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.7595.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 12.32
//
[ok]

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

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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:

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:

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:

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:

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