Alignments for a candidate for aroA in Thauera aminoaromatica S2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Thauera aminoaromatica S2

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_040828306.1 C665_RS02150 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidylate kinase

Query= BRENDA::Q9KRB0
         (426 letters)



>NCBI__GCF_000310185.1:WP_040828306.1
          Length = 653

 Score =  471 bits (1211), Expect = e-137
 Identities = 250/430 (58%), Positives = 307/430 (71%), Gaps = 5/430 (1%)

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

Query: 61  GVNYRLSADKTTCEVEGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPR 120
           GV++R   D     V G+G  F   +  +LFLGNAGTA RPL AAL L  G+Y L+G PR
Sbjct: 61  GVDWRREGDSLNYRVCGVGGPF-PVKTGDLFLGNAGTAFRPLTAALALSGGEYRLSGVPR 119

Query: 121 MKERPIGHLVDALRQAGAQIEYLEQENFPPLRIQGTGLQ-AGTVTIDGSISSQFLTAFLM 179
           M ERPIG LVDALRQ GA I     E +PPL ++   ++  G V + G +SSQFLTA LM
Sbjct: 120 MHERPIGDLVDALRQLGADITCTANEGYPPLHLKPATIRPGGVVRVRGDVSSQFLTALLM 179

Query: 180 SAPLAQGKVTIKIVGELVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPGQFL 239
           + PL   + TI++VGEL+SKPYI ITL +M +FGVQV    ++ FV+P G  Y SPG   
Sbjct: 180 ALPLTGVETTIEVVGELISKPYIRITLELMARFGVQVGQQGWERFVVPGGARYRSPGTVF 239

Query: 240 VEGDASSASYFLAAAAIKGGEVKVTGIGKNSIQGDIQFADALEKMGAQIEWGDDYVIARR 299
           VEGDASSASYFLAA AI GG V+V G+G+ SIQGD++FA+ALE++GA+I  GD+++ A  
Sbjct: 240 VEGDASSASYFLAAGAIGGGPVRVEGVGRTSIQGDVRFAEALEQLGARITLGDNWIEAAA 299

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

Query: 357 GATVEEGEDFIVITPPTKLIHAAIDTYDDHRMAMCFSLVALSDTPVTINDPKCTSKTFPD 416
           GA VEEG D++V+  P +L  AAIDTYDDHRMAMCFSL +L    V INDPKC +KTFP 
Sbjct: 360 GAEVEEGADYLVVQRPPRLQPAAIDTYDDHRMAMCFSLASLGGCRVRINDPKCVNKTFPG 419

Query: 417 YFDKFAQLSR 426
           YF+ FAQ++R
Sbjct: 420 YFEAFAQVAR 429


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: 690
Number of extensions: 28
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: 653
Length adjustment: 35
Effective length of query: 391
Effective length of database: 618
Effective search space:   241638
Effective search space used:   241638
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_040828306.1 C665_RS02150 (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.8703.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     7e-141  455.7   0.0   9.2e-141  455.3   0.0    1.1  1  lcl|NCBI__GCF_000310185.1:WP_040828306.1  C665_RS02150 bifunctional 3-phos


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000310185.1:WP_040828306.1  C665_RS02150 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cyti
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.3   0.0  9.2e-141  9.2e-141       1     412 [.      14     427 ..      14     429 .. 0.95

  Alignments for each domain:
  == domain 1  score: 455.3 bits;  conditional E-value: 9.2e-141
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelv..iegvgg.l 66 
                                               g++++pgsKSis+R+lllaaLaeget +++lL s+D++ +lealr+lG++ ++e+++l   + gvgg +
  lcl|NCBI__GCF_000310185.1:WP_040828306.1  14 GSVRLPGSKSISNRVLLLAALAEGETDIRDLLLSDDVERMLEALRALGVDWRREGDSLNyrVCGVGGpF 82 
                                               789*************************************************99887652277777777 PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                                 ++  l lgn+Gt++R+lt++lal++ge+ l+g +++++RPi++lv+aLr+lga+i ++ +eg++Pl+
  lcl|NCBI__GCF_000310185.1:WP_040828306.1  83 PVKTGDLFLGNAGTAFRPLTAALALSGGEYRLSGVPRMHERPIGDLVDALRQLGADITCTANEGYPPLH 151
                                               78889**************************************************************** PP

                                 TIGR01356 136 isgp..lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveee 202
                                               ++     +gg+v+++g++SsQ+++all+a pl+  + t+e+vg +lis+pyi+itL+l+++fgv+v ++
  lcl|NCBI__GCF_000310185.1:WP_040828306.1 152 LKPAtiRPGGVVRVRGDVSSQFLTALLMALPLTGVETTIEVVG-ELISKPYIRITLELMARFGVQVGQQ 219
                                               **9886777**********************999999999999.************************9 PP

                                 TIGR01356 203 derkivvkggqkykqk.evevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadv 270
                                                 +++vv+gg+ y+++ +v vegDaSsA++flaa+ai g+ v+ve++g +s qgd+++++ Le++Ga++
  lcl|NCBI__GCF_000310185.1:WP_040828306.1 220 GWERFVVPGGARYRSPgTVFVEGDASSASYFLAAGAIGGGPVRVEGVGRTSIQGDVRFAEALEQLGARI 288
                                               99**********99888**************************************************** PP

                                 TIGR01356 271 eveeqrdvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaee 338
                                               ++ ++ ++e   +     +k+ d d+++++D+++tlav+a+fA+g++r++ni+++RvkE+dRiaa+a+e
  lcl|NCBI__GCF_000310185.1:WP_040828306.1 289 TLGDN-WIEAAAPA-GGVLKAfDLDLNHIPDAAMTLAVAALFADGPCRLRNIASWRVKETDRIAAMATE 355
                                               *****.9**99654.44678888********************************************** PP

                                 TIGR01356 339 LeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfe 407
                                               L+klG+evee++d+l+++    +l++a +dtydDHR+am++++++l    +v+i+d++cv+k+fP +fe
  lcl|NCBI__GCF_000310185.1:WP_040828306.1 356 LRKLGAEVEEGADYLVVQRP-PRLQPAAIDTYDDHRMAMCFSLASLGGC-RVRINDPKCVNKTFPGYFE 422
                                               *****************999.6*************************97.9****************** PP

                                 TIGR01356 408 vleql 412
                                               + +q+
  lcl|NCBI__GCF_000310185.1:WP_040828306.1 423 AFAQV 427
                                               99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (653 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: 00:00:00.01
# Mc/sec: 14.62
//
[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