Align candidate AZOBR_RS06415 AZOBR_RS06415 (anthranilate synthase subunit I)
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.24040.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 1298.3 0.0 0 1298.1 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS06415 AZOBR_RS06415 anthranilate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS06415 AZOBR_RS06415 anthranilate synthase subunit I # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1298.1 0.0 0 0 1 717 [] 18 736 .. 18 736 .. 0.99 Alignments for each domain: == domain 1 score: 1298.1 bits; conditional E-value: 0 TIGR01815 1 yrtkGgvvvtrratevkletaleevvdalderrGallsssyeypGrykrwalgfvdppvalsasGrtlr 69 ++t+Ggv vtr at+++++ al++v+dald+rrG+llss++e+pGry+r+algf+dpp+a++a+Grtlr lcl|FitnessBrowser__azobra:AZOBR_RS06415 18 FQTRGGVAVTRCATALDPQGALDPVIDALDRRRGLLLSSGVEAPGRYRRHALGFTDPPLAVTARGRTLR 86 89******************************************************************* PP TIGR01815 70 iealnerGevllpviaealkkvedlakleeaarrvtasvkspdevlaeeerskqpsvftvlravldlfa 138 i+aln rG+vllp++aeal+++e+la+leea++rvta+v++p+++++eeers+qps f+vlravl+lfa lcl|FitnessBrowser__azobra:AZOBR_RS06415 87 IDALNARGRVLLPAVAEALRGLEALAGLEEAPSRVTALVRKPQHPFPEEERSRQPSLFSVLRAVLNLFA 155 ********************************************************************* PP TIGR01815 139 seedellGlyGafgydlafqfeaieqklerpddqrdlvlylpdelvvvdyyaakaflveydfitaagst 207 +++d+llGlyGaf+ydlafqfe+i+++lerpddqrdlvlylpd+lvv+d++a+ a+lvey+f+taagst lcl|FitnessBrowser__azobra:AZOBR_RS06415 156 APDDPLLGLYGAFAYDLAFQFEPIRLRLERPDDQRDLVLYLPDRLVVLDPVAGLARLVEYEFATAAGST 224 ********************************************************************* PP TIGR01815 208 egleadgedepyrsdtsiepqadhkpGeyaklvekakeafrrGdlfevvpgqkffeaceaapsevferl 276 egle+ g+d+pyr+dt++e ++dh+pG y+++ve+ak+afrrGdlfevvpgq+f+e+c++aps vf+rl lcl|FitnessBrowser__azobra:AZOBR_RS06415 225 EGLERAGRDHPYRPDTNAEGGCDHAPGAYQRVVETAKAAFRRGDLFEVVPGQTFAEPCADAPSAVFRRL 293 ********************************************************************* PP TIGR01815 277 kainpspyeffvnlGrgeylvgaspemfvrveGr....rvetcpisGtikrGddaiddaaqilkllnsk 341 +a+np+pye+fvnlGrge+lv+aspem+vrv+G+ rvetcpisGt++rG+da++daaq+l+ll+s+ lcl|FitnessBrowser__azobra:AZOBR_RS06415 294 RAANPAPYEAFVNLGRGEFLVAASPEMYVRVAGGrmggRVETCPISGTVARGADALGDAAQVLRLLTSA 362 *******************************975222279***************************** PP TIGR01815 342 kdeaeltmctdvdrndksrvcepGsvkviGrrqielysrlihtvdhveGrlrdeldaldaflshawavt 410 kd+aeltmctdvdrndk+rvcepGsv+viGrr+ielysrlihtvdhveGrlr++ldaldafl+h+wavt lcl|FitnessBrowser__azobra:AZOBR_RS06415 363 KDAAELTMCTDVDRNDKARVCEPGSVRVIGRRMIELYSRLIHTVDHVEGRLRPGLDALDAFLTHTWAVT 431 ********************************************************************* PP TIGR01815 411 vtGapkraalqfiekteksprrwyGGavGrlgfnGdlntGltlrtirlkdgiaevraGatllydsdpea 479 vtGapkr+a+qf+e+te+sprrwyGGa+Grlgf+G+++tGltlrtir+++g+a+vraGatll+dsdp+a lcl|FitnessBrowser__azobra:AZOBR_RS06415 432 VTGAPKRWAMQFLEDTEQSPRRWYGGAFGRLGFDGGMDTGLTLRTIRMAEGVAYVRAGATLLSDSDPDA 500 ********************************************************************* PP TIGR01815 480 eeaetelkaaalieairdakaadaakeesavakvgeGkrillvdhedsfvhtlanylrqtGasvttlrh 548 e+ae++lkaaa+++air + + + a ++a++++g G+r+llvdh+dsfvhtla+ylrqtGasv tlrh lcl|FitnessBrowser__azobra:AZOBR_RS06415 501 EDAECRLKAAAFRDAIR-GVTEGVACALPAAPNGGRGRRVLLVDHDDSFVHTLADYLRQTGASVMTLRH 568 *****************.888999********************************************* PP TIGR01815 549 svaeelldeerpdlvvlspGpGrpkdfdvketikaalardlpvfGvclGlqglveafGGeldvlaepvh 617 ++a+++l+e+rpdlvvlspGpGrp+df+v++ti+aala++lpvfGvclGlqg+ve+fGG+ldvl+epvh lcl|FitnessBrowser__azobra:AZOBR_RS06415 569 GHARAALAERRPDLVVLSPGPGRPADFNVAGTIDAALALGLPVFGVCLGLQGMVERFGGALDVLPEPVH 637 ********************************************************************* PP TIGR01815 618 GkasrirvlepdvlfaglpeeltvGryhslfarsdrlpkelkvtaesedgvimaiehrklpvaavqfhp 686 Gka+++rvl++ +lfaglpe++ vGryhsl+ar+drlp++l+vtae++dg++ma+ehr+lp+aavqfhp lcl|FitnessBrowser__azobra:AZOBR_RS06415 638 GKATEVRVLGG-ALFAGLPERMRVGRYHSLVARRDRLPADLTVTAETADGLVMAVEHRRLPLAAVQFHP 705 *********99.********************************************************* PP TIGR01815 687 esiltlaGeaGlalienvvdklaksaktkaa 717 esil+l+G+aGlal++nv+d+la++a t+aa lcl|FitnessBrowser__azobra:AZOBR_RS06415 706 ESILSLDGGAGLALLGNVMDRLAAGALTDAA 736 ****************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (717 nodes) Target sequences: 1 (737 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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06 # Mc/sec: 8.30 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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