Alignments for a candidate for aroA in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Polaromonas naphthalenivorans CJ2

Align 3-phosphoshikimate 1-carboxyvinyltransferase; 5-enolpyruvylshikimate-3-phosphate synthase; EPSP synthase; EPSPS; EC 2.5.1.19 (characterized)
to candidate WP_011802174.1 PNAP_RS13960 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidylate kinase

Query= SwissProt::P24497
         (427 letters)



>NCBI__GCF_000015505.1:WP_011802174.1
          Length = 667

 Score =  429 bits (1102), Expect = e-124
 Identities = 245/439 (55%), Positives = 299/439 (68%), Gaps = 18/439 (4%)

Query: 1   MESLTLQPIARVDGTVNLPGSKSVSNRALLLAALARGTTVLTNLLDSDDVRHMLNALSAL 60
           +E L + P+ +  GTV LPGSKS+SNR LLLAAL+ G T + +LL SDD   ML AL  L
Sbjct: 4   IEYLDIPPLTQAGGTVCLPGSKSISNRVLLLAALSHGQTTVHDLLASDDTAVMLTALEQL 63

Query: 61  GVHYVLSSDRTRCEVTGTGGPLQAGSALELFLGNAGTAMRPLAAALCLGSNDIVLTGEPR 120
           G   V S +     + G GG L    A  LF+GNAGTAMRPL AAL L   +  L+G PR
Sbjct: 64  GCTVVQSGNTA--VIGGLGGQLVQRKAA-LFMGNAGTAMRPLTAALALLGGEFELSGVPR 120

Query: 121 MKERPIGHLVDALRQGGAQIDYLEQENYPPLRLRGGFTGGD--VEVDGSVSSQFLTALLM 178
           M ERPIG LVDALRQ G  IDYL  E +PPLRLR G    D  + V G VSSQFLTALLM
Sbjct: 121 MHERPIGDLVDALRQLGCAIDYLGNEGFPPLRLRPGVLKLDDAIRVRGDVSSQFLTALLM 180

Query: 179 ASPLAPQDTV-IAIKGELVSRPYIDITLHLMKTFGVEVENQAYQRFIVRGNQQYQSPGDY 237
           A PL  Q  + I + GEL+SRPYI+ITL+L+K FG++VE + +QRF +    QYQSPG+ 
Sbjct: 181 ALPLVAQQAIRIEVVGELISRPYIEITLNLLKRFGIQVEREGWQRFTIPAGSQYQSPGEI 240

Query: 238 LVEGDASSASYFLAAGAI----KG-GTVKVTGIGRNSVQGDIRFADVLEKMGATVTWGED 292
            VE DASSASYF+A GAI    KG   +K+ G+G +S+QGDIRF +    MGA +    +
Sbjct: 241 HVEADASSASYFIALGAIAACAKGINDIKIMGVGADSIQGDIRFIEAARMMGAKIDSTPN 300

Query: 293 YIACTRGE--LNAIDMDMNHIPDAAMTIATAALFARGTTTLRNIYNWRVKETDRLFAMAT 350
            +  +RG   L AID+D NHIPDAAMT+A  AL+A GTT LRNI +WRVKETDR+ AMA 
Sbjct: 301 SLQISRGAWPLKAIDLDCNHIPDAAMTLAVMALYADGTTVLRNIASWRVKETDRIAAMAC 360

Query: 351 ELRKVGAEVEEGEDYIRITPPL---TLQFAEIGTYNDHRMAMCFSLVAL--SDTPVTILD 405
           EL+K+GA VEEG DY++ITPP      + A I TY+DHR+AMCFSL A   ++ PV ILD
Sbjct: 361 ELQKLGATVEEGADYLKITPPAQAGAWKPAVIHTYDDHRIAMCFSLAAFNPAELPVRILD 420

Query: 406 PKCTAKTFPDYFGQLARIS 424
           PKC AKTFPDYF  L  ++
Sbjct: 421 PKCVAKTFPDYFEALFSVA 439


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: 717
Number of extensions: 38
Number of successful extensions: 10
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: 667
Length adjustment: 35
Effective length of query: 392
Effective length of database: 632
Effective search space:   247744
Effective search space used:   247744
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: 52 (24.6 bits)

Align candidate WP_011802174.1 PNAP_RS13960 (bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidylate kinase)
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.25713.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-139  451.0   0.0   2.8e-139  450.4   0.0    1.2  1  lcl|NCBI__GCF_000015505.1:WP_011802174.1  PNAP_RS13960 bifunctional 3-phos


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011802174.1  PNAP_RS13960 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cyti
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.4   0.0  2.8e-139  2.8e-139       1     412 [.      17     438 ..      17     441 .. 0.95

  Alignments for each domain:
  == domain 1  score: 450.4 bits;  conditional E-value: 2.8e-139
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg.lke 68 
                                               g + +pgsKSis+R+lllaaL++g+t+v++lL s+Dt ++l al++lG +v ++++++vi g gg l +
  lcl|NCBI__GCF_000015505.1:WP_011802174.1  17 GTVCLPGSKSISNRVLLLAALSHGQTTVHDLLASDDTAVMLTALEQLGCTVVQSGNTAVIGGLGGqLVQ 85 
                                               67889***********************************************99**********98888 PP

                                 TIGR01356  69 peaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlais 137
                                                +a+l +gn+Gt++R+lt++lal++ge++l+g +++++RPi++lv+aLr+lg+ i++  +eg++Pl+++
  lcl|NCBI__GCF_000015505.1:WP_011802174.1  86 RKAALFMGNAGTAMRPLTAALALLGGEFELSGVPRMHERPIGDLVDALRQLGCAIDYLGNEGFPPLRLR 154
                                               99******************************************************************* PP

                                 TIGR01356 138 gp.lkg.givelsgsaSsQyksalllaap.lalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                                + lk+ + ++++g++SsQ+++all+a p +a+qa  +e+vg +lisrpyieitL+llk+fg++ve+e 
  lcl|NCBI__GCF_000015505.1:WP_011802174.1 155 PGvLKLdDAIRVRGDVSSQFLTALLMALPlVAQQAIRIEVVG-ELISRPYIEITLNLLKRFGIQVEREG 222
                                               9988889**********************8889999999999.*************************9 PP

                                 TIGR01356 204 erkivvkggqkykqk.evevegDaSsAafflaaaaitge.....evtvenlgenstqgdkaiiivLeem 266
                                                ++++++ g +y+++ e++ve+DaSsA++f+a++ai+       ++++ ++g++s qgd ++i+  + m
  lcl|NCBI__GCF_000015505.1:WP_011802174.1 223 WQRFTIPAGSQYQSPgEIHVEADASSASYFIALGAIAACakginDIKIMGVGADSIQGDIRFIEAARMM 291
                                               9********9988888*******************9864334779************************ PP

                                 TIGR01356 267 Gadveveeqrdveveg.asklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaa 334
                                               Ga+++ + + ++++ + a  lk+++   d+++++D+++tlav+a++A+g+t+++ni+++RvkE+dRiaa
  lcl|NCBI__GCF_000015505.1:WP_011802174.1 292 GAKIDSTPN-SLQISRgAWPLKAID--LDCNHIPDAAMTLAVMALYADGTTVLRNIASWRVKETDRIAA 357
                                               *********.699886577777777..****************************************** PP

                                 TIGR01356 335 iaeeLeklGveveeledgllieGkk..kelkgavvdtydDHRiamalavlglaae.geveiedaecvak 400
                                               +a eL+klG++vee++d+l+i++ +    +k+av++tydDHRiam+++++++  +  +v+i d++cvak
  lcl|NCBI__GCF_000015505.1:WP_011802174.1 358 MACELQKLGATVEEGADYLKITPPAqaGAWKPAVIHTYDDHRIAMCFSLAAFNPAeLPVRILDPKCVAK 426
                                               ***********************999999***********************98758************ PP

                                 TIGR01356 401 sfPeFfevleql 412
                                               +fP++fe+l ++
  lcl|NCBI__GCF_000015505.1:WP_011802174.1 427 TFPDYFEALFSV 438
                                               *******98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (667 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: 00:00:00.02
# Mc/sec: 13.48
//
[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