Align candidate WP_025273780.1 HALAL_RS0109490 (anthranilate synthase component 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.22700.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-287 939.0 0.0 8.2e-287 938.8 0.0 1.0 1 lcl|NCBI__GCF_000527155.1:WP_025273780.1 HALAL_RS0109490 anthranilate syn Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000527155.1:WP_025273780.1 HALAL_RS0109490 anthranilate synthase component I # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 938.8 0.0 8.2e-287 8.2e-287 1 706 [. 4 703 .. 4 708 .] 0.95 Alignments for each domain: == domain 1 score: 938.8 bits; conditional E-value: 8.2e-287 TIGR01815 1 yrtkGgvvvtrratevkletaleevvdalderrGallsssyeypGrykrwalgfvdppvalsasGrtlr 69 y+t Gg ++tr a +++ + l+ + + +++rrG++lss++eypGry r+ l++v+p+ ++ sGrt++ lcl|NCBI__GCF_000527155.1:WP_025273780.1 4 YTTAGGARITRTAATLNT-DDLDYISELVESRRGGVLSSGMEYPGRYSRFHLAYVNPAAEVVVSGRTVT 71 89**********999986.5699999999**************************************** PP TIGR01815 70 iealnerGevllpviaealkkvedlakleeaarrvtasvkspdevlaeeerskqpsvftvlravldlfa 138 +alnerG+v+lpv al++v+ ++ v+ v + v++ee+rs+q +vft lra++ f lcl|NCBI__GCF_000527155.1:WP_025273780.1 72 AQALNERGQVVLPVFEHALSQVAPVKVEG---DAVSIEVPTDPGVVTEEQRSRQLTVFTALRAIVSAFG 137 ******************99998876544...446677777889************************8 PP TIGR01815 139 seedellGlyGafgydlafqfeaieqklerpddqrdlvlylpdelvvvdyyaakaflveydfitaagst 207 + ed+ lGl+Gafgydla+qfe+ie erp d rd vl+l de+ vvd + a l +ydf + +st lcl|NCBI__GCF_000527155.1:WP_025273780.1 138 C-EDPYLGLWGAFGYDLAYQFEPIEFAKERPSDVRDAVLHLADEVYVVDRKRETASLYRYDFEVDGAST 205 7.79***************************************************************** PP TIGR01815 208 egleadgedepyrsdtsiepqadhkpGeyaklvekakeafrrGdlfevvpgqkffeaceaapsevferl 276 gle++ge+ +yr+ ++++++ pG y+++v +ake fr G+lfevvpg +++++c++ p++ +erl lcl|NCBI__GCF_000527155.1:WP_025273780.1 206 VGLERTGEHFDYRPAEEVPAG--PTPGAYSEVVRQAKEEFREGNLFEVVPGHEMYTTCDS-PASFYERL 271 *****************9987..57*********************************75.8899**** PP TIGR01815 277 kainpspyeffvnlGrgeylvgaspemfvrveGrrvetcpisGtikrGddaiddaaqilkllnskkdea 345 k+ npspyeff+nlG++eylvg+spemfvrv+G+rvetcpisGti+rG+d+++da qil llns+k+ea lcl|NCBI__GCF_000527155.1:WP_025273780.1 272 KKSNPSPYEFFFNLGHDEYLVGTSPEMFVRVNGNRVETCPISGTIARGNDPLQDAGQILSLLNSEKEEA 340 ********************************************************************* PP TIGR01815 346 eltmctdvdrndksrvcepGsvkviGrrqielysrlihtvdhveGrlrdeldaldaflshawavtvtGa 414 eltmctdvdrndk+rvc+pGsv+viGrrqielys+lihtvdh+eGrlr+++da+dafl+h wavtvtGa lcl|NCBI__GCF_000527155.1:WP_025273780.1 341 ELTMCTDVDRNDKARVCVPGSVRVIGRRQIELYSHLIHTVDHIEGRLREDMDAFDAFLTHMWAVTVTGA 409 ********************************************************************* PP TIGR01815 415 pkraalqfiekteksprrwyGGavGrlgfnGdlntGltlrtirlkdgiaevraGatllydsdpeaeeae 483 pk +a++fie +e +prrwyGGavG++gf+G +ntGltlrt ++dg++ vraGatlly sdp+ eeae lcl|NCBI__GCF_000527155.1:WP_025273780.1 410 PKTWAMRFIERNETTPRRWYGGAVGYVGFDGSMNTGLTLRTAHIRDGLTSVRAGATLLYYSDPDMEEAE 478 ********************************************************************* PP TIGR01815 484 telkaaalieairdakaadaakees...avakvgeGkrillvdhedsfvhtlanylrqtGasvttlrhs 549 t lka+al+ea + + +++ ++ a + g+G+r+ll+dhedsfv tla+y+rq a vttlr + lcl|NCBI__GCF_000527155.1:WP_025273780.1 479 TFLKASALLEAAEGKHRMRPEPPAAidvAGGAAGTGRRVLLIDHEDSFVNTLADYFRQHDAEVTTLRYG 547 ***********997777766554331003445669********************************** PP TIGR01815 550 va.eelldeerpdlvvlspGpGrpkdfdvketikaalardlpvfGvclGlqglveafGGeldvlaepvh 617 + ++ld+ +pdlvvlspGpGrp+df +++ + +r+lpvfGvclGlq++ve GG+l+ l+ep h lcl|NCBI__GCF_000527155.1:WP_025273780.1 548 FDlGQALDDINPDLVVLSPGPGRPTDFACQALLRDLERRELPVFGVCLGLQAMVEYTGGKLSLLDEPAH 616 973689*************************************************************** PP TIGR01815 618 GkasrirvlepdvlfaglpeeltvGryhslfarsdrlpkelkvtaesedgvimaiehrklpvaavqfhp 686 Gk+ +++v ++ lf++++++lt ryhsl a+ d++ ++ t+ + d++ m+ie vqfhp lcl|NCBI__GCF_000527155.1:WP_025273780.1 617 GKPGNVKVFGG-GLFSDVGDRLTTARYHSLHATIDQVQGGFV-TTSALDDIAMSIEDPMRGWYGVQFHP 683 *********99.79***********************99986.55677889****************** PP TIGR01815 687 esiltlaGeaGlalienvvd 706 esilt + Gl+li+nv+ lcl|NCBI__GCF_000527155.1:WP_025273780.1 684 ESILTSERASGLRLIGNVLR 703 *****************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (717 nodes) Target sequences: 1 (708 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 0.02s 00:00:00.06 Elapsed: 00:00:00.06 # Mc/sec: 7.82 // [ok]
This GapMind analysis is from Apr 10 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