Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate 7024327 Shewana3_1519 anthranilate synthase component II (RefSeq)
Query= SwissProt::P00900 (193 letters) >FitnessBrowser__ANA3:7024327 Length = 202 Score = 205 bits (521), Expect = 5e-58 Identities = 104/185 (56%), Positives = 133/185 (71%), Gaps = 1/185 (0%) Query: 4 ILLLDNVDSFTYNLVDQLRASGHQVVIYRNQIGAEVIIERLQHMEQP-VLMLSPGPGTPS 62 + LLDN DSFTYNLVDQ R+ G +VVIYRN + A+ I +L +P L+LSPGPG P Sbjct: 3 LYLLDNFDSFTYNLVDQFRSLGCEVVIYRNDVAADYIANKLLAETEPSALVLSPGPGAPH 62 Query: 63 EAGCMPELLQRLRGQLPIIGICLGHQAIVEAYGGQVGQAGEILHGKASAIAHDGEGMFAG 122 EAG M L+ ++ G++P++GICLGHQA+VE YGG+V +A ++HGKAS H+G G+FA Sbjct: 63 EAGSMMSLIDKVAGKVPMLGICLGHQAMVEYYGGKVERAPFVVHGKASPTFHNGTGVFAN 122 Query: 123 MANPLPVARYHSLVGSNIPADLTVNARSGEMVMAVRDDRRRVCGFQFHPESILTTHGARL 182 + +PLPVARYHSLV + +P L V A + EM MA+ R GFQFHPESILTT G+ L Sbjct: 123 LPSPLPVARYHSLVATKVPDCLEVIATTEEMPMAILHAEHRAVGFQFHPESILTTLGSTL 182 Query: 183 LEQTL 187 L QTL Sbjct: 183 LTQTL 187 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: 137 Number of extensions: 6 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 7024327 Shewana3_1519 (anthranilate synthase component II (RefSeq))
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.20692.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-58 182.0 0.0 6.5e-58 181.7 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7024327 Shewana3_1519 anthranilate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7024327 Shewana3_1519 anthranilate synthase component II (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 181.7 0.0 6.5e-58 6.5e-58 2 190 .. 3 187 .. 2 189 .. 0.95 Alignments for each domain: == domain 1 score: 181.7 bits; conditional E-value: 6.5e-58 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallplls...ivisPGPctPdeaaissleliehlaGkl 75 + l+dn+dsftynlv+++ lg evv+ rnd + ++ll+++ +v+sPGP+ P+ea+ ++li+++aGk+ lcl|FitnessBrowser__ANA3:7024327 3 LYLLDNFDSFTYNLVDQFRSLGCEVVIYRNDVAADYIANKLLAETEpsaLVLSPGPGAPHEAGSM-MSLIDKVAGKV 78 5699***************************999999999999987788*************976.9********** PP TIGR00566 76 PilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtalee 152 P+lG+ClGhqa+ G++v ra v hGk s hng++vfa l +P l+++ryhslv a +++++lev a++e lcl|FitnessBrowser__ANA3:7024327 79 PMLGICLGHQAMVEYYGGKVERAPFVVHGKASPTFHNGTGVFANLPSP--LPVARYHSLV--ATKVPDCLEVIATTE 151 ************************************************..*********8..689*******99998 PP TIGR00566 153 eeieimairhrdlpleGvqfhPesilselGkellanfl 190 e mai h + G qfhPesil+ lG++ll+ l lcl|FitnessBrowser__ANA3:7024327 152 EM--PMAILHAEHRAVGFQFHPESILTTLGSTLLTQTL 187 87..79***************************98765 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.37 // [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