Alignments for a candidate for aroG in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Mycolicibacterium vanbaalenii PYR-1

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011780739.1 MVAN_RS17780 3-deoxy-7-phosphoheptulonate synthase class II

Query= BRENDA::O53512
         (462 letters)



>NCBI__GCF_000015305.1:WP_011780739.1
          Length = 468

 Score =  825 bits (2130), Expect = 0.0
 Identities = 404/467 (86%), Positives = 435/467 (93%), Gaps = 6/467 (1%)

Query: 1   MNWTVDIPIDQLPSLPPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTV 60
           MNWTVD+PIDQLP+LPPLP DLR RLDAALA+PA QQP+W A QA AMR VLESVPPVTV
Sbjct: 1   MNWTVDVPIDQLPALPPLPEDLRQRLDAALARPALQQPSWDAGQAAAMRKVLESVPPVTV 60

Query: 61  PSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMP 120
           PSEI RL+ QLA VA+G+AFLLQGGDCAETF+DNTEPHIR N+R LLQMAVVLTYGASMP
Sbjct: 61  PSEIERLKSQLADVARGQAFLLQGGDCAETFVDNTEPHIRANIRTLLQMAVVLTYGASMP 120

Query: 121 VVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAM 180
           VVKVARIAGQYAKPRS+D DALGL+SYRGDM+NGFAPDAA REHDPSRLVRAYANASAAM
Sbjct: 121 VVKVARIAGQYAKPRSSDTDALGLKSYRGDMVNGFAPDAAVREHDPSRLVRAYANASAAM 180

Query: 181 NLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQT 240
           NLVRALTSSG+ASLH VHDWNREFVRTSPAGARYEALA EIDRGLRFMSAC V DRNL T
Sbjct: 181 NLVRALTSSGMASLHQVHDWNREFVRTSPAGARYEALAGEIDRGLRFMSACRVDDRNLDT 240

Query: 241 AEIYASHEALVLDYERAMLRLSDGD------DGEPQLFDLSAHTVWIGERTRQIDGAHIA 294
           AEIYASHEALVLDYERAMLR++  D      DG P+L+DLSAH VWIGERTRQ+DGAH+A
Sbjct: 241 AEIYASHEALVLDYERAMLRMNIADSADPASDGPPKLYDLSAHYVWIGERTRQLDGAHVA 300

Query: 295 FAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKV 354
           FA+VIANPVG+K+GP  +PELAVEYVERLDP+N+PGRLTLVSRMGNHKVRD+LPPI+EKV
Sbjct: 301 FAEVIANPVGIKIGPTTSPELAVEYVERLDPNNEPGRLTLVSRMGNHKVRDVLPPIIEKV 360

Query: 355 QATGHQVIWQCDPMHGNTHESSTGFKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITG 414
           QA+GHQV+WQCDPMHGNTHESSTG+KTRHFDRIVDEVQGFFEVH ALGTHPGGIHVEITG
Sbjct: 361 QASGHQVVWQCDPMHGNTHESSTGYKTRHFDRIVDEVQGFFEVHHALGTHPGGIHVEITG 420

Query: 415 ENVTECLGGAQDISETDLAGRYETACDPRLNTQQSLELAFLVAEMLR 461
           ENVTECLGGAQDIS+TDLAGRYETACDPRLNTQQSLELAFLVAEMLR
Sbjct: 421 ENVTECLGGAQDISDTDLAGRYETACDPRLNTQQSLELAFLVAEMLR 467


Lambda     K      H
   0.319    0.134    0.399 

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: 750
Number of extensions: 13
Number of successful extensions: 2
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: 462
Length of database: 468
Length adjustment: 33
Effective length of query: 429
Effective length of database: 435
Effective search space:   186615
Effective search space used:   186615
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_011780739.1 MVAN_RS17780 (3-deoxy-7-phosphoheptulonate synthase class II)
to HMM TIGR01358 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# 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/TIGR01358.hmm
# target sequence database:        /tmp/gapView.29672.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01358  [M=443]
Accession:   TIGR01358
Description: DAHP_synth_II: 3-deoxy-7-phosphoheptulonate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.3e-220  716.4   0.1   6.1e-220  716.2   0.1    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011780739.1  MVAN_RS17780 3-deoxy-7-phosphohe


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011780739.1  MVAN_RS17780 3-deoxy-7-phosphoheptulonate synthase class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  716.2   0.1  6.1e-220  6.1e-220       3     440 ..      26     467 ..      24     468 .] 0.97

  Alignments for each domain:
  == domain 1  score: 716.2 bits;  conditional E-value: 6.1e-220
                                 TIGR01358   3 leswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfke 71 
                                               l+++ ++pa+q+P + da+++ a+++ les+PP+++++ei++lk++la+va+G+afllqgGdcae+f +
  lcl|NCBI__GCF_000015305.1:WP_011780739.1  26 LDAALARPALQQPSW-DAGQAAAMRKVLESVPPVTVPSEIERLKSQLADVARGQAFLLQGGDCAETFVD 93 
                                               68999**********.69*************************************************** PP

                                 TIGR01358  72 veadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafde 140
                                               +++++ir ++r+llqmavvltygas+Pvvkv+riaGqyakPrs++++a +   l+syrGd++ng+a+d+
  lcl|NCBI__GCF_000015305.1:WP_011780739.1  94 NTEPHIRANIRTLLQMAVVLTYGASMPVVKVARIAGQYAKPRSSDTDALG---LKSYRGDMVNGFAPDA 159
                                               ***********************************************999...**************** PP

                                 TIGR01358 141 aarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfm 209
                                               a r++dp+rlvraya+++a++nl+ralts+G+a+l++vh+Wn+efv++spagarye+la eid++lrfm
  lcl|NCBI__GCF_000015305.1:WP_011780739.1 160 AVREHDPSRLVRAYANASAAMNLVRALTSSGMASLHQVHDWNREFVRTSPAGARYEALAGEIDRGLRFM 228
                                               ********************************************************************* PP

                                 TIGR01358 210 savgvaeaealkrvelytsheallldyeealtrvds.........kegqlfdlsahllWiGertrqldg 269
                                               sa+ v++++ l+++e+y+sheal+ldye+a++r++             +l+dlsah++WiGertrqldg
  lcl|NCBI__GCF_000015305.1:WP_011780739.1 229 SACRVDDRN-LDTAEIYASHEALVLDYERAMLRMNIadsadpasdGPPKLYDLSAHYVWIGERTRQLDG 296
                                               *******99.***********************8643345555445679******************** PP

                                 TIGR01358 270 ahveflrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGr 338
                                               ahv+f+++++nP+gik+gp+++++ +++++e+ldP+nePGrltl+sr+G++k+++ lP+++e+v+a+G+
  lcl|NCBI__GCF_000015305.1:WP_011780739.1 297 AHVAFAEVIANPVGIKIGPTTSPELAVEYVERLDPNNEPGRLTLVSRMGNHKVRDVLPPIIEKVQASGH 365
                                               ********************************************************************* PP

                                 TIGR01358 339 avvWvtdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareit 407
                                               +vvW++dpmhGnt+e+++Gyktr+fd+i++ev++ffevh+a+GthpGG+h+e+tGe+vteclGGa++i+
  lcl|NCBI__GCF_000015305.1:WP_011780739.1 366 QVVWQCDPMHGNTHESSTGYKTRHFDRIVDEVQGFFEVHHALGTHPGGIHVEITGENVTECLGGAQDIS 434
                                               ********************************************************************* PP

                                 TIGR01358 408 etdlasryetacdPrlnaeqslelaflvaeklr 440
                                               +tdla ryetacdPrln++qslelaflvae+lr
  lcl|NCBI__GCF_000015305.1:WP_011780739.1 435 DTDLAGRYETACDPRLNTQQSLELAFLVAEMLR 467
                                               *******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (468 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 7.36
//
[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