Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate 202142 SO3020 glutamine amido-transferase (NCBI ptt file)
Query= SwissProt::P00900 (193 letters) >FitnessBrowser__MR1:202142 Length = 202 Score = 207 bits (527), Expect = 1e-58 Identities = 104/187 (55%), Positives = 136/187 (72%), Gaps = 1/187 (0%) Query: 4 ILLLDNVDSFTYNLVDQLRASGHQVVIYRNQIGAEVIIERLQHMEQPV-LMLSPGPGTPS 62 + LLDN DSFTYNLVDQ R+ G +VVIYRN + A+ I ++L P L+LSPGPG P Sbjct: 3 LYLLDNFDSFTYNLVDQFRSLGCEVVIYRNDVAADYIADKLLAETAPTALVLSPGPGAPH 62 Query: 63 EAGCMPELLQRLRGQLPIIGICLGHQAIVEAYGGQVGQAGEILHGKASAIAHDGEGMFAG 122 EAG M EL+ ++ G++P++GICLGHQA+VE YGG+V +A ++HGKAS H+G G+FA Sbjct: 63 EAGSMMELIDKVAGKVPMLGICLGHQAMVEYYGGKVERAPFVVHGKASPTFHNGTGVFAN 122 Query: 123 MANPLPVARYHSLVGSNIPADLTVNARSGEMVMAVRDDRRRVCGFQFHPESILTTHGARL 182 + +PLPVARYHSLV + +P L V A + +M MA+ + R GFQFHPESILTT G+ L Sbjct: 123 LPSPLPVARYHSLVATKVPNCLDVIATTDDMPMAILHAKHRAVGFQFHPESILTTLGSTL 182 Query: 183 LEQTLAW 189 L QTL + Sbjct: 183 LTQTLVY 189 Lambda K H 0.322 0.138 0.410 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: 134 Number of extensions: 5 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: 193 Length of database: 202 Length adjustment: 20 Effective length of query: 173 Effective length of database: 182 Effective search space: 31486 Effective search space used: 31486 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 (21.9 bits) S2: 45 (21.9 bits)
Align candidate 202142 SO3020 (glutamine amido-transferase (NCBI ptt file))
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.7400.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-58 182.7 0.0 3.8e-58 182.5 0.0 1.0 1 lcl|FitnessBrowser__MR1:202142 SO3020 glutamine amido-transfera Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:202142 SO3020 glutamine amido-transferase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 182.5 0.0 3.8e-58 3.8e-58 2 188 .. 3 185 .. 2 189 .. 0.94 Alignments for each domain: == domain 1 score: 182.5 bits; conditional E-value: 3.8e-58 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallplls...ivisPGPctPdeaaissleliehlaGklPi 77 + l+dn+dsftynlv+++ lg evv+ rnd + ++ll++++ +v+sPGP+ P+ea+ +eli+++aGk+P+ lcl|FitnessBrowser__MR1:202142 3 LYLLDNFDSFTYNLVDQFRSLGCEVVIYRNDVAADYIADKLLAETAptaLVLSPGPGAPHEAGSM-MELIDKVAGKVPM 80 5699****************************999999**999987788*************975.9************ PP TIGR00566 78 lGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtaleeeeie 156 lG+ClGhqa+ G++v ra v hGk s hng++vfa l +P l+++ryhslv a +++++l+v a+++ lcl|FitnessBrowser__MR1:202142 81 LGICLGHQAMVEYYGGKVERAPFVVHGKASPTFHNGTGVFANLPSP--LPVARYHSLV--ATKVPNCLDVIATTDDM-- 153 **********************************************..*********8..689*******9998876.. PP TIGR00566 157 imairhrdlpleGvqfhPesilselGkellan 188 mai h + G qfhPesil+ lG++ll+ lcl|FitnessBrowser__MR1:202142 154 PMAILHAKHRAVGFQFHPESILTTLGSTLLTQ 185 799999999999****************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (202 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 5.44 // [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