Alignments for a candidate for cmutase in Archaeoglobus veneficus SNP6

GapMind for Amino acid biosynthesis

Alignments for a candidate for cmutase in Archaeoglobus veneficus SNP6

Align prephenate dehydrogenase (EC 1.3.1.12); prephenate dehydratase (EC 4.2.1.51); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_013683139.1 ARCVE_RS02150 prephenate dehydratase

Query= BRENDA::O30012
         (620 letters)



>NCBI__GCF_000194625.1:WP_013683139.1
          Length = 620

 Score =  764 bits (1973), Expect = 0.0
 Identities = 388/617 (62%), Positives = 486/617 (78%), Gaps = 10/617 (1%)

Query: 6   ILIYGVGNMGKLFRDIFYGKGYYVRGYDIDQMKR--DTNSISGFDVIFVCTPMYALEEAL 63
           ILIYG+G MGK F D F+ +GY V GYD+   +R  + + I  +DVIF+C PM A+ +A+
Sbjct: 5   ILIYGMGRMGKFFYDFFFSRGYDVAGYDVVPERRTIEEDKIESYDVIFLCVPMQAVGDAI 64

Query: 64  EHIKREAKKEALLVDVSSVKKVSVPLFEESGFDFLSIHPMLGGDSEISLSNVIVVRESGR 123
             I R +   AL+VD+SS+K   +P  + SGFD+LSIHPM G DSEI LSN+IVV++SGR
Sbjct: 65  ARIPRSS---ALIVDISSIKGFVLPYLDASGFDYLSIHPMFGPDSEIGLSNIIVVKKSGR 121

Query: 124 EEEKVILEELRKCGAVLSRLDVEEHDRKMAEIQGIAHFALVSMADFL--RYGKEELKYAS 181
           +EE+VILEE RK GAVLS L  E+HD KMAEIQG+AHF LV MA FL  R+ +E+LKYAS
Sbjct: 122 KEEEVILEEFRKAGAVLSELPPEKHDAKMAEIQGLAHFLLVGMAHFLAERFDREDLKYAS 181

Query: 182 PIFTVLYKLASRIINQNWEMYFQIQKNAEDVREEYLRRAMELHEKMKDRESFREIFESLR 241
           PIF  LYKL+SRI+NQ+W MY+ IQKNAE +R E+++   +L  K  D E FR++FE L 
Sbjct: 182 PIFATLYKLSSRILNQDWRMYYYIQKNAEILRREFIKSLADLDAKFSDEEKFRKLFEELG 241

Query: 242 KIYTDYESSTIILESYKATKKAESIEELRGLIKSIDSLILRLIERRIDAARQIARIKMER 301
             + DY +ST+IL++ KAT    +IE LRG I+++DSLILRL+ERR  A R+IA  K +R
Sbjct: 242 SKFDDYGNSTLILDACKATWDVSTIELLRGYIRAVDSLILRLLERRTQAGRKIALHKRDR 301

Query: 302 GEPIELKDVEEEKLWEVMSKTTLNPVKLKEIFEGIMSLAKEEEYKVAGVKYTIAVLGPQG 361
            EPIE+ D+EE K+ +++ +T+LNP+ +++IFE IM L KEEEY+V G+K T+AVLGP G
Sbjct: 302 NEPIEIADLEEVKIKDLLLRTSLNPIYVQDIFENIMGLTKEEEYRVLGIKKTLAVLGPAG 361

Query: 362 SFSEEMALKLVGSRVPLRYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNH 421
           SFSEE ALKLVGSR+PL+YC+TTDEIIK VE+G  DYGLVPIENSVNGTV+ V+DALLNH
Sbjct: 362 SFSEEAALKLVGSRLPLKYCATTDEIIKCVENGSADYGLVPIENSVNGTVISVLDALLNH 421

Query: 422 DVEVFGEAKLEVNHCLVAKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTS 481
           DVEVFGE  LE+ HCL A+R + LKEI+ +YSHPQA+AQCMGFINNYL    +RYT+STS
Sbjct: 422 DVEVFGETTLEIVHCLAARRYMPLKEIRVVYSHPQAIAQCMGFINNYL-KAELRYTSSTS 480

Query: 482 DAARMLDDYSAAIMSENAARFYRLHVLRKGIQDLKGRNITRFYLIRRR-SGRSEGKITSL 540
           DA  +LDDYSAAI+SENAA+ ++L+VLRKGIQD K  N TRFYLIR++ SG   G ITSL
Sbjct: 481 DAIALLDDYSAAIVSENAAKLHKLYVLRKGIQDAKA-NTTRFYLIRKKGSGEMRGSITSL 539

Query: 541 FFGVEDKPGALKDVLEVFHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPLREEDLLDLKQ 600
           FFGVED+PGALKDVLEVF++KG N+RKLESRPA TGLGDYVFFVEVE  L  EDL +L+ 
Sbjct: 540 FFGVEDRPGALKDVLEVFYRKGINMRKLESRPARTGLGDYVFFVEVEKDLSSEDLRELRN 599

Query: 601 VTTFYKVVGVFDEVKRM 617
           VTTFY +VGVFD V+R+
Sbjct: 600 VTTFYHIVGVFDRVERL 616


Lambda     K      H
   0.320    0.137    0.380 

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: 1121
Number of extensions: 40
Number of successful extensions: 6
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: 620
Length of database: 620
Length adjustment: 37
Effective length of query: 583
Effective length of database: 583
Effective search space:   339889
Effective search space used:   339889
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: 53 (25.0 bits)

Align candidate WP_013683139.1 ARCVE_RS02150 (prephenate dehydratase)
to HMM PF01817 (CM_2)

# 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/PF01817.25.hmm
# target sequence database:        /tmp/gapView.20097.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       CM_2  [M=79]
Accession:   PF01817.25
Description: Chorismate mutase type II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      2e-14   40.1   1.3    5.9e-14   38.6   1.3    1.9  1  lcl|NCBI__GCF_000194625.1:WP_013683139.1  ARCVE_RS02150 prephenate dehydra


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000194625.1:WP_013683139.1  ARCVE_RS02150 prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   1.3   5.9e-14   5.9e-14       1      78 [.     270     344 ..     270     345 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 5.9e-14
                                      CM_2   1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlregaeelgldpeavekifre 69 
                                               R  I ++D+ +l+Ll++R++  ++ia  K++++ p+   + ee +++ l        l+p +v++if++
  lcl|NCBI__GCF_000194625.1:WP_013683139.1 270 RGYIRAVDSLILRLLERRTQAGRKIALHKRDRNEPIEIADLEEVKIKDLLLRT---SLNPIYVQDIFEN 335
                                               6789*********************************************9954...6************ PP

                                      CM_2  70 iisesralQ 78 
                                               i+  +++ +
  lcl|NCBI__GCF_000194625.1:WP_013683139.1 336 IMGLTKEEE 344
                                               **9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (79 nodes)
Target sequences:                          1  (620 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 13.03
//
[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