Alignments for a candidate for aroA in Nitratifractor salsuginis DSM 16511

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Nitratifractor salsuginis DSM 16511

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_013553296.1 NITSA_RS01685 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::A6TL04
         (425 letters)



>NCBI__GCF_000186245.1:WP_013553296.1
          Length = 430

 Score =  309 bits (792), Expect = 9e-89
 Identities = 190/412 (46%), Positives = 251/412 (60%), Gaps = 14/412 (3%)

Query: 15  TVPGDKSISHRAIMLSSISKGTSRVKGFLRGEDCLSTISCFRDLGIDIED--RGTEIIIQ 72
           T+  DKSISHR  M S  S   S V+ FL+GED L+++S  R LG ++E+   GT  I  
Sbjct: 19  TIAPDKSISHRCAMFSLFSDRPSTVRNFLKGEDTLASLSIARQLGAEVEEDEAGTLRITP 78

Query: 73  GKGLHGLSEPLNVLDAGNSGTTIRLISGILAGQKFLTIVTGDASLRKRPMERIATPLRKM 132
              L    EP ++LD GN+GT +RL  G+LAG +   ++TGD  LR RPM+R+  PL+ +
Sbjct: 79  PVELR---EPDDILDCGNAGTGMRLYCGLLAGVEGSFVLTGDRYLRSRPMKRVTGPLQSI 135

Query: 133 GAFIEGRDYGNLAPLVIRGGNLKGMDYASPVSSAQVKSAILLAGLYGEGDTIVREKITSR 192
           GA I+GR+ GNLAPL IRGG LK   Y SP+ SAQVKSA++LA L G+  +  RE   SR
Sbjct: 136 GAKIDGREEGNLAPLHIRGGKLKAFRYESPIDSAQVKSAMILAALRGDAPSYYRENFLSR 195

Query: 193 DHTEKMLKGLGANISTDQG---VTRLGKSELYGQSIEVPGDISSAAFFMAGAAALPGSFL 249
           DHTE+ML+G+GA+I TD     V +     L    I VP D SSA FF   AA +PG+ +
Sbjct: 196 DHTERMLRGMGASIETDAEGWIVVKPLTKPLNPLDITVPADPSSAFFFAVAAAIVPGAKV 255

Query: 250 ITEGVGLNPTRTGIIDVLRDMGGDIEIHNLRQSGGEEIGDIMIR-GKKLYGTEIGKEIIP 308
              GV LNPTR     VL  MG  +E + LR+   E IG+I +    +L   E+    I 
Sbjct: 256 RIPGVTLNPTRIEAYKVLEAMGAAVE-YALREDRYEPIGEIRVAYDGRLSAVEVSHR-IA 313

Query: 309 RLIDEIPVLAIIAATAEGKTIITGAEELKVKESNRITAMVTEMQKVGIKVTELPDGMEIE 368
            LIDE+P LA+  ATAEG + +  A EL+VKES+RI  +VT ++  GI+  E PDG  I 
Sbjct: 314 WLIDELPALAVAMATAEGVSRVRNAAELRVKESDRIATVVTALKACGIEAEEYPDGYAIR 373

Query: 369 GGQVITGGRVESYGDHRIAMAMAICGLFAQEPIKINDSQCIDISFPNFEEKL 420
           GG  +    ++S+GDHRIAM+ AI GL     ++I D  C+  SFPNF E L
Sbjct: 374 GG-TLRRAVIDSHGDHRIAMSFAIAGLLC--GMEIEDIDCVATSFPNFFEIL 422


Lambda     K      H
   0.317    0.138    0.383 

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: 490
Number of extensions: 27
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: 425
Length of database: 430
Length adjustment: 32
Effective length of query: 393
Effective length of database: 398
Effective search space:   156414
Effective search space used:   156414
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_013553296.1 NITSA_RS01685 (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.21306.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-125  405.4   0.0   1.6e-125  405.1   0.0    1.0  1  lcl|NCBI__GCF_000186245.1:WP_013553296.1  NITSA_RS01685 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000186245.1:WP_013553296.1  NITSA_RS01685 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.1   0.0  1.6e-125  1.6e-125       4     413 ..      19     426 ..      18     428 .. 0.96

  Alignments for each domain:
  == domain 1  score: 405.1 bits;  conditional E-value: 1.6e-125
                                 TIGR01356   4 kipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgglkepea 71 
                                               +i+++KSishR  +++++++ +++v+n+Lk+eDtla+l++ r+lGa+ve +e ++l i++   l+ep++
  lcl|NCBI__GCF_000186245.1:WP_013553296.1  19 TIAPDKSISHRCAMFSLFSDRPSTVRNFLKGEDTLASLSIARQLGAEVEeDEAGTLRITPPVELREPDD 87 
                                               589**********************************************5559*******999****** PP

                                 TIGR01356  72 eldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgpl 140
                                               +ld+gn+Gt +Rl+ g+la ++g++vltgd  l+ RP++r++ +L+++ga+i+ +ee + +Pl+i+g++
  lcl|NCBI__GCF_000186245.1:WP_013553296.1  88 ILDCGNAGTGMRLYCGLLAGVEGSFVLTGDRYLRSRPMKRVTGPLQSIGAKIDGREEGNLAPLHIRGGK 156
                                               *******************************************************************98 PP

                                 TIGR01356 141 kggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivv 209
                                                 +  + s+  S+Q+ksa++laa   l+++  + + e+ +sr+++e++L  +++    +e + e  ivv
  lcl|NCBI__GCF_000186245.1:WP_013553296.1 157 LKAFRYESPIDSAQVKSAMILAA---LRGDAPSYYRENFLSRDHTERMLRGMGAS---IETDAEGWIVV 219
                                               88*********************...8899999*******************988...77777778999 PP

                                 TIGR01356 210 kggqkykqk.evevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr 276
                                               k+  k  ++ +++v++D+SsA+ff++aaai ++ +v++ +++ n+t+ +  +  vLe+mGa ve++  +
  lcl|NCBI__GCF_000186245.1:WP_013553296.1 220 KPLTKPLNPlDITVPADPSSAFFFAVAAAIVPGaKVRIPGVTLNPTRIE--AYKVLEAMGAAVEYALRE 286
                                               9999955555***************************************..555***********9888 PP

                                 TIGR01356 277 .......dvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaee 338
                                                      +++v     l++v+v ++++ liDelp+lav++a Aeg++r++n++elRvkEsdRia ++++
  lcl|NCBI__GCF_000186245.1:WP_013553296.1 287 dryepigEIRVAYDGRLSAVEVSHRIAWLIDELPALAVAMATAEGVSRVRNAAELRVKESDRIATVVTA 355
                                               88***********99****************************************************** PP

                                 TIGR01356 339 LeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfe 407
                                               L++ G+e+ee +dg  i+G+  +l+ av+d+++DHRiam++a++gl +   +eied  cva+sfP+Ffe
  lcl|NCBI__GCF_000186245.1:WP_013553296.1 356 LKACGIEAEEYPDGYAIRGG--TLRRAVIDSHGDHRIAMSFAIAGLLCG--MEIEDIDCVATSFPNFFE 420
                                               ********************..6*************************6..****************** PP

                                 TIGR01356 408 vleqlg 413
                                                l +l+
  lcl|NCBI__GCF_000186245.1:WP_013553296.1 421 ILSNLT 426
                                               **9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (430 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: 10.94
//
[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