Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate GFF3347 HP15_3289 para-aminobenzoate/anthranilate synthase glutamine amidotransferase component II
Query= SwissProt::P00901 (198 letters) >FitnessBrowser__Marino:GFF3347 Length = 193 Score = 316 bits (810), Expect = 2e-91 Identities = 145/191 (75%), Positives = 172/191 (90%) Query: 2 LLMMIDNYDSFTYNVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAG 61 +L+MIDNYDSFTYNVVQYL ELGA+V+V RNDE+TI QIEALNPER+V+SPGPCTP+EAG Sbjct: 1 MLLMIDNYDSFTYNVVQYLAELGADVQVHRNDEITIEQIEALNPERLVISPGPCTPNEAG 60 Query: 62 VSIEAILHFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVHHRDLGVFTGLNN 121 +S+ AI HFAGK+PILG+CLGHQ+IGQ +GGDV+RA +VMHGK SPV H+D GVF GL+N Sbjct: 61 ISMAAIRHFAGKVPILGICLGHQAIGQVYGGDVIRAGRVMHGKVSPVFHKDTGVFRGLSN 120 Query: 122 PLTVTRYHSLVVKRETLPDCLEVTAWTAHEDGSVDEIMGLRHKTLNIEGVQFHPESILTE 181 PL TRYHSLV+ + TLPDCLEVTAWT ++DGS++EIMG+RHKTL IEGVQFHPESI+TE Sbjct: 121 PLQATRYHSLVIDKATLPDCLEVTAWTRNDDGSIEEIMGVRHKTLPIEGVQFHPESIMTE 180 Query: 182 QGHELFANFLK 192 QGHEL NFL+ Sbjct: 181 QGHELLRNFLR 191 Lambda K H 0.320 0.138 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: 206 Number of extensions: 2 Number of successful extensions: 1 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: 198 Length of database: 193 Length adjustment: 20 Effective length of query: 178 Effective length of database: 173 Effective search space: 30794 Effective search space used: 30794 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 (21.8 bits) S2: 44 (21.6 bits)
Align candidate GFF3347 HP15_3289 (para-aminobenzoate/anthranilate synthase glutamine amidotransferase component II)
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.9099.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-92 294.4 0.0 2.1e-92 294.2 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF3347 HP15_3289 para-aminobenzoate/ant Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF3347 HP15_3289 para-aminobenzoate/anthranilate synthase glutamine amidotransferase com # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 294.2 0.0 2.1e-92 2.1e-92 1 191 [. 1 191 [. 1 192 [. 0.98 Alignments for each domain: == domain 1 score: 294.2 bits; conditional E-value: 2.1e-92 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGkl 75 m+l+idnydsftyn+vq+l+elga+v v+rnd++t+++ieal p+ +visPGPctP+ea+is +++i+h+aGk+ lcl|FitnessBrowser__Marino:GFF3347 1 MLLMIDNYDSFTYNVVQYLAELGADVQVHRNDEITIEQIEALNPER-LVISPGPCTPNEAGIS-MAAIRHFAGKV 73 79********************************************.****************.899******** PP TIGR00566 76 PilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtal 150 PilG+ClGhqa++q+ G+dv+ra +v+hGkvs + h++++vf+gl+nP l+atryhslv++ +tl+++levta+ lcl|FitnessBrowser__Marino:GFF3347 74 PILGICLGHQAIGQVYGGDVIRAGRVMHGKVSPVFHKDTGVFRGLSNP--LQATRYHSLVIDKATLPDCLEVTAW 146 ************************************************..************************* PP TIGR00566 151 eeee....ieimairhrdlpleGvqfhPesilselGkellanflk 191 + ++ +eim++rh+ lp+eGvqfhPesi++e+G+ell+nfl+ lcl|FitnessBrowser__Marino:GFF3347 147 TRNDdgsiEEIMGVRHKTLPIEGVQFHPESIMTEQGHELLRNFLR 191 998878888**********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (193 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: 5.79 // [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