Alignments for a candidate for trpE in Methanococcus maripaludis C5

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Methanococcus maripaludis C5

Align anthranilate synthase component I (EC 4.1.3.27) (characterized)
to candidate WP_011868356.1 MMARC5_RS02980 anthranilate synthase component I

Query= metacyc::MONOMER-281
         (461 letters)



>NCBI__GCF_000016125.1:WP_011868356.1
          Length = 439

 Score =  276 bits (706), Expect = 1e-78
 Identities = 179/448 (39%), Positives = 250/448 (55%), Gaps = 28/448 (6%)

Query: 13  DLETPVSTFMKVSRGEEFAFLLESVELGSAFGRHSFIGIGKKDVLVFEKGILRTSNQQLD 72
           D   P+  +  +    ++  +LES   G    R+++I    + +L       +  N+ + 
Sbjct: 5   DYVNPLKLYGVLRDEGKYPVMLESRAKGQINARYTYISSNPEYMLRIGNKT-KMDNETIS 63

Query: 73  YTSSPLKAIKDWLEVYRYSVKHDELPSFRGGAVGFVSYDYI-SYIEKVKVKASVFPTFYF 131
             S+P KA+K   E ++ + K D    F GG VG+++YD I +YI     + SVF  +  
Sbjct: 64  KESNPFKALK---ENFKITQKGDR---FTGGYVGYIAYDCIHNYIGGKIEEPSVFGYY-- 115

Query: 132 VVPEHLIIFDHLKNNVFIISDSPEELTSKVLSPFEEKPEKNVFVTEPESNFE-------R 184
              +H+ ++DH   N +  S++      +      EK  KN  + E +   E        
Sbjct: 116 ---DHMYVYDHETRNFYYHSETNNSEELRNAEATVEKA-KNFKIEEEDGGIEVLGCDADL 171

Query: 185 EQFYKVVEKAKKYIVEGDIFQVVLSQAFTFKTTLDPFYIYRALRMINPSPYMFYLKFGDT 244
           + + K+VEK K+YI  GD FQVV S+ +  K     F +YR LR +NPSPYMF L+F D 
Sbjct: 172 DDYVKMVEKTKEYIYSGDAFQVVPSREYRLKNKFSAFQLYRNLRNVNPSPYMFLLEF-DK 230

Query: 245 VVLGSSPETMAKVEGDKATVKPIAGTRPRGRTVEEDLKLERELLNDEKEIAEHVMLVDLG 304
            V+G+SPETMA V+ +   V PIAGT P G+T  E  KL   LL DEKE AEH+MLVDL 
Sbjct: 231 DVVGASPETMASVQNNILKVNPIAGTAPIGKTENETQKLAEMLLKDEKERAEHMMLVDLA 290

Query: 305 RNDLGRVCKEGTVRVEKKMVIERYSHVMHIVSQVSGELKDDKDAVDVFEATFPAGTVSGA 364
           RND+ +V K G++ +E+   + RYSHV HI S+V G LKD+    D  EA FPAGT++GA
Sbjct: 291 RNDVRKVSKSGSIVLERFFDVVRYSHVQHIESEVLGTLKDNSTIFDAIEAAFPAGTLTGA 350

Query: 365 PKVRAMEIIEELEPTPRGPYAGAVGYFSFPDDKGRMNMDSAITIRSFFFKGKQGWLQAGA 424
           PK RAMEII+E+E + R  Y GAVGYFS        N D AI IR          ++AG 
Sbjct: 351 PKFRAMEIIDEVEKSRRKIYGGAVGYFS-----NSGNADLAIGIRMAEIDSVCR-VRAGG 404

Query: 425 GIVYDSVPEREYQETLNKLRALFRSLEV 452
           G+V DSVPE EY ET  K+ A+ ++L V
Sbjct: 405 GVVADSVPENEYYETERKMAAMMKALGV 432


Lambda     K      H
   0.319    0.137    0.392 

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: 546
Number of extensions: 29
Number of successful extensions: 4
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: 461
Length of database: 439
Length adjustment: 33
Effective length of query: 428
Effective length of database: 406
Effective search space:   173768
Effective search space used:   173768
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_011868356.1 MMARC5_RS02980 (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.30306.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.5e-160  519.7   4.9     8e-160  518.9   4.9    1.4  1  lcl|NCBI__GCF_000016125.1:WP_011868356.1  MMARC5_RS02980 anthranilate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016125.1:WP_011868356.1  MMARC5_RS02980 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  518.9   4.9    8e-160    8e-160       1     449 []       9     431 ..       9     431 .. 0.97

  Alignments for each domain:
  == domain 1  score: 518.9 bits;  conditional E-value: 8e-160
                                 TIGR01820   1 PlelykalrkeseysflLesvekqskkaryslvgaspeavvkinerkavelfeeivskvkklegkkkae 69 
                                               Pl+ly +lr+e +y+++Les  k + +ary++++ +pe++++i ++             +k+++     
  lcl|NCBI__GCF_000016125.1:WP_011868356.1   9 PLKLYGVLRDEGKYPVMLESRAKGQINARYTYISSNPEYMLRIGNK-------------TKMDN----- 59 
                                               99*******************************************8.............67774..... PP

                                 TIGR01820  70 gkdvldalrkalkklkeielleeerqtflGglvGyvaYdavrdywedaekekeseipeaefllvtkvlv 138
                                                 +++++ ++++k+lke  + +++ ++f+Gg vGy+aYd +++y+ ++ +e      +++f ++++++v
  lcl|NCBI__GCF_000016125.1:WP_011868356.1  60 --ETISKESNPFKALKENFKITQKGDRFTGGYVGYIAYDCIHNYIGGKIEE------PSVFGYYDHMYV 120
                                               ..78999999999999988888999***********************999......99********** PP

                                 TIGR01820 139 fdhleeevslvvteevsad..eaekiveklkeaekeeeekkeaeleslaekeefeeavekakekifeGd 205
                                               +dh +++ ++ ++ ++s +  +ae+ vek+k+ + eee++  ++l  +a+ +++ ++vek+ke+i +Gd
  lcl|NCBI__GCF_000016125.1:WP_011868356.1 121 YDHETRNFYYHSETNNSEElrNAEATVEKAKNFKIEEEDGGIEVLGCDADLDDYVKMVEKTKEYIYSGD 189
                                               *******8888876665546699*************99999999999999******************* PP

                                 TIGR01820 206 ifqvvlSrklelrldldplelYaklreiNPSPYmyllefgdraivGaSPEtlvrvekrtveinPiAGta 274
                                                fqvv Sr+++l+ + + ++lY++lr++NPSPYm+llef d+ +vGaSPEt+ +v+++++++nPiAGta
  lcl|NCBI__GCF_000016125.1:WP_011868356.1 190 AFQVVPSREYRLKNKFSAFQLYRNLRNVNPSPYMFLLEF-DKDVVGASPETMASVQNNILKVNPIAGTA 257
                                               ***************************************.***************************** PP

                                 TIGR01820 275 pRgkseeeDeelakelLsdeKerAEHvmLvDLaRNDvrkvsesgsvkvsefmkvlkyshvqHieSevvg 343
                                               p gk+e+e ++la+ lL+deKerAEH+mLvDLaRNDvrkvs+sgs+ +++f++v++yshvqHieSev+g
  lcl|NCBI__GCF_000016125.1:WP_011868356.1 258 PIGKTENETQKLAEMLLKDEKERAEHMMLVDLARNDVRKVSKSGSIVLERFFDVVRYSHVQHIESEVLG 326
                                               ********************************************************************* PP

                                 TIGR01820 344 tLkkeadafdalkAvfPAGtlsGaPKirAmeiieelEkepRgvYgGgvGyfslngdadlAiviRtalie 412
                                               tLk++ + fda++A+fPAGtl+GaPK rAmeii+e+Ek++R++YgG+vGyfs  g+adlAi iR+a+i+
  lcl|NCBI__GCF_000016125.1:WP_011868356.1 327 TLKDNSTIFDAIEAAFPAGTLTGAPKFRAMEIIDEVEKSRRKIYGGAVGYFSNSGNADLAIGIRMAEID 395
                                               ********************************************************************9 PP

                                 TIGR01820 413 kkklriqaGAGivaDSdPekEfeEterKmkavlkaig 449
                                                + +r++aG G+vaDS+Pe+E++EterKm+a++ka+g
  lcl|NCBI__GCF_000016125.1:WP_011868356.1 396 -SVCRVRAGGGVVADSVPENEYYETERKMAAMMKALG 431
                                               .89********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (449 nodes)
Target sequences:                          1  (439 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 4.46
//
[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