Alignments for a candidate for aroA in Desulfobacca acetoxidans DSM 11109

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Desulfobacca acetoxidans DSM 11109

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_013705642.1 DESAC_RS03210 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q8YMB5
         (425 letters)



>NCBI__GCF_000195295.1:WP_013705642.1
          Length = 432

 Score =  350 bits (899), Expect = e-101
 Identities = 186/413 (45%), Positives = 268/413 (64%), Gaps = 3/413 (0%)

Query: 11  RPVDATVEIPGSKSITNRALLVAALAQGDSTLENALFSEDSEYFAKCVEQLGIPITLHPH 70
           + ++A + +PGSKS ++RAL+ A LA+G S+L N L ++D+   A+ +EQLG+ IT    
Sbjct: 10  KAMEAVITLPGSKSFSHRALIAAGLARGSSSLRNLLRADDTLMTARALEQLGVRITWQEK 69

Query: 71  LAQIQVSGKGGDIPAKQADLFVGLAGTAARFITALVALGNGEYRLDGVPRMRERPMGDLV 130
             +  + G GG +      +++G +GT+ RF+TA+ ALGNG Y L G PR+ +RP+ DL+
Sbjct: 70  --ECLLEGAGGRLKVPTEPIYLGDSGTSMRFLTAVAALGNGRYVLTGSPRLCQRPIQDLL 127

Query: 131 TVLQNSGITINFEGNSGFMPYTIYGQQFAGGHFRLKANQTSQQLSALLMIAPYAQQDTTI 190
             L   G+  + E ++G  P  I  +  AGG  R+    +SQ LSALL+I+P+A +D  I
Sbjct: 128 DALTLLGVVAHCENHNGCPPVIIQARGLAGGESRVSGGISSQFLSALLLISPFAARDVEI 187

Query: 191 EVEGTLVSQSYVKMTCRLMADFGVDVTQTDDNQFHIKAGQRYQARHYTIEPDASNASYFF 250
           EV G LVS+ YV +T  +M  FG+   +     F + AGQRYQAR Y +E DAS+ASYF 
Sbjct: 188 EVVGELVSRPYVDITLSVMEAFGIAYYRRGYQNFCVPAGQRYQARDYEVEGDASSASYFL 247

Query: 251 AAAAVTGGRVRVNHLTKQSCQGDILWLNVLEQMGCQVIEGADYTEVIGPEQLQGIDIDMN 310
            AAA+TGGR+ + +L  QSCQGDI +L VL+QMGCQV E      V+   QLQ I I+M 
Sbjct: 248 GAAALTGGRITLTNLNPQSCQGDIGFLEVLQQMGCQV-EPTGSGVVLRGRQLQAIRINMA 306

Query: 311 DMSDLVQTLGAIAPYASSPVIIRNVEHIRYKETERIRAVVTELRRLGVKVEEFADGMKIE 370
            M DLV TL  +A YA    +I  V H+R+KE++R++AV TEL ++G+ V +  DG+ I+
Sbjct: 307 HMPDLVPTLAVLAAYAQGETVITGVPHLRHKESDRLQAVATELAKMGITVNQTKDGLIIQ 366

Query: 371 PTPITPAAIETYHDHRMAMAFAVTGLKTPGIVIQDPGCTAKTFPDYFTRFFKM 423
                   IETY+DHR+AM+FA+ GLKTPG++I +P C AK+FPD++  F K+
Sbjct: 367 GGKPRGVVIETYNDHRIAMSFALAGLKTPGVMIANPDCVAKSFPDFWDYFAKL 419



 Score = 32.7 bits (73), Expect = 2e-05
 Identities = 38/142 (26%), Positives = 56/142 (39%), Gaps = 13/142 (9%)

Query: 6   IPALNRPVDATVEIPGSKSITNRALLVAALAQGDSTLENALFSEDSEYFAKCVEQLGIPI 65
           +PA  R      E+ G  S  +  L  AAL  G  TL N   +  S     C   +G   
Sbjct: 223 VPAGQRYQARDYEVEGDASSASYFLGAAALTGGRITLTN--LNPQS-----CQGDIGFLE 275

Query: 66  TLHPHLAQIQVSGKGGDIPAKQAD-LFVGLA--GTAARFITALVALGNGEYRLDGVPRMR 122
            L     Q++ +G G  +  +Q   + + +A        +  L A   GE  + GVP +R
Sbjct: 276 VLQQMGCQVEPTGSGVVLRGRQLQAIRINMAHMPDLVPTLAVLAAYAQGETVITGVPHLR 335

Query: 123 ERPMGDL---VTVLQNSGITIN 141
            +    L    T L   GIT+N
Sbjct: 336 HKESDRLQAVATELAKMGITVN 357


Lambda     K      H
   0.320    0.136    0.393 

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: 445
Number of extensions: 16
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 425
Length of database: 432
Length adjustment: 32
Effective length of query: 393
Effective length of database: 400
Effective search space:   157200
Effective search space used:   157200
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: 51 (24.3 bits)

Align candidate WP_013705642.1 DESAC_RS03210 (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.11572.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     5e-142  459.5   0.0   5.7e-142  459.3   0.0    1.0  1  lcl|NCBI__GCF_000195295.1:WP_013705642.1  DESAC_RS03210 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195295.1:WP_013705642.1  DESAC_RS03210 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.3   0.0  5.7e-142  5.7e-142       3     414 ..      16     421 ..      14     422 .. 0.98

  Alignments for each domain:
  == domain 1  score: 459.3 bits;  conditional E-value: 5.7e-142
                                 TIGR01356   3 ikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg.lkepe 70 
                                               i++pgsKS+shRal++a+La+g++ ++nlL+++Dtl+t +al++lG++++ +++e+  eg gg lk p+
  lcl|NCBI__GCF_000195295.1:WP_013705642.1  16 ITLPGSKSFSHRALIAAGLARGSSSLRNLLRADDTLMTARALEQLGVRITWQEKECLLEGAGGrLKVPT 84 
                                               89************************************************888899****9999***** PP

                                 TIGR01356  71 aeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp 139
                                               + ++lg+sGt++R+lt+v+al +g +vltg+++l +RPi++l++aL  lg+  ++++++g++P+ i++ 
  lcl|NCBI__GCF_000195295.1:WP_013705642.1  85 EPIYLGDSGTSMRFLTAVAALGNGRYVLTGSPRLCQRPIQDLLDALTLLGVVAHCENHNGCPPVIIQAR 153
                                               ********************************************************************9 PP

                                 TIGR01356 140 .lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederki 207
                                                l gg +++sg +SsQ++salll  p a ++v++e+vg +l+srpy++itL ++++fg+   +   +++
  lcl|NCBI__GCF_000195295.1:WP_013705642.1 154 gLAGGESRVSGGISSQFLSALLLISPFAARDVEIEVVG-ELVSRPYVDITLSVMEAFGIAYYRRGYQNF 221
                                               8999**********************************.*************************99*** PP

                                 TIGR01356 208 vvkggqkykqkevevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadveveeqr 276
                                                v+ gq y+ +++evegDaSsA++fl aaa+tg+++t++nl  +s qgd  +++vL++mG++ve + + 
  lcl|NCBI__GCF_000195295.1:WP_013705642.1 222 CVPAGQRYQARDYEVEGDASSASYFLGAAALTGGRITLTNLNPQSCQGDIGFLEVLQQMGCQVEPTGS- 289
                                               ********************************************************************. PP

                                 TIGR01356 277 dvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGve 345
                                                v+++g ++l++++  i++++++D++ptlavlaa+A+get+i+++ +lR kEsdR++a+a+eL+k+G++
  lcl|NCBI__GCF_000195295.1:WP_013705642.1 290 GVVLRG-RQLQAIR--INMAHMPDLVPTLAVLAAYAQGETVITGVPHLRHKESDRLQAVATELAKMGIT 355
                                               799996.68*9***..***************************************************** PP

                                 TIGR01356 346 veeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlga 414
                                               v++++dgl+i+G+  + +g v++ty+DHRiam++a++gl+   +v i ++ cvaksfP+F++  ++lg 
  lcl|NCBI__GCF_000195295.1:WP_013705642.1 356 VNQTKDGLIIQGG--KPRGVVIETYNDHRIAMSFALAGLKTP-GVMIANPDCVAKSFPDFWDYFAKLGT 421
                                               *************..6*************************9.********************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (432 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.29
//
[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