Alignments for a candidate for aroA in Chlorobium limicola DSM 245

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Chlorobium limicola DSM 245

Align 3-phosphoshikimate 1-carboxyvinyltransferase; EC 2.5.1.19; 5-enolpyruvylshikimate-3-phosphate synthase; EPSP synthase; EPSPS (uncharacterized)
to candidate WP_012467016.1 CLIM_RS10675 3-phosphoshikimate 1-carboxyvinyltransferase

Query= curated2:Q3B659
         (433 letters)



>NCBI__GCF_000020465.1:WP_012467016.1
          Length = 434

 Score =  578 bits (1491), Expect = e-170
 Identities = 299/433 (69%), Positives = 344/433 (79%), Gaps = 1/433 (0%)

Query: 1   MSVFKGEVTSLPPDKSISHRAALIASLSDGETEIMNFSAGFDNQSTLGVLQACGIPVRQE 60
           M+VFKGEVT+LPPDKSISHRAALI SLS+G TEI NFSAGFDNQSTLGVL   GI V Q 
Sbjct: 1   MAVFKGEVTALPPDKSISHRAALIGSLSEGVTEITNFSAGFDNQSTLGVLHDAGIEVSQH 60

Query: 61  EVPGPWGTAILRVVIKSKGLWSLTPPSAPLQCNNSGSTMRMFSGILAGQPFQSELVGDAS 120
           E+ G +G  I +V+I S+GLWS T P  PL CNNSGSTMRMF+GILA QPF+SELVGD+S
Sbjct: 61  EIDGAYGRRIRKVIISSRGLWSFTAPEKPLMCNNSGSTMRMFAGILAAQPFESELVGDSS 120

Query: 121 LLKRPMRRIADPLIQMGAGVSLSPIGTAPVVITGSKDLHAIDYRLPVASAQVKSLVAFAG 180
           L+KRPM+R+ADPL QMGAGV LSP GTAPV I G++DL  ++YRLPV SAQVKSLV FA 
Sbjct: 121 LMKRPMKRVADPLRQMGAGVDLSPAGTAPVRIRGTRDLTPLEYRLPVPSAQVKSLVTFAA 180

Query: 181 LHAEGETRIYEPLSSRNHTELMLGLEPRVENE-ERVIVVPGRRQREARPFQIPADPSAAC 239
           LHA+GETRI E + SRNHTELMLGLE     + ERVIV+PGR+   AR F IPADPSAAC
Sbjct: 181 LHADGETRIIESIRSRNHTELMLGLETIDRPDGERVIVIPGRKTIVARSFYIPADPSAAC 240

Query: 240 FIVSLGLLARGSEIMIRDVCLNPTRAAFLDILIRAGAAVTIENRRTVGGESIGDILVEGT 299
           FIV+LGLL   SEI+IRDVCLNPTR  F+ +L  AGA +TIEN R +GGE+IGDILV  T
Sbjct: 241 FIVALGLLGSNSEIIIRDVCLNPTRVEFIPLLTGAGADITIENSRIIGGETIGDILVRST 300

Query: 300 RDMEPLVISDPQEVAIAIDELPMLGVLSAFATERFELMNAGELRTKESDRIEALALNLER 359
           R ++PLVIS+P  VA  IDELPML VLSAF++  FEL NA ELRTKESDRI A+ +NLER
Sbjct: 301 RTLKPLVISNPTVVAGVIDELPMLSVLSAFSSGEFELHNAEELRTKESDRINAIVVNLER 360

Query: 360 LGFVCHQEPGGLSVTGRKGRPSGPVVVECFDDHRIAMSFAVASKACGEDIELSDREVAGV 419
           LGF C Q P G  V GR+ RP G V V CFDDHRIAMSFAVA++A GE I LSD +V GV
Sbjct: 361 LGFDCEQYPDGFRVIGRRCRPVGQVTVACFDDHRIAMSFAVAARATGEGIALSDSDVVGV 420

Query: 420 SFPNFFSLLDALE 432
           SFPNFF +++ L+
Sbjct: 421 SFPNFFEIIENLK 433


Lambda     K      H
   0.319    0.136    0.391 

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: 599
Number of extensions: 19
Number of successful extensions: 2
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: 433
Length of database: 434
Length adjustment: 32
Effective length of query: 401
Effective length of database: 402
Effective search space:   161202
Effective search space used:   161202
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: 51 (24.3 bits)

Align candidate WP_012467016.1 CLIM_RS10675 (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.3496.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-103  333.3   0.0   1.2e-103  333.1   0.0    1.0  1  lcl|NCBI__GCF_000020465.1:WP_012467016.1  CLIM_RS10675 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020465.1:WP_012467016.1  CLIM_RS10675 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.1   0.0  1.2e-103  1.2e-103       4     413 ..      10     433 ..       6     434 .] 0.92

  Alignments for each domain:
  == domain 1  score: 333.1 bits;  conditional E-value: 1.2e-103
                                 TIGR01356   4 kipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee.ke.......elviegv 63 
                                               ++p++KSishRa l+++L+eg t++tn+  + D ++tl +l++ G++v+ +e ++       +++i   
  lcl|NCBI__GCF_000020465.1:WP_012467016.1  10 ALPPDKSISHRAALIGSLSEGVTEITNFSAGFDNQSTLGVLHDAGIEVSqHEiDGaygrrirKVIISSR 78 
                                               57**********************************************943333222222224556665 PP

                                 TIGR01356  64 gg..lkepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeeg 130
                                               g   +  pe+ l ++nsG t+R+  g+la++++e++l gd sl kRP++r+ ++Lr++ga ++ +  +g
  lcl|NCBI__GCF_000020465.1:WP_012467016.1  79 GLwsFTAPEKPLMCNNSGSTMRMFAGILAAQPFESELVGDSSLMKRPMKRVADPLRQMGAGVDLSP-AG 146
                                               557788888******************************************************766.79 PP

                                 TIGR01356 131 slPlaisgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgve 198
                                               ++P++i+g+  + +  +  +  S+Q+ks + +aa   l+a++++ ++e++ sr+++e++L l       
  lcl|NCBI__GCF_000020465.1:WP_012467016.1 147 TAPVRIRGTRDLtPLEYRLPVPSAQVKSLVTFAA---LHADGETRIIESIRSRNHTELMLGLET----- 207
                                               *********88889********************...89999999999***********97644..... PP

                                 TIGR01356 199 veeede.rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLee 265
                                               +++ d+ r iv++g +++  +++++++D+S+A+f++a++++ ++ e+ ++++  n+t+ +  +i +L  
  lcl|NCBI__GCF_000020465.1:WP_012467016.1 208 IDRPDGeRVIVIPGRKTIVARSFYIPADPSAACFIVALGLLGSNsEIIIRDVCLNPTRVE--FIPLLTG 274
                                               5666663677777777788889*********************99***************..777**** PP

                                 TIGR01356 266 mGadveveeqr........dvevegasklkgvkv..didvdsliDelptlavlaafAegetriknieel 324
                                                Gad+++e++r        d+ v++++ lk++ +  +  v+ +iDelp+l+vl+af +ge +++n+eel
  lcl|NCBI__GCF_000020465.1:WP_012467016.1 275 AGADITIENSRiiggetigDILVRSTRTLKPLVIsnPTVVAGVIDELPMLSVLSAFSSGEFELHNAEEL 343
                                               *********************************995699****************************** PP

                                 TIGR01356 325 RvkEsdRiaaiaeeLeklGveveeledgllieGkk.kelkgavvdtydDHRiamalavlglaaegevei 392
                                               R kEsdRi+ai+ +Le+lG ++e+ +dg+ + G++ + + + +v ++dDHRiam++av++ a  +++ +
  lcl|NCBI__GCF_000020465.1:WP_012467016.1 344 RTKESDRINAIVVNLERLGFDCEQYPDGFRVIGRRcRPVGQVTVACFDDHRIAMSFAVAARATGEGIAL 412
                                               ***********************************888999**************************** PP

                                 TIGR01356 393 edaecvaksfPeFfevleqlg 413
                                                d+ +v +sfP+Ffe +e+l+
  lcl|NCBI__GCF_000020465.1:WP_012467016.1 413 SDSDVVGVSFPNFFEIIENLK 433
                                               *****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (434 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: 10.60
//
[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