Alignments for a candidate for trpE in Methanosarcina barkeri Fusaro

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Methanosarcina barkeri Fusaro

Align Anthranilate synthase component 1 2; EC 4.1.3.27; Anthranilate synthase component I 2 (uncharacterized)
to candidate WP_011308530.1 MBAR_RS19240 anthranilate synthase component I

Query= curated2:Q5V213
         (536 letters)



>NCBI__GCF_000195895.1:WP_011308530.1
          Length = 547

 Score =  397 bits (1020), Expect = e-115
 Identities = 245/570 (42%), Positives = 323/570 (56%), Gaps = 80/570 (14%)

Query: 1   MTLDISREEFVEHAKA-DRPVVVRTAAELD-VDVEPLTAYAALTGRTSDVAANDYTFLLE 58
           ++ D+ +EEF + A    +P  ++  A +D +   PL  Y AL         + Y++LLE
Sbjct: 2   LSFDLGKEEFKKLASGVSQPGFIQLLARIDNLTCSPLELYHALRAS----GTSGYSYLLE 57

Query: 59  SAEKVASSDPDGAFAPETDDRHARFSFVGYDPRAVVTV---------------------- 96
           S EK               +  AR+SFVG DP AVV +                      
Sbjct: 58  SVEK--------------QETKARYSFVGNDPDAVVKIGDRKISLELLNPNASPFFEEIQ 103

Query: 97  ----------TGDESEVEAFDDRYADLVTT----DGGDVVDDLRAAMPD---VALRNFPA 139
                     T +E   E  +    +L  T     G D  D LR   P    + L N   
Sbjct: 104 SKTKDACGCETIEEENPEKENSELGNLKFTAPIPKGKDGFDALRLVFPSANGMGLLNTKR 163

Query: 140 MDRQHLEGGLVGFLSYDAVYDLWLDEVGLDRP-DSRFPDAQFVLTTSTVRFDHVEDTVSL 198
            DRQ   GG +G+ +YDA+YD WL   G+ +  +S  P+ Q++L + T  FDH+ + + +
Sbjct: 164 FDRQTFLGGAIGYTAYDAIYDSWL---GVKKGFESEIPELQYLLVSKTFVFDHMTEEIYI 220

Query: 199 VFTPVVRQGEDAGERYGELVAEAERVEAVLSDLSPLSTG------------GFRREDEVA 246
           V TP +  G + GE Y + + EAE++   L + +                 G    D  A
Sbjct: 221 VVTPFIIPGANVGEIYEKALLEAEKLYTTLKEAALSGDSVEIAIPGGSIFPGLPVSDCNA 280

Query: 247 GPRDEYEDAVERAKEYVLSGDIYQGVISRTRELYGDVDPLGFYEALRAVNPSPYMYLLGY 306
           G + ++ED+V +AKE++ +GDI+Q V+SR  E   +  P   Y  LRA+NPSPYMY+  +
Sbjct: 281 GKK-KFEDSVVQAKEHIFAGDIFQVVLSRKCEFTLEQSPFELYMQLRAINPSPYMYIFEF 339

Query: 307 DDLTIVGASPETLVSVAGDHVVSNPIAGTCPRGNSPVEDRRLAGEMLADGKERAEHTMLV 366
            DL IVGASPETL++V    +++NPIAGTCPRG +  ED   A  M+ D KERAEH MLV
Sbjct: 340 GDLAIVGASPETLLTVHERTLITNPIAGTCPRGKTEAEDEAFAAHMMHDEKERAEHVMLV 399

Query: 367 DLARNDVRRVAEAGSVRVPEFMNVLKYSHVQHIESTVTGRLAEDKDAFDAARATFPAGTL 426
           DL RNDVR V E+GSV+V EFM VLKYSHVQHIES V G L  + D FDA RA FPAGTL
Sbjct: 400 DLGRNDVRMVTESGSVKVSEFMKVLKYSHVQHIESKVIGTLRPECDQFDAFRAIFPAGTL 459

Query: 427 SGAPKIRAMEIIDELERSPRGPYGGGVGYFDWDGDTDFAIVIRSATVEDEGDRDRITVQA 486
           SGAPKIRAMEII ELE SPRG YGGGVGY+ W+GD DFAIVIR+  V+ +    + +VQA
Sbjct: 460 SGAPKIRAMEIISELETSPRGIYGGGVGYYSWNGDADFAIVIRTIIVQGK----KASVQA 515

Query: 487 GAGIVADSDPESEYVETEQKMDGVLTALEE 516
           GAGIVADSDP  E+ ETE+KM  +L A+ E
Sbjct: 516 GAGIVADSDPGYEFRETERKMGAMLAAIGE 545


Lambda     K      H
   0.315    0.135    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: 786
Number of extensions: 38
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: 536
Length of database: 547
Length adjustment: 35
Effective length of query: 501
Effective length of database: 512
Effective search space:   256512
Effective search space used:   256512
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: 52 (24.6 bits)

Align candidate WP_011308530.1 MBAR_RS19240 (anthranilate synthase component I)
to HMM TIGR01820 (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/TIGR01820.hmm
# target sequence database:        /tmp/gapView.649.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01820  [M=449]
Accession:   TIGR01820
Description: TrpE-arch: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.7e-204  664.7   0.0   5.6e-204  664.4   0.0    1.0  1  lcl|NCBI__GCF_000195895.1:WP_011308530.1  MBAR_RS19240 anthranilate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195895.1:WP_011308530.1  MBAR_RS19240 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  664.4   0.0  5.6e-204  5.6e-204       1     449 []      37     544 ..      37     544 .. 0.94

  Alignments for each domain:
  == domain 1  score: 664.4 bits;  conditional E-value: 5.6e-204
                                 TIGR01820   1 Plelykalrk..eseysflLesvekqskkaryslvgaspeavvkiner.........kavelfeeivsk 58 
                                               Plely+alr+  +s+ys+lLesvekq++karys+vg++p+avvki +r         +a+ +feei+sk
  lcl|NCBI__GCF_000195895.1:WP_011308530.1  37 PLELYHALRAsgTSGYSYLLESVEKQETKARYSFVGNDPDAVVKIGDRkislellnpNASPFFEEIQSK 105
                                               9********988888****************************************************** PP

                                 TIGR01820  59 vkkleg......kkkae...................gkdvldalrkalkklkeiellee...erqtflG 99 
                                               +k+ +g      +   +                   gkd +dalr ++++++++ ll++   +rqtflG
  lcl|NCBI__GCF_000195895.1:WP_011308530.1 106 TKDACGcetieeE---NpekenselgnlkftapipkGKDGFDALRLVFPSANGMGLLNTkrfDRQTFLG 171
                                               ******7655441...145556789999999**********************99988877899***** PP

                                 TIGR01820 100 glvGyvaYdavrdywedaekekeseipeaefllvtkvlvfdhleeevslvvteevsad........... 157
                                               g++Gy+aYda++d+w++++k +eseipe+++llv+k++vfdh++ee+++vvt+++ +            
  lcl|NCBI__GCF_000195895.1:WP_011308530.1 172 GAIGYTAYDAIYDSWLGVKKGFESEIPELQYLLVSKTFVFDHMTEEIYIVVTPFIIPGanvgeiyekal 240
                                               ******************************************************999899999999999 PP

                                 TIGR01820 158 .eaekiveklkeaekeeeekkeaeleslae............keefeeavekakekifeGdifqvvlSr 213
                                                eaek++++lkea    ++   a+    +             k++fe++v +ake+if+GdifqvvlSr
  lcl|NCBI__GCF_000195895.1:WP_011308530.1 241 lEAEKLYTTLKEAALSGDSVEIAIP-GGSIfpglpvsdcnagKKKFEDSVVQAKEHIFAGDIFQVVLSR 308
                                               9999999999999887665433322.2222245666667777999************************ PP

                                 TIGR01820 214 klelrldldplelYaklreiNPSPYmyllefgdraivGaSPEtlvrvekrtveinPiAGtapRgkseee 282
                                               k+e++l+++p+elY +lr+iNPSPYmy++efgd+aivGaSPEtl++v++rt+++nPiAGt+pRgk+e+e
  lcl|NCBI__GCF_000195895.1:WP_011308530.1 309 KCEFTLEQSPFELYMQLRAINPSPYMYIFEFGDLAIVGASPETLLTVHERTLITNPIAGTCPRGKTEAE 377
                                               ********************************************************************* PP

                                 TIGR01820 283 DeelakelLsdeKerAEHvmLvDLaRNDvrkvsesgsvkvsefmkvlkyshvqHieSevvgtLkkeada 351
                                               De++a+++++deKerAEHvmLvDL+RNDvr+v+esgsvkvsefmkvlkyshvqHieS+v+gtL++e+d+
  lcl|NCBI__GCF_000195895.1:WP_011308530.1 378 DEAFAAHMMHDEKERAEHVMLVDLGRNDVRMVTESGSVKVSEFMKVLKYSHVQHIESKVIGTLRPECDQ 446
                                               ********************************************************************* PP

                                 TIGR01820 352 fdalkAvfPAGtlsGaPKirAmeiieelEkepRgvYgGgvGyfslngdadlAiviRtaliekkklriqa 420
                                               fda++A+fPAGtlsGaPKirAmeii+elE++pRg+YgGgvGy+s+ngdad+AiviRt+++++kk+++qa
  lcl|NCBI__GCF_000195895.1:WP_011308530.1 447 FDAFRAIFPAGTLSGAPKIRAMEIISELETSPRGIYGGGVGYYSWNGDADFAIVIRTIIVQGKKASVQA 515
                                               ********************************************************************* PP

                                 TIGR01820 421 GAGivaDSdPekEfeEterKmkavlkaig 449
                                               GAGivaDSdP +Ef+EterKm a+l+aig
  lcl|NCBI__GCF_000195895.1:WP_011308530.1 516 GAGIVADSDPGYEFRETERKMGAMLAAIG 544
                                               ***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (449 nodes)
Target sequences:                          1  (547 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.25
//
[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