Alignments for a candidate for aroA in Ammonifex degensii KC4

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Ammonifex degensii KC4

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_015739144.1 ADEG_RS05805 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::F5A7Q0
         (429 letters)



>NCBI__GCF_000024605.1:WP_015739144.1
          Length = 434

 Score =  465 bits (1196), Expect = e-135
 Identities = 233/410 (56%), Positives = 308/410 (75%), Gaps = 2/410 (0%)

Query: 13  LNGNITIPGDKSISHRAVMFGSIAEGKTTIKGFLSGADCLSTISCFKEMGVEITQNGD-E 71
           L G IT+PGDKSISHRA++ GS+A G+T I+ FL G DCL+T+ C +++GV+I + G+  
Sbjct: 11  LEGTITVPGDKSISHRALLLGSLAHGETVIENFLQGKDCLATLRCLRQLGVKIEEEGEGR 70

Query: 72  VTVVGKGLEGLQEPKAVLDVGNSGTTIRLMSGILANTPFFSCVQGDESIAKRPMKRVTNP 131
           + V G+GL  LQEP+ VLD GNSGTT+RL+ G+LA  P F+ + GD S+ +RPM RVT P
Sbjct: 71  LRVEGRGLGNLQEPEEVLDAGNSGTTMRLLLGVLAGNPIFAVLTGDASLRRRPMDRVTLP 130

Query: 132 LKQMGANIDGREEGTFTPLTIRGG-DLKAIEYISPVASAQVKSAILLAGLRAEGVTAVTE 190
           LK MGA I GR+EG   PL IRG   L+ +EY SPVASAQVKSA+LLAGL AEG T+VTE
Sbjct: 131 LKLMGAEIWGRQEGKLAPLAIRGQRKLRPLEYTSPVASAQVKSAVLLAGLYAEGETSVTE 190

Query: 191 PHISRDHTERMLEAFGVKVTREGKTVKLSGGQKLTATNIQVPGDVSSAAFFLVAGAIIPN 250
           P +SRDHTERML  FGV V REG TV+L G   L    ++VPGD S+AAFFL A AI+P 
Sbjct: 191 PALSRDHTERMLGYFGVPVKREGLTVRLKGRALLQGRPVRVPGDFSAAAFFLAAAAILPE 250

Query: 251 SKLVLQNVGMNPTRTGIIDVLEKMGATFTVDLINEGASEPAANITIETSSLKGIEIGGDI 310
            ++ ++ VG+NPTRTG ++VLE MGA  +V++  E A EP  N+T+E+S+L+G+EIGG+I
Sbjct: 251 GRVTVREVGLNPTRTGFLEVLEAMGARLSVEVTGEWAGEPVGNVTVESSALRGVEIGGEI 310

Query: 311 IPRLIDEIPVIALAATQAEGITVIKDAHELKVKETNRIDTVVAELTKLGARIEATDDGMI 370
           IPRLIDEIPV+ + A  A G TVI+ A EL+ KE++R+ T+  EL +LGA++E   DG+I
Sbjct: 311 IPRLIDEIPVLTVVAACAAGKTVIRGAEELRYKESDRLATMAQELGRLGAKVEVLPDGLI 370

Query: 371 IYGKSALKGNTVNSYGDHRIGMMLAIAGCLAEGKTIIEDAEAVGVSYPTF 420
           I+G   L+G+ V S+GDHR+ M +A+AG +AEG+TIIE AEA+ VS+P F
Sbjct: 371 IHGGYPLQGSRVQSHGDHRVAMAMAVAGLVAEGETIIEGAEAIDVSFPNF 420



 Score = 24.6 bits (52), Expect = 0.006
 Identities = 12/37 (32%), Positives = 19/37 (51%)

Query: 373 GKSALKGNTVNSYGDHRIGMMLAIAGCLAEGKTIIED 409
           G++     T+   GD  I     + G LA G+T+IE+
Sbjct: 6   GQAKRLEGTITVPGDKSISHRALLLGSLAHGETVIEN 42


Lambda     K      H
   0.315    0.134    0.369 

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: 586
Number of extensions: 31
Number of successful extensions: 6
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: 429
Length of database: 434
Length adjustment: 32
Effective length of query: 397
Effective length of database: 402
Effective search space:   159594
Effective search space used:   159594
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: 42 (22.0 bits)
S2: 51 (24.3 bits)

Align candidate WP_015739144.1 ADEG_RS05805 (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.2654.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-137  443.8   0.0   3.3e-137  443.6   0.0    1.0  1  lcl|NCBI__GCF_000024605.1:WP_015739144.1  ADEG_RS05805 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024605.1:WP_015739144.1  ADEG_RS05805 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  443.6   0.0  3.3e-137  3.3e-137       1     414 [.      13     429 ..      13     430 .. 0.96

  Alignments for each domain:
  == domain 1  score: 443.6 bits;  conditional E-value: 3.3e-137
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 
                                               g i++pg+KSishRalll++La+getv++n+L+++D+latl++lr+lG+k+eee +++l +eg g   l
  lcl|NCBI__GCF_000024605.1:WP_015739144.1  13 GTITVPGDKSISHRALLLGSLAHGETVIENFLQGKDCLATLRCLRQLGVKIEEEgEGRLRVEGRGLgnL 81 
                                               789*************************************************77699*****998788* PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                               +epe++ld+gnsGtt+Rll+gvla  +   vltgd sl++RP++r++ +L+ +gaei  ++e + +Pla
  lcl|NCBI__GCF_000024605.1:WP_015739144.1  82 QEPEEVLDAGNSGTTMRLLLGVLAGNPIFAVLTGDASLRRRPMDRVTLPLKLMGAEIWGRQEGKLAPLA 150
                                               ********************************************************************* PP

                                 TIGR01356 136 isgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               i+g+ k+ +  + s+ aS+Q+ksa+lla+   l a++++ v+e+ +sr+++e++L     fgv v++e 
  lcl|NCBI__GCF_000024605.1:WP_015739144.1 151 IRGQRKLrPLEYTSPVASAQVKSAVLLAG---LYAEGETSVTEPALSRDHTERMLGY---FGVPVKREG 213
                                               ****8888*********************...67789999999**********9866...5688***98 PP

                                 TIGR01356 204 erkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadve 271
                                                 ++++kg +  + + v+v+gD+S+Aafflaaaai +e +vtv+++g n+t+++  +++vLe+mGa+++
  lcl|NCBI__GCF_000024605.1:WP_015739144.1 214 L-TVRLKGRALLQGRPVRVPGDFSAAAFFLAAAAILPEgRVTVREVGLNPTRTG--FLEVLEAMGARLS 279
                                               7.9****999966667*********************99***************..999********99 PP

                                 TIGR01356 272 veeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdR 331
                                               ve +         +v+ve +s l+gv++  + +++liDe+p+l+v+aa+A g+t+i+++eelR+kEsdR
  lcl|NCBI__GCF_000024605.1:WP_015739144.1 280 VEVTGewagepvgNVTVE-SSALRGVEIgGEIIPRLIDEIPVLTVVAACAAGKTVIRGAEELRYKESDR 347
                                               9999889***********.799******99*************************************** PP

                                 TIGR01356 332 iaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvak 400
                                               +a +a+eL +lG++ve+l+dgl+i+G+   l+g +v++++DHR+ama+av+gl+aege++ie+ae++++
  lcl|NCBI__GCF_000024605.1:WP_015739144.1 348 LATMAQELGRLGAKVEVLPDGLIIHGG-YPLQGSRVQSHGDHRVAMAMAVAGLVAEGETIIEGAEAIDV 415
                                               ***************************.6**************************************** PP

                                 TIGR01356 401 sfPeFfevleqlga 414
                                               sfP+F  +l++l++
  lcl|NCBI__GCF_000024605.1:WP_015739144.1 416 SFPNFPTLLATLTE 429
                                               ********999875 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: 00:00:00.02
# Mc/sec: 7.72
//
[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