Alignments for a candidate for aroA in Arcobacter nitrofigilis DSM 7299

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Arcobacter nitrofigilis DSM 7299

Align 3-phosphoshikimate 1-carboxyvinyltransferase 1; 5-enolpyruvylshikimate-3-phosphate synthase 1; EPSP synthase 1; EPSPS 1; EC 2.5.1.19 (characterized)
to candidate WP_013134300.1 ARNIT_RS02460 3-phosphoshikimate 1-carboxyvinyltransferase

Query= SwissProt::Q9KCA6
         (431 letters)



>NCBI__GCF_000092245.1:WP_013134300.1
          Length = 426

 Score =  303 bits (776), Expect = 7e-87
 Identities = 176/416 (42%), Positives = 258/416 (62%), Gaps = 13/416 (3%)

Query: 19  VPGDKSISHRAVMFGALAKGTTTVEGFLPGADCLSTISCFQKLGVSIEQAEERVTVKGKG 78
           +  DKSISHR  MF  L+  T+ ++ FL   D L+T+S  ++LG  I++    VT+  KG
Sbjct: 20  IASDKSISHRCAMFSLLSNETSHIKNFLTAEDTLNTLSIVEQLGAEIKRDGSTVTITPKG 79

Query: 79  WDGLREPSDILDVGNSGTTTRLILGILSTLPFHSVIIGDESIGKRPMKRVTEPLKSMGAQ 138
              L EPS++LD GNSGT  RL  G L+++     ++GD+ +  RPMKRV  PL+S+GA+
Sbjct: 80  T--LTEPSNVLDCGNSGTAMRLFCGFLASIDGAFTLVGDKYLHSRPMKRVANPLRSIGAK 137

Query: 139 IDGRDHGNLTPLSIRG-GQLKGIDFHSPVASAQMKSAILLAGLRAEGKTSVTEPAKTRDH 197
           IDGR+ GN  PL IRG  +LK   +HSPV SAQ+KSA++LA LRA G +   E   TRDH
Sbjct: 138 IDGREDGNKAPLFIRGVKELKAFTYHSPVDSAQVKSAMILAALRANGVSKYKENELTRDH 197

Query: 198 TERMLEAFGVNIEKD--GLTVSIEGGQMLTGQHVVVPGDISSAAFFLVAGAMVPHSRITL 255
           TERML+  G  +E D  G        + L   ++ VP D SSA FF +A A+ P++++T+
Sbjct: 198 TERMLKGMGAKLENDSEGFIHIYPLTKPLKPLNITVPTDPSSAFFFALAAAITPNAKVTI 257

Query: 256 TNVGINPTRAGILEVLKQMGATLA-MENERVQGGEPVADLTIETSVLQGVEIGGDIIPRL 314
            NV +NPTR     VLK+MGA +  +E E V   EP+ D+ +  + L GV++  + I  L
Sbjct: 258 KNVTLNPTRTEAYVVLKRMGANVEFIEKENVY--EPMGDIVVSANELNGVDV-SENISWL 314

Query: 315 IDEIPIIAVLATQASGRTVIKDAEELKVKETNRIDTVVSELTKLGASIHATDDGMIIEGP 374
           IDE+P +++  + A+G++ + +A+EL+VKE++RI +VV+ L   G +    +DG  I G 
Sbjct: 315 IDELPALSIAMSLANGKSKVSNAKELRVKESDRISSVVNNLKLCGVTYKEFEDGYEITGG 374

Query: 375 TPLKGGVTVSSHGDHRIGMAMAIAALLAEKPVTVEGTEAIAVSYPSFFDHLDRLKS 430
              K   T++SHGDHRI M+ AIA L     + ++  + I  S+P+F + LD LKS
Sbjct: 375 KLKK--ATINSHGDHRIAMSFAIAGL--NSGMQIQDVDCILTSFPNFKEILDTLKS 426


Lambda     K      H
   0.315    0.134    0.375 

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: 434
Number of extensions: 19
Number of successful extensions: 8
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: 431
Length of database: 426
Length adjustment: 32
Effective length of query: 399
Effective length of database: 394
Effective search space:   157206
Effective search space used:   157206
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate WP_013134300.1 ARNIT_RS02460 (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.14882.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.4e-128  413.5   0.0   5.4e-128  413.3   0.0    1.0  1  lcl|NCBI__GCF_000092245.1:WP_013134300.1  ARNIT_RS02460 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092245.1:WP_013134300.1  ARNIT_RS02460 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.3   0.0  5.4e-128  5.4e-128       5     412 ..      20     424 ..      17     426 .] 0.97

  Alignments for each domain:
  == domain 1  score: 413.3 bits;  conditional E-value: 5.4e-128
                                 TIGR01356   5 ipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgglkepeael 73 
                                               i+++KSishR  ++++L++ ++ ++n+L++eDtl+tl+++++lGa++++++ +++i+++g+l ep+++l
  lcl|NCBI__GCF_000092245.1:WP_013134300.1  20 IASDKSISHRCAMFSLLSNETSHIKNFLTAEDTLNTLSIVEQLGAEIKRDGSTVTITPKGTLTEPSNVL 88 
                                               789****************************************************************** PP

                                 TIGR01356  74 dlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgplkg 142
                                               d+gnsGt++Rl  g la ++g ++l gd+ l+ RP++r+ ++Lr++ga+i+ +e+ +++Pl i+g +++
  lcl|NCBI__GCF_000092245.1:WP_013134300.1  89 DCGNSGTAMRLFCGFLASIDGAFTLVGDKYLHSRPMKRVANPLRSIGAKIDGREDGNKAPLFIRGVKEL 157
                                               *****************************************************************9999 PP

                                 TIGR01356 143 .givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvk 210
                                                + ++ s+  S+Q+ksa++laa   l+a++++ ++e++++r+++e++Lk ++++   +e++ e  i++ 
  lcl|NCBI__GCF_000092245.1:WP_013134300.1 158 kAFTYHSPVDSAQVKSAMILAA---LRANGVSKYKENELTRDHTERMLKGMGAK---LENDSEGFIHIY 220
                                               9*********************...8999**********************988...999999999999 PP

                                 TIGR01356 211 ggqk.ykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr. 276
                                               +  k  k+ +++v+ D+SsA+ff++aaait++ +vt++n++ n+t+++  + +vL++mGa+ve+ e++ 
  lcl|NCBI__GCF_000092245.1:WP_013134300.1 221 PLTKpLKPLNITVPTDPSSAFFFALAAAITPNaKVTIKNVTLNPTRTE--AYVVLKRMGANVEFIEKEn 287
                                               999967777***************************************..555**********999999 PP

                                 TIGR01356 277 ......dvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeL 339
                                                     d++v  a++l+gv+v ++++ liDelp+l++++++A+g++++ n++elRvkEsdRi++++++L
  lcl|NCBI__GCF_000092245.1:WP_013134300.1 288 vyepmgDIVVS-ANELNGVDVSENISWLIDELPALSIAMSLANGKSKVSNAKELRVKESDRISSVVNNL 355
                                               ******9*999.789****************************************************** PP

                                 TIGR01356 340 eklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfev 408
                                               +  Gv+ +e+edg +i+G+  +lk+a++++++DHRiam++a++gl     ++i+d  c+ +sfP+F e 
  lcl|NCBI__GCF_000092245.1:WP_013134300.1 356 KLCGVTYKEFEDGYEITGG--KLKKATINSHGDHRIAMSFAIAGLNSG--MQIQDVDCILTSFPNFKEI 420
                                               *******************..6***********************996..******************9 PP

                                 TIGR01356 409 leql 412
                                               l +l
  lcl|NCBI__GCF_000092245.1:WP_013134300.1 421 LDTL 424
                                               9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (426 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: 10.96
//
[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