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

GapMind for Amino acid biosynthesis

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

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_011780029.1 MVAN_RS14135 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_000015305.1:WP_011780029.1
          Length = 508

 Score =  385 bits (988), Expect = e-111
 Identities = 227/499 (45%), Positives = 303/499 (60%), Gaps = 21/499 (4%)

Query: 3   REEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLA-DAPNSYLLESVQGGEKWGRYSII 61
           RE+F  LAA+ +  +P++ + LAD +TPLS Y KLA + P ++LLES + G  W R+S I
Sbjct: 13  REDFRALAAE-HRVVPVTRKVLADSETPLSAYRKLAANRPGTFLLESAENGRSWSRWSFI 71

Query: 62  GLPCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLVG 121
           G    + L V D +  + +  +  +     DPL  +       +   +PGLP    GLVG
Sbjct: 72  GAGAPSALTVRDGEA-VWLGVIPQDAPSGGDPLQALRATLTLLETAPLPGLPPLSSGLVG 130

Query: 122 YFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLA------DP 175
           +F YD VR +E+        D L  PD++L+++  V   D+  G I  I  A      D 
Sbjct: 131 FFAYDLVRRLERLPEL--TVDDLALPDMMLLLATDVAAVDHHEGTITLIANAVNWNGTDE 188

Query: 176 SEENAYERGQARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKD 235
             + AY+   ARL+ +   L +P+       +       P  R+  T E+Y   V ++  
Sbjct: 189 RVDWAYDDAVARLDVMTAALAEPLAST----VATFSRPVPEHRSQRTVEEYTAIVDKLVG 244

Query: 236 YILAGDCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFG------DFHVVGSS 289
            I AG+  QVVPSQR  ++  A P+D+YR LR  NP+PYMY  N        DF +VGSS
Sbjct: 245 DIEAGEAFQVVPSQRFEMDTDADPLDVYRMLRVTNPSPYMYLLNVPNADGGLDFSIVGSS 304

Query: 290 PEVLVRVEDGLVTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGR 349
           PE LV V+DG  T  PIAGTR RG  EE DL LE++LL D KE AEHLML+DLGRND+GR
Sbjct: 305 PEALVTVKDGRATTHPIAGTRWRGDTEEEDLLLEKELLCDEKERAEHLMLVDLGRNDLGR 364

Query: 350 VSDIGAVKVTEKMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAM 409
           V   G VKV +   IERYS+VMH+VS VTG L +G +A+DA+ A  PAGTLSGAPK+RAM
Sbjct: 365 VCRPGTVKVEDYSHIERYSHVMHLVSTVTGLLADGKTALDAVTACFPAGTLSGAPKVRAM 424

Query: 410 EIIDELEPVKRGVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALE 469
           E+I+E+E  +RG+YGG +GYL + GN D AIAIRTA+I+NG  +VQAGGG+VADS    E
Sbjct: 425 ELIEEVEKTRRGLYGGVLGYLDFAGNADFAIAIRTALIRNGTAYVQAGGGVVADSNGPYE 484

Query: 470 WEETINKRRAMFRAVALAE 488
           + E  NK RA+  A+A AE
Sbjct: 485 YNEASNKARAVLAAIAAAE 503


Lambda     K      H
   0.321    0.139    0.408 

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: 652
Number of extensions: 42
Number of successful extensions: 5
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: 492
Length of database: 508
Length adjustment: 34
Effective length of query: 458
Effective length of database: 474
Effective search space:   217092
Effective search space used:   217092
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: 52 (24.6 bits)

Align candidate WP_011780029.1 MVAN_RS14135 (anthranilate synthase component I)
to HMM TIGR00564 (trpE: anthranilate synthase component I (EC 4.1.3.27))

# 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/TIGR00564.hmm
# target sequence database:        /tmp/gapView.14547.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00564  [M=455]
Accession:   TIGR00564
Description: trpE_most: anthranilate synthase component I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-167  544.6   0.0   1.3e-167  544.3   0.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011780029.1  MVAN_RS14135 anthranilate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011780029.1  MVAN_RS14135 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  544.3   0.0  1.3e-167  1.3e-167       1     454 [.      34     499 ..      34     500 .. 0.96

  Alignments for each domain:
  == domain 1  score: 544.3 bits;  conditional E-value: 1.3e-167
                                 TIGR00564   1 adtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieede 68 
                                               ad++tp+s+y+kla  r+ +fllEs+e++ +++R+S+ig+     ++++dg+av+l +  ++a   +d+
  lcl|NCBI__GCF_000015305.1:WP_011780029.1  34 ADSETPLSAYRKLAAnRPGTFLLESAENGRSWSRWSFIGAGAPSALTVRDGEAVWLGVIPQDAPSGGDP 102
                                               589***********988*****************************************99999999*** PP

                                 TIGR00564  69 lkelrkllekaeesedeld..eplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDh 135
                                               l++lr++l+ +e  +  l+  +pls+g+vG+++yd+vr +e+l+e + d+l lpd++lll ++v++ Dh
  lcl|NCBI__GCF_000015305.1:WP_011780029.1 103 LQALRATLTLLE--TAPLPglPPLSSGLVGFFAYDLVRRLERLPELTVDDLALPDMMLLLATDVAAVDH 169
                                               ********9964..555666678********************************************** PP

                                 TIGR00564 136 vekkvilienarteaers.....aeeeaaarleellaelqkelekavkaleekkesftsnvekeeyeek 199
                                                e +++li+na + ++++     a+++a arl+ ++a l ++l+++v +  +   +  s+ + eey++ 
  lcl|NCBI__GCF_000015305.1:WP_011780029.1 170 HEGTITLIANAVNWNGTDervdwAYDDAVARLDVMTAALAEPLASTVATFSRPVPEHRSQRTVEEYTAI 238
                                               **********9998888888999********************99888777777788899999****** PP

                                 TIGR00564 200 vakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldled......felvgsSPEl 262
                                               v+k+   i+aG+ fqvv+Sqr+e++++a+p+++Yr LR++NPSpy+y l++ +      f++vgsSPE+
  lcl|NCBI__GCF_000015305.1:WP_011780029.1 239 VDKLVGDIEAGEAFQVVPSQRFEMDTDADPLDVYRMLRVTNPSPYMYLLNVPNadggldFSIVGSSPEA 307
                                               ***************************************************87677777********** PP

                                 TIGR00564 263 lvkvkgkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkel 331
                                               lv+vk+ r +t+PiAGtr RG+t+eeD  le+eLl deKerAEHlmLvDL+RND+g+v+++g+v+v+++
  lcl|NCBI__GCF_000015305.1:WP_011780029.1 308 LVTVKDGRATTHPIAGTRWRGDTEEEDLLLEKELLCDEKERAEHLMLVDLGRNDLGRVCRPGTVKVEDY 376
                                               ********************************************************************* PP

                                 TIGR00564 332 lkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgyl 400
                                                +ie+yshvmH+vS+V+G l+d++ta+Da++a++PaGTlsGAPKvrAmeli+e+Ek++Rg+YgG++gyl
  lcl|NCBI__GCF_000015305.1:WP_011780029.1 377 SHIERYSHVMHLVSTVTGLLADGKTALDAVTACFPAGTLSGAPKVRAMELIEEVEKTRRGLYGGVLGYL 445
                                               ********************************************************************* PP

                                 TIGR00564 401 sfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               +f+g+ d+aiaiRt+++++g+ayvqAg+G+VaDS+   Ey+E+ nKa+a+l ai
  lcl|NCBI__GCF_000015305.1:WP_011780029.1 446 DFAGNADFAIAIRTALIRNGTAYVQAGGGVVADSNGPYEYNEASNKARAVLAAI 499
                                               *************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (508 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: 9.90
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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