Alignments for a candidate for aroA in Azoarcus sp. BH72

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Azoarcus sp. BH72

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_041642367.1 AZO_RS05430 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidylate kinase

Query= BRENDA::Q9KRB0
         (426 letters)



>NCBI__GCF_000061505.1:WP_041642367.1
          Length = 651

 Score =  475 bits (1223), Expect = e-138
 Identities = 253/429 (58%), Positives = 305/429 (71%), Gaps = 5/429 (1%)

Query: 1   MESLTLQPIELISGEVNLPGSKSVSNRALLLAALASGTTRLTNLLDSDDIRHMLNALTKL 60
           ME L L P+    G+V LPGSKS+SNR+LLLAALA G T + +LL SDD+  ML AL  L
Sbjct: 1   MEFLDLPPMLAARGQVRLPGSKSISNRSLLLAALAEGETDIRDLLASDDVERMLEALQAL 60

Query: 61  GVNYRLSADKTTCEVEGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPR 120
           GV +          V G+G  F   +  +LFLGNAGTA RPL AAL L  GDY L+G  R
Sbjct: 61  GVRWSREEGTDNYRVHGVGGPFPVKKG-DLFLGNAGTAFRPLTAALALSGGDYRLSGVAR 119

Query: 121 MKERPIGHLVDALRQAGAQIEYLEQENFPPLRIQGTGLQAGTVT-IDGSISSQFLTAFLM 179
           M ERPIG LVDALRQAGA IEY+  E FPPL I+   ++ G V  + G +SSQFLTA LM
Sbjct: 120 MHERPIGDLVDALRQAGADIEYVGNEGFPPLHIRPATIRPGGVLKVRGDVSSQFLTALLM 179

Query: 180 SAPLAQGKVTIKIVGELVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPGQFL 239
           + PL   + TI++VGEL+SKPYI ITL +M +FGV V+  D+Q F +P G  Y SPG   
Sbjct: 180 ALPLTGVETTIEVVGELISKPYIAITLDLMARFGVDVVREDWQRFTVPGGARYRSPGVLY 239

Query: 240 VEGDASSASYFLAAAAIKGGEVKVTGIGKNSIQGDIQFADALEKMGAQIEWGDDYVIARR 299
           VEGDASSASYFLAA AI GG V+V G+G++SIQGD++FADAL ++GA I  GD+++ A  
Sbjct: 240 VEGDASSASYFLAAGAIGGGPVRVEGVGRDSIQGDVRFADALAQLGAVITVGDNWIEAAA 299

Query: 300 ---GELNAVDLDFNHIPDAAMTIATTALFAKGTTAIRNVYNWRVKETDRLAAMATELRKV 356
              G L A DLD NHIPDAAMT+A  ALFA G   +RN+ +WRVKETDR+AAMATELRKV
Sbjct: 300 PAGGRLRAFDLDLNHIPDAAMTLAVAALFADGPCTLRNIASWRVKETDRIAAMATELRKV 359

Query: 357 GATVEEGEDFIVITPPTKLIHAAIDTYDDHRMAMCFSLVALSDTPVTINDPKCTSKTFPD 416
           GA VEEG D++ I PP  L  AAIDTYDDHRMAMCFSLV+L    V INDP+C +KTFP 
Sbjct: 360 GAEVEEGADYLRIMPPAVLRPAAIDTYDDHRMAMCFSLVSLGGCRVRINDPRCVNKTFPS 419

Query: 417 YFDKFAQLS 425
           YF+ FA ++
Sbjct: 420 YFEAFATVA 428


Lambda     K      H
   0.318    0.135    0.384 

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: 687
Number of extensions: 36
Number of successful extensions: 6
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: 651
Length adjustment: 35
Effective length of query: 391
Effective length of database: 616
Effective search space:   240856
Effective search space used:   240856
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: 52 (24.6 bits)

Align candidate WP_041642367.1 AZO_RS05430 (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.30654.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-140  453.7   0.0   3.5e-140  453.4   0.0    1.1  1  lcl|NCBI__GCF_000061505.1:WP_041642367.1  AZO_RS05430 bifunctional 3-phosp


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000061505.1:WP_041642367.1  AZO_RS05430 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.4   0.0  3.5e-140  3.5e-140       1     413 [.      14     428 ..      14     430 .. 0.96

  Alignments for each domain:
  == domain 1  score: 453.4 bits;  conditional E-value: 3.5e-140
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee.keelviegvgg.l 66 
                                               g++++pgsKSis+R+lllaaLaeget +++lL s+D++ +leal++lG++ + ee  ++  ++gvgg +
  lcl|NCBI__GCF_000061505.1:WP_041642367.1  14 GQVRLPGSKSISNRSLLLAALAEGETDIRDLLASDDVERMLEALQALGVRWSrEEgTDNYRVHGVGGpF 82 
                                               789************************************************9655799********988 PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                                 ++  l lgn+Gt++R+lt++lal++g++ l+g  ++++RPi++lv+aLr+ ga+ie+  +eg++Pl+
  lcl|NCBI__GCF_000061505.1:WP_041642367.1  83 PVKKGDLFLGNAGTAFRPLTAALALSGGDYRLSGVARMHERPIGDLVDALRQAGADIEYVGNEGFPPLH 151
                                               8888***************************************************************** PP

                                 TIGR01356 136 isgp..lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveee 202
                                               i+     +gg+ +++g++SsQ+++all+a pl+  + t+e+vg +lis+pyi itL+l+++fgv+v +e
  lcl|NCBI__GCF_000061505.1:WP_041642367.1 152 IRPAtiRPGGVLKVRGDVSSQFLTALLMALPLTGVETTIEVVG-ELISKPYIAITLDLMARFGVDVVRE 219
                                               **9886777**********************999999999999.************************* PP

                                 TIGR01356 203 derkivvkggqkykqk.evevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadv 270
                                               d ++++v+gg+ y+++  ++vegDaSsA++flaa+ai g+ v+ve++g +s qgd+++++ L ++Ga +
  lcl|NCBI__GCF_000061505.1:WP_041642367.1 220 DWQRFTVPGGARYRSPgVLYVEGDASSASYFLAAGAIGGGPVRVEGVGRDSIQGDVRFADALAQLGAVI 288
                                               99**********9988899************************************************** PP

                                 TIGR01356 271 eveeqrdvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaee 338
                                               +v ++ ++e   + + + +++ d d+++++D+++tlav+a+fA+g+++++ni+++RvkE+dRiaa+a+e
  lcl|NCBI__GCF_000061505.1:WP_041642367.1 289 TVGDN-WIEAAAPAGGR-LRAfDLDLNHIPDAAMTLAVAALFADGPCTLRNIASWRVKETDRIAAMATE 355
                                               *****.9****866664.66668********************************************** PP

                                 TIGR01356 339 LeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfe 407
                                               L+k+G+evee++d+l i +  + l++a +dtydDHR+am++++++l    +v+i+d+ cv+k+fP++fe
  lcl|NCBI__GCF_000061505.1:WP_041642367.1 356 LRKVGAEVEEGADYLRIMPP-AVLRPAAIDTYDDHRMAMCFSLVSLGGC-RVRINDPRCVNKTFPSYFE 422
                                               ********************.6*************************97.9****************** PP

                                 TIGR01356 408 vleqlg 413
                                               + +++ 
  lcl|NCBI__GCF_000061505.1:WP_041642367.1 423 AFATVA 428
                                               998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (651 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: 15.58
//
[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