Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate HSERO_RS19440 HSERO_RS19440 anthranilate synthase subunit II
Query= SwissProt::P00901 (198 letters) >FitnessBrowser__HerbieS:HSERO_RS19440 Length = 191 Score = 266 bits (680), Expect = 2e-76 Identities = 125/190 (65%), Positives = 154/190 (81%), Gaps = 5/190 (2%) Query: 2 LLMMIDNYDSFTYNVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAG 61 +L+MIDNYDSFTYN+VQY GELG EV IRNDE+T+ I LNPERI +SPGPC+P EAG Sbjct: 1 MLLMIDNYDSFTYNLVQYFGELGEEVLTIRNDEITLDDIRKLNPERICLSPGPCSPKEAG 60 Query: 62 VSIEAILHFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVHHRDLGVFTGLNN 121 + ++ + F+GKLPILGVCLGHQ+IG+AFGG+++RA+QVMHGKTS + H +GVF L + Sbjct: 61 ICVDLLKEFSGKLPILGVCLGHQAIGEAFGGNIIRAKQVMHGKTSKIAHTGVGVFQDLPS 120 Query: 122 PLTVTRYHSLVVKRETLPDCLEVTAWTAHEDGSVDEIMGLRHKTLNIEGVQFHPESILTE 181 P TV RYHSL ++R TLPDCLEVTAWT +DG EIMG+RHK +++GVQFHPESIL+E Sbjct: 121 PYTVIRYHSLAIERATLPDCLEVTAWT--DDG---EIMGVRHKEFDLQGVQFHPESILSE 175 Query: 182 QGHELFANFL 191 GH L NFL Sbjct: 176 HGHALLKNFL 185 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: 190 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: 198 Length of database: 191 Length adjustment: 20 Effective length of query: 178 Effective length of database: 171 Effective search space: 30438 Effective search space used: 30438 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: 44 (21.6 bits)
Align candidate HSERO_RS19440 HSERO_RS19440 (anthranilate synthase subunit II)
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.14739.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-85 270.0 0.0 6.5e-85 269.8 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS19440 HSERO_RS19440 anthranilate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS19440 HSERO_RS19440 anthranilate synthase subunit II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 269.8 0.0 6.5e-85 6.5e-85 1 190 [. 1 185 [. 1 187 [. 0.99 Alignments for each domain: == domain 1 score: 269.8 bits; conditional E-value: 6.5e-85 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleli 68 m+l+idnydsftynlvq++ elg+ev+ rnd++tl++i +l p+ i++sPGPc+P+ea+i ++l+ lcl|FitnessBrowser__HerbieS:HSERO_RS19440 1 MLLMIDNYDSFTYNLVQYFGELGEEVLTIRNDEITLDDIRKLNPER-ICLSPGPCSPKEAGIC-VDLL 66 79********************************************.***************9.**** PP TIGR00566 69 ehlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvv 136 ++++GklPilGvClGhqa++ afG++++ra++v+hGk+s+i h g++vf+ l +P +++ ryhsl + lcl|FitnessBrowser__HerbieS:HSERO_RS19440 67 KEFSGKLPILGVCLGHQAIGEAFGGNIIRAKQVMHGKTSKIAHTGVGVFQDLPSP--YTVIRYHSLAI 132 *******************************************************..*********** PP TIGR00566 137 eaetldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanfl 190 e +tl+++levta+++ eim++rh++ +l+GvqfhPesilse+G++ll+nfl lcl|FitnessBrowser__HerbieS:HSERO_RS19440 133 ERATLPDCLEVTAWTDDG-EIMGVRHKEFDLQGVQFHPESILSEHGHALLKNFL 185 ****************99.**********************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (191 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 5.63 // [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