Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate Pf1N1B4_2547 Anthranilate synthase, amidotransferase component (EC 4.1.3.27) @ Para-aminobenzoate synthase, amidotransferase component (EC 2.6.1.85)
Query= SwissProt::P00901 (198 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2547 Length = 197 Score = 369 bits (947), Expect = e-107 Identities = 178/197 (90%), Positives = 188/197 (95%) Query: 2 LLMMIDNYDSFTYNVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAG 61 +L+MIDNYDSFTYNVVQYLGELG+EVKV+RNDE+TIA+IEALNPERIVVSPGPCTP+EAG Sbjct: 1 MLLMIDNYDSFTYNVVQYLGELGSEVKVVRNDELTIAEIEALNPERIVVSPGPCTPTEAG 60 Query: 62 VSIEAILHFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVHHRDLGVFTGLNN 121 +SIEAI HFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPV H D GVF GLN Sbjct: 61 ISIEAIKHFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVFHEDKGVFEGLNR 120 Query: 122 PLTVTRYHSLVVKRETLPDCLEVTAWTAHEDGSVDEIMGLRHKTLNIEGVQFHPESILTE 181 PLTVTRYHSL+VKRETLPDCLE+TAWT EDGSVDEIMGLRHKTLNIEGVQFHPESILTE Sbjct: 121 PLTVTRYHSLIVKRETLPDCLELTAWTQLEDGSVDEIMGLRHKTLNIEGVQFHPESILTE 180 Query: 182 QGHELFANFLKQTGGRR 198 QGHELFANFLKQTGG R Sbjct: 181 QGHELFANFLKQTGGTR 197 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: 237 Number of extensions: 1 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: 197 Length adjustment: 20 Effective length of query: 178 Effective length of database: 177 Effective search space: 31506 Effective search space used: 31506 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: 45 (21.9 bits)
Align candidate Pf1N1B4_2547 (Anthranilate synthase, amidotransferase component (EC 4.1.3.27) @ Para-aminobenzoate synthase, amidotransferase component (EC 2.6.1.85))
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.31626.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-91 291.9 0.0 1.2e-91 291.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2547 Anthranilate synthase, amidotran Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2547 Anthranilate synthase, amidotransferase component (EC 4.1.3.27) @ Para # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 291.8 0.0 1.2e-91 1.2e-91 1 191 [. 1 191 [. 1 192 [. 0.98 Alignments for each domain: == domain 1 score: 291.8 bits; conditional E-value: 1.2e-91 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaiss 64 m+l+idnydsftyn+vq+l elg+ev v rnd+lt++eieal p+ iv+sPGPctP ea+is lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2547 1 MLLMIDNYDSFTYNVVQYLGELGSEVKVVRNDELTIAEIEALNPER-IVVSPGPCTPTEAGIS- 62 79********************************************.****************. PP TIGR00566 65 leliehlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalka 128 +e+i+h+aGklPilGvClGhq+++qafG+dvvra++v+hGk+s + h++++vf+gl P l++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2547 63 IEAIKHFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVFHEDKGVFEGLNRP--LTV 124 ***********************************************************..*** PP TIGR00566 129 tryhslvveaetldtllevtaleeee....ieimairhrdlpleGvqfhPesilselGkellan 188 tryhsl+v+ etl+++le+ta+++ e +eim++rh+ l++eGvqfhPesil+e+G+el an lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2547 125 TRYHSLIVKRETLPDCLELTAWTQLEdgsvDEIMGLRHKTLNIEGVQFHPESILTEQGHELFAN 188 **********************987767889********************************* PP TIGR00566 189 flk 191 flk lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2547 189 FLK 191 *98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (197 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: 5.51 // [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