Alignments for a candidate for trpED in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpED in Sinorhizobium meliloti 1021

Align candidate SMc02725 SMc02725 (anthranilate synthase)
to HMM TIGR01815 (anthranilate synthase (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/TIGR01815.hmm
# target sequence database:        /tmp/gapView.27935.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01815  [M=717]
Accession:   TIGR01815
Description: TrpE-clade3: anthranilate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
          0 1408.6   0.0          0 1408.4   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc02725  SMc02725 anthranilate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02725  SMc02725 anthranilate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1408.4   0.0         0         0       1     717 []      13     729 .]      13     729 .] 1.00

  Alignments for each domain:
  == domain 1  score: 1408.4 bits;  conditional E-value: 0
                           TIGR01815   1 yrtkGgvvvtrratevkletaleevvdalderrGallsssyeypGrykrwalgfvdppvalsasGrtlriealne 75 
                                         y+tkGg+vvtrr++e+++++a++++vd+lderrGa++ss+yeypGry+rw++++vdpp+a+s++Gr+l+iea+ne
  lcl|FitnessBrowser__Smeli:SMc02725  13 YTTKGGIVVTRRRREASYSDAIAGYVDRLDERRGAVFSSNYEYPGRYTRWDTAVVDPPLAISSFGRSLWIEAYNE 87 
                                         89************************************************************************* PP

                           TIGR01815  76 rGevllpviaealkkvedlakleeaarrvtasvkspdevlaeeerskqpsvftvlravldlfaseedellGlyGa 150
                                         rGevll++iae+lk+v+d++ +++aarr+++++++pd+v++eeersk+p+vftvlrav++lf+seed++lGlyGa
  lcl|FitnessBrowser__Smeli:SMc02725  88 RGEVLLALIAEDLKSVADITLGSLAARRLDLTINEPDRVFTEEERSKMPTVFTVLRAVTNLFHSEEDSNLGLYGA 162
                                         *************************************************************************** PP

                           TIGR01815 151 fgydlafqfeaieqklerpddqrdlvlylpdelvvvdyyaakaflveydfitaagstegleadgedepyrsdtsi 225
                                         fgydlafqf+aie+kl+rpddqrd+vl+lpde++vvd+yaaka++++ydf+++++steg++ad+++ep+rs++si
  lcl|FitnessBrowser__Smeli:SMc02725 163 FGYDLAFQFDAIELKLSRPDDQRDMVLFLPDEILVVDHYAAKAWIDRYDFARENLSTEGKAADIAPEPFRSVDSI 237
                                         *************************************************************************** PP

                           TIGR01815 226 epqadhkpGeyaklvekakeafrrGdlfevvpgqkffeaceaapsevferlkainpspyeffvnlGrgeylvgas 300
                                         +p++dh+pGeya+lv+kake+frrGdlfevvpgqkf+e+ce++pse+++rlkainpspy+ff+nlG++eylvgas
  lcl|FitnessBrowser__Smeli:SMc02725 238 PPHGDHRPGEYAELVVKAKESFRRGDLFEVVPGQKFYERCESRPSEISNRLKAINPSPYSFFINLGNQEYLVGAS 312
                                         *************************************************************************** PP

                           TIGR01815 301 pemfvrveGrrvetcpisGtikrGddaiddaaqilkllnskkdeaeltmctdvdrndksrvcepGsvkviGrrqi 375
                                         pemfvrv+Grr+etcpisGtikrGdd+i+d++qilkllnskkde+eltmc+dvdrndksrvc+pGsvkviGrrqi
  lcl|FitnessBrowser__Smeli:SMc02725 313 PEMFVRVSGRRIETCPISGTIKRGDDPIADSEQILKLLNSKKDESELTMCSDVDRNDKSRVCVPGSVKVIGRRQI 387
                                         *************************************************************************** PP

                           TIGR01815 376 elysrlihtvdhveGrlrdeldaldaflshawavtvtGapkraalqfiekteksprrwyGGavGrlgfnGdlntG 450
                                         e+ysrlihtvdh+eGrlrd++da+d+flshawavtvtGapk++a++fie++ekspr+wyGGa+G++gfnGd+ntG
  lcl|FitnessBrowser__Smeli:SMc02725 388 EMYSRLIHTVDHIEGRLRDDMDAFDGFLSHAWAVTVTGAPKLWAMRFIESHEKSPRAWYGGAIGMVGFNGDMNTG 462
                                         *************************************************************************** PP

                           TIGR01815 451 ltlrtirlkdgiaevraGatllydsdpeaeeaetelkaaalieairdakaadaakeesavakvgeGkrillvdhe 525
                                         ltlrtir+kdgiaevraGatllyds+pe+eeaetelka+a+i+airdak+a++ak++++va+vg+G++illvdhe
  lcl|FitnessBrowser__Smeli:SMc02725 463 LTLRTIRIKDGIAEVRAGATLLYDSNPEEEEAETELKASAMIAAIRDAKSANSAKSARDVAAVGAGVSILLVDHE 537
                                         *************************************************************************** PP

                           TIGR01815 526 dsfvhtlanylrqtGasvttlrhsvaeelldeerpdlvvlspGpGrpkdfdvketikaalardlpvfGvclGlqg 600
                                         dsfvhtlany+rqtGasvtt+r++vaee++d+++pdlvvlspGpG+pkdfd+k+tik+a+ardlp+fGvclGlq+
  lcl|FitnessBrowser__Smeli:SMc02725 538 DSFVHTLANYFRQTGASVTTVRTPVAEEIFDRVKPDLVVLSPGPGTPKDFDCKATIKKARARDLPIFGVCLGLQA 612
                                         *************************************************************************** PP

                           TIGR01815 601 lveafGGeldvlaepvhGkasrirvlepdvlfaglpeeltvGryhslfarsdrlpkelkvtaesedgvimaiehr 675
                                         l+ea+GG+l++la+p+hGk+srirvlep+++f+gl++e+tvGryhs+fa++++lp+e+++taesedg+im+ieh+
  lcl|FitnessBrowser__Smeli:SMc02725 613 LAEAYGGDLRQLAIPMHGKPSRIRVLEPGIVFSGLGKEVTVGRYHSIFADPSNLPREFVITAESEDGTIMGIEHS 687
                                         *************************************************************************** PP

                           TIGR01815 676 klpvaavqfhpesiltlaGeaGlalienvvdklaksaktkaa 717
                                         k+pvaavqfhpesi+tl+G+aG+++ienvv++lak+aktkaa
  lcl|FitnessBrowser__Smeli:SMc02725 688 KEPVAAVQFHPESIMTLGGDAGMRMIENVVAHLAKRAKTKAA 729
                                         ***************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (717 nodes)
Target sequences:                          1  (729 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: 00:00:00.05
# Mc/sec: 10.11
//
[ok]

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

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Protein sequences (fasta format)
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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