Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate 17423 b3360 para-aminobenzoate synthase component II (NCBI)
Query= BRENDA::P20576 (201 letters) >FitnessBrowser__Keio:17423 Length = 187 Score = 268 bits (685), Expect = 5e-77 Identities = 129/192 (67%), Positives = 160/192 (83%), Gaps = 5/192 (2%) Query: 1 MLLMIDNYDSFTYNLVQYFGELKAEVKVVRNDELSVEQIEALAPERIVLSPGPCTPNEAG 60 M+L+IDNYDSFT+NL QYF EL A+V V RND L++ I+AL P++IV+SPGPCTP+EAG Sbjct: 1 MILLIDNYDSFTWNLYQYFCELGADVLVKRNDALTLADIDALKPQKIVISPGPCTPDEAG 60 Query: 61 VSLAVIERFAGKLPLLGVCLGHQSIGQAFGGEVVRARQVMHGKTSPIHHKDLGVFAGLAN 120 +SL VI +AG+LP+LGVCLGHQ++ QAFGG+VVRA +VMHGKTSPI H GVF GLAN Sbjct: 61 ISLDVIRHYAGRLPILGVCLGHQAMAQAFGGKVVRAAKVMHGKTSPITHNGEGVFRGLAN 120 Query: 121 PLTVTRYHSLVVKRESLPECLEVTAWTQHADGSLDEIMGVRHKTLNVEGVQFHPESILTE 180 PLTVTRYHSLVV+ +SLP C +VTAW++ EIMG+RH+ ++EGVQFHPESIL+E Sbjct: 121 PLTVTRYHSLVVEPDSLPACFDVTAWSE-----TREIMGIRHRQWDLEGVQFHPESILSE 175 Query: 181 QGHELLANFLRQ 192 QGH+LLANFL + Sbjct: 176 QGHQLLANFLHR 187 Lambda K H 0.319 0.137 0.403 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: 172 Number of extensions: 4 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: 201 Length of database: 187 Length adjustment: 20 Effective length of query: 181 Effective length of database: 167 Effective search space: 30227 Effective search space used: 30227 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 (21.7 bits) S2: 44 (21.6 bits)
Align candidate 17423 b3360 (para-aminobenzoate synthase component II (NCBI))
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.10250.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-103 329.1 0.0 4.8e-103 328.9 0.0 1.0 1 lcl|FitnessBrowser__Keio:17423 b3360 para-aminobenzoate synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17423 b3360 para-aminobenzoate synthase component II (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 328.9 0.0 4.8e-103 4.8e-103 1 192 [] 1 187 [] 1 187 [] 0.99 Alignments for each domain: == domain 1 score: 328.9 bits; conditional E-value: 4.8e-103 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGklPilG 79 m+llidnydsft+nl+q+++elga+v+vkrnd+ltl++i+al+p++ ivisPGPctPdea+is l++i+h+aG+lPilG lcl|FitnessBrowser__Keio:17423 1 MILLIDNYDSFTWNLYQYFCELGADVLVKRNDALTLADIDALKPQK-IVISPGPCTPDEAGIS-LDVIRHYAGRLPILG 77 79********************************************.****************.*************** PP TIGR00566 80 vClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtaleeeeieim 158 vClGhqa+aqafG++vvra+kv+hGk+s i+hng++vf+gl+nP l++tryhslvve+++l+++++vta++e++ eim lcl|FitnessBrowser__Keio:17423 78 VCLGHQAMAQAFGGKVVRAAKVMHGKTSPITHNGEGVFRGLANP--LTVTRYHSLVVEPDSLPACFDVTAWSETR-EIM 153 ********************************************..****************************9.*** PP TIGR00566 159 airhrdlpleGvqfhPesilselGkellanflkr 192 +irhr+++leGvqfhPesilse+G++llanfl+r lcl|FitnessBrowser__Keio:17423 154 GIRHRQWDLEGVQFHPESILSEQGHQLLANFLHR 187 ********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (187 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: 5.23 // [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