxy:BWI76_RS09760 226 RGNQHYLAPgDYLVEGDASSASYFLAAGAIKGGTVKVTGIGRNSVQGDIRFADVLEKMGATVTWGDD-FIA 295
                                             *****76666*********************************************************.999 PP

                               TIGR01356 280 vegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveele 350
                                              + + +l++++  +d+++++D+++t+a++a+fA+g+t+++ni ++RvkE+dR+ a+a+eL+k+G+evee+e
  lcl|FitnessBrowser__Koxy:BWI76_RS09760 296 CT-HGELNAID--MDMNHIPDAAMTIATAALFAKGTTTLRNIYNWRVKETDRLFAMATELRKVGAEVEEGE 363
                                             99.67899999..********************************************************** PP

                               TIGR01356 351 dgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleql 412
                                             d++ i++  ++l+ a++ t++DHR+am++++++l    +v+i d++c+ak+fP++fe l+++
  lcl|FitnessBrowser__Koxy:BWI76_RS09760 364 DYIRITPP-AKLQFAEIGTWNDHRMAMCFSLVALSDT-PVTILDPKCTAKTFPDYFEQLARI 423
                                             ********.6*************************98.********************9987 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.39
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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