Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate 6937997 Sama_2130 anthranilate synthase component II (RefSeq)
Query= SwissProt::P00900 (193 letters) >FitnessBrowser__SB2B:6937997 Length = 199 Score = 212 bits (540), Expect = 3e-60 Identities = 105/186 (56%), Positives = 134/186 (72%) Query: 4 ILLLDNVDSFTYNLVDQLRASGHQVVIYRNQIGAEVIIERLQHMEQPVLMLSPGPGTPSE 63 + LLDN DSFTYNLVDQ RA G +VVIYRN + + + +L Q L+LSPGPG P E Sbjct: 3 LYLLDNFDSFTYNLVDQFRALGFEVVIYRNDVDPQQLAAKLLAEPQTALVLSPGPGAPHE 62 Query: 64 AGCMPELLQRLRGQLPIIGICLGHQAIVEAYGGQVGQAGEILHGKASAIAHDGEGMFAGM 123 AGCM L++ + G+LPI+GICLGHQA+VE YGG+V +A ++HGKAS HDG+G+F G+ Sbjct: 63 AGCMMALIKLVAGKLPILGICLGHQALVEHYGGKVERAPSVVHGKASPTVHDGQGIFRGL 122 Query: 124 ANPLPVARYHSLVGSNIPADLTVNARSGEMVMAVRDDRRRVCGFQFHPESILTTHGARLL 183 +PLPVARYHSLV + +P L V A + M MAV + + GFQFHPESILTT G+ LL Sbjct: 123 PSPLPVARYHSLVATKVPDALKVIATTEGMPMAVLHEEDKALGFQFHPESILTTLGSTLL 182 Query: 184 EQTLAW 189 Q+L + Sbjct: 183 VQSLQY 188 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: 139 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: 193 Length of database: 199 Length adjustment: 20 Effective length of query: 173 Effective length of database: 179 Effective search space: 30967 Effective search space used: 30967 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 6937997 Sama_2130 (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.32223.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-57 180.8 0.0 1.4e-57 180.6 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6937997 Sama_2130 anthranilate synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937997 Sama_2130 anthranilate synthase component II (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 180.6 0.0 1.4e-57 1.4e-57 2 188 .. 3 184 .. 2 188 .. 0.93 Alignments for each domain: == domain 1 score: 180.6 bits; conditional E-value: 1.4e-57 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieall..pllsivisPGPctPdeaaissleliehlaGklP 76 + l+dn+dsftynlv+++ lg evv+ rnd + q +ll p++++v+sPGP+ P+ea+ ++li+ +aGklP lcl|FitnessBrowser__SB2B:6937997 3 LYLLDNFDSFTYNLVDQFRALGFEVVIYRNDVDPQQLAAKLLaePQTALVLSPGPGAPHEAGCM-MALIKLVAGKLP 78 5699***************************99999888886337888**************98.9*********** PP TIGR00566 77 ilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtaleee 153 ilG+ClGhqal G++v ra +v hGk s h+g+++f+gl +P l+++ryhslv a ++++ l+v a++e lcl|FitnessBrowser__SB2B:6937997 79 ILGICLGHQALVEHYGGKVERAPSVVHGKASPTVHDGQGIFRGLPSP--LPVARYHSLV--ATKVPDALKVIATTEG 151 ***********************************************..*********8..6789999999998876 PP TIGR00566 154 eieimairhrdlpleGvqfhPesilselGkellan 188 ma+ h++ + G qfhPesil+ lG++ll lcl|FitnessBrowser__SB2B:6937997 152 M--PMAVLHEEDKALGFQFHPESILTTLGSTLLVQ 184 6..7**************************99865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (199 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: 6.23 // [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