Alignments for a candidate for aroA in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Dechlorosoma suillum PS

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate Dsui_1942 Dsui_1942 cytidylate kinase/3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q9KRB0
         (426 letters)



>FitnessBrowser__PS:Dsui_1942
          Length = 644

 Score =  476 bits (1224), Expect = e-138
 Identities = 254/430 (59%), Positives = 310/430 (72%), Gaps = 7/430 (1%)

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

Query: 61  GVNYRLSADKTTCEVEGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPR 120
           GV    S       + G+G  F   +  ELFLGNAGTA RPL AAL L  G YVL G  R
Sbjct: 61  GVGVE-SLGGEAYRITGVGGPFPVKEA-ELFLGNAGTAFRPLTAALALAGGHYVLKGVAR 118

Query: 121 MKERPIGHLVDALRQAGAQIEYLEQENFPPLRIQGTGLQAGTVT-IDGSISSQFLTAFLM 179
           M ERPIG LVD LRQ GA++ YL  + FPPL I    ++AG V  + G +SSQFLTA LM
Sbjct: 119 MHERPIGDLVDGLRQLGAEVRYLGNDGFPPLEIFPASIRAGGVLQVRGDVSSQFLTALLM 178

Query: 180 SAPLAQGKVTIKIVGELVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPGQFL 239
           + PL   +  +++VGEL+SKPYI+ITL  M +FGV+V    +Q FV+PAG  YVSPG   
Sbjct: 179 ALPLTGVETRVEVVGELISKPYIEITLATMARFGVEVQREGWQAFVVPAGVRYVSPGTVY 238

Query: 240 VEGDASSASYFLAAAAIKGGEVKVTGIGKNSIQGDIQFADALEKMGAQIEWGDDYVIAR- 298
           VEGDASSASYFLAA AI GG ++V G+GK+SIQGD++FA+AL  MGA+IE G +++ AR 
Sbjct: 239 VEGDASSASYFLAAGAIGGGPLRVEGVGKDSIQGDVRFAEALALMGARIEMGPNWIEARA 298

Query: 299 --RGELNAVDLDFNHIPDAAMTIATTALFAKGTTAIRNVYNWRVKETDRLAAMATELRKV 356
              G+L A+DLD NHIPDAAMT+AT ALFA+GTT +RN+ +WRVKETDR+AAMATEL+K+
Sbjct: 299 PASGKLQAIDLDCNHIPDAAMTLATAALFAEGTTVLRNIASWRVKETDRIAAMATELQKL 358

Query: 357 GATVEEGEDFIVITPPTKLIHAAIDTYDDHRMAMCFSLVALSDTPVTINDPKCTSKTFPD 416
           GA VEEG D++ +TP   L  AAIDTYDDHRMAMCFSL A + TP+ INDPKC +KTFPD
Sbjct: 359 GAVVEEGPDYLKVTPVPALKPAAIDTYDDHRMAMCFSLAAFA-TPLRINDPKCVAKTFPD 417

Query: 417 YFDKFAQLSR 426
           YF++ A ++R
Sbjct: 418 YFERLATVTR 427


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: 669
Number of extensions: 31
Number of successful extensions: 7
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: 644
Length adjustment: 35
Effective length of query: 391
Effective length of database: 609
Effective search space:   238119
Effective search space used:   238119
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 Dsui_1942 Dsui_1942 (cytidylate kinase/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.1228.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.5e-143  464.5   0.0   1.9e-143  464.2   0.0    1.1  1  lcl|FitnessBrowser__PS:Dsui_1942  Dsui_1942 cytidylate kinase/3-ph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1942  Dsui_1942 cytidylate kinase/3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.2   0.0  1.9e-143  1.9e-143       1     413 [.      14     426 ..      14     428 .. 0.96

  Alignments for each domain:
  == domain 1  score: 464.2 bits;  conditional E-value: 1.9e-143
                         TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg.lkepeaeldl 75 
                                       g +++pgsKSis+R+lllaaLaeg t+v++lL+s+Dt+ +leal++lG+ ve  ++e   i+gvgg +  +eael l
  lcl|FitnessBrowser__PS:Dsui_1942  14 GTVRLPGSKSISNRVLLLAALAEGVTEVRDLLHSDDTERMLEALQQLGVGVEsLGGEAYRITGVGGpFPVKEAELFL 90 
                                       789*************************************************666**********9889999***** PP

                         TIGR01356  76 gnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.lkg.givelsgs 150
                                       gn+Gt++R+lt++lala+g++vl+g  ++++RPi++lv+ Lr+lgae+++  ++g++Pl+i    +++ g+ +++g+
  lcl|FitnessBrowser__PS:Dsui_1942  91 GNAGTAFRPLTAALALAGGHYVLKGVARMHERPIGDLVDGLRQLGAEVRYLGNDGFPPLEIFPAsIRAgGVLQVRGD 167
                                       *************************************************************87776655******** PP

                         TIGR01356 151 aSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqkykqk.evevegDa 226
                                       +SsQ+++all+a pl+  +  +e+vg +lis+pyieitL+++++fgvev++e  + +vv+ g  y ++ +v+vegDa
  lcl|FitnessBrowser__PS:Dsui_1942 168 VSSQFLTALLMALPLTGVETRVEVVG-ELISKPYIEITLATMARFGVEVQREGWQAFVVPAGVRYVSPgTVYVEGDA 243
                                       **************999889999999.*************************99********9976666******** PP

                         TIGR01356 227 SsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadveveeqrdvevegasklkgvkv.didvdsliDel 302
                                       SsA++flaa+ai g+ ++ve++g++s qgd+++++ L  mGa++e+  + ++e + + + k +++ d d+++++D++
  lcl|FitnessBrowser__PS:Dsui_1942 244 SSASYFLAAGAIGGGPLRVEGVGKDSIQGDVRFAEALALMGARIEMGPN-WIEARAPASGK-LQAiDLDCNHIPDAA 318
                                       *************************************************.9****966665.44448********** PP

                         TIGR01356 303 ptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamal 379
                                       +tla++a+fAeg+t+++ni+++RvkE+dRiaa+a+eL+klG+ vee++d+l++++    lk+a +dtydDHR+am++
  lcl|FitnessBrowser__PS:Dsui_1942 319 MTLATAALFAEGTTVLRNIASWRVKETDRIAAMATELQKLGAVVEEGPDYLKVTPV-PALKPAAIDTYDDHRMAMCF 394
                                       ********************************************************.6******************* PP

                         TIGR01356 380 avlglaaegeveiedaecvaksfPeFfevleqlg 413
                                       +++++a    ++i+d++cvak+fP++fe l++++
  lcl|FitnessBrowser__PS:Dsui_1942 395 SLAAFATP--LRINDPKCVAKTFPDYFERLATVT 426
                                       *****995..*******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (644 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: 00:00:00.01
# Mc/sec: 15.53
//
[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