Align Anthranilate synthase component II (characterized, see rationale)
to candidate SMc02725 SMc02725 anthranilate synthase
Query= uniprot:Q8AAD4_BACTN (188 letters) >FitnessBrowser__Smeli:SMc02725 Length = 729 Score = 128 bits (321), Expect = 3e-34 Identities = 70/178 (39%), Positives = 99/178 (55%) Query: 1 MKILLLDNYDSFTYNLLHAVKELGATDVEVVRNDQINLDEVERFDKIILSPGPGIPEEAG 60 + ILL+D+ DSF + L + ++ GA+ V + + + D ++LSPGPG P++ Sbjct: 529 VSILLVDHEDSFVHTLANYFRQTGASVTTVRTPVAEEIFDRVKPDLVVLSPGPGTPKDFD 588 Query: 61 LLLPIIKRYAPTKSILGVCLGHQAIGEAFGARLENLKEVYHGVQTPISILQKDVLFEGLG 120 I K A I GVCLG QA+ EA+G L L HG + I +L+ ++F GLG Sbjct: 589 CKATIKKARARDLPIFGVCLGLQALAEAYGGDLRQLAIPMHGKPSRIRVLEPGIVFSGLG 648 Query: 121 KEIPVGRYHSWVVSREGFPECLEITAESQEGQIMALRHKTYDVHGIQFHPESVLTPQG 178 KE+ VGRYHS P ITAES++G IM + H V +QFHPES++T G Sbjct: 649 KEVTVGRYHSIFADPSNLPREFVITAESEDGTIMGIEHSKEPVAAVQFHPESIMTLGG 706 Lambda K H 0.319 0.141 0.411 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: 308 Number of extensions: 10 Number of successful extensions: 2 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: 188 Length of database: 729 Length adjustment: 29 Effective length of query: 159 Effective length of database: 700 Effective search space: 111300 Effective search space used: 111300 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: 49 (23.5 bits)
Align candidate SMc02725 SMc02725 (anthranilate synthase)
to HMM TIGR00566 (glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase)
# 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/TIGR00566.hmm # target sequence database: /tmp/gapView.18062.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00566 [M=192] Accession: TIGR00566 Description: trpG_papA: glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-44 137.1 0.0 4.8e-44 136.5 0.0 1.3 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 ! 136.5 0.0 4.8e-44 4.8e-44 2 190 .. 531 717 .. 530 719 .. 0.88 Alignments for each domain: == domain 1 score: 136.5 bits; conditional E-value: 4.8e-44 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGklP 76 +ll+d dsf + l +++ + ga+v+ r ++ + ++++p+l +v+sPGP+tP++ + + + + a lP lcl|FitnessBrowser__Smeli:SMc02725 531 ILLVDHEDSFVHTLANYFRQTGASVTTVRT-PVAEEIFDRVKPDL-VVLSPGPGTPKDFDCK-ATIKKARARDLP 602 9*********************99875554.5566677*******.************9888.56666667779* PP TIGR00566 77 ilGvClGhqalaqafGadvvraekvkhGkvseiehngaa.vfaglfnPdalkatryhslvveaetldtllevtal 150 i+GvClG qala a G+d+ +++ +hGk s i+ + + vf gl + ++++ryhs+ ++ +l+ + +ta lcl|FitnessBrowser__Smeli:SMc02725 603 IFGVCLGLQALAEAYGGDLRQLAIPMHGKPSRIRVLEPGiVFSGLGKE--VTVGRYHSIFADPSNLPREFVITAE 675 **********************************98877369999998..9********************9999 PP TIGR00566 151 eeeeieimairhrdlpleGvqfhPesils...elGkellanfl 190 +e im+i h + p+ vqfhPesi++ + G ++++n++ lcl|FitnessBrowser__Smeli:SMc02725 676 SEDG-TIMGIEHSKEPVAAVQFHPESIMTlggDAGMRMIENVV 717 8888.9**********************844456677888875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 16.98 // [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