Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate WP_041551064.1 SARO_RS11380 acetolactate synthase small subunit
Query= BRENDA::P00894 (163 letters) >NCBI__GCF_000013325.1:WP_041551064.1 Length = 171 Score = 129 bits (324), Expect = 2e-35 Identities = 66/159 (41%), Positives = 109/159 (68%), Gaps = 3/159 (1%) Query: 2 RRILSVLLENESGALSRVIGLFSQRGYNIESLTVAP-TDDPTLSRMTIQTVGDEKVLEQI 60 R +L++ ++NE+G L+++ GLF+ RGYNI+SLTVA TD +SR+TI T G +++QI Sbjct: 10 RHVLTITVDNEAGILAKIAGLFTARGYNIDSLTVADITDGHDVSRITIVTHGPPPIIDQI 69 Query: 61 EKQLHKLVDVLRVSELGQ-GAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSL 119 QL +LV V +V++L + G VERE+ L+K+ G R E R ++FR +++D T S Sbjct: 70 RAQLERLVPVHKVTDLTEVGPFVERELALIKVSGKGENRVEALRLADVFRAKVVDTTTSS 129 Query: 120 YTVQLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRG 158 + +L G K+D+F++ ++++ +VEV R+G+VG+ RG Sbjct: 130 FIFELTGAPDKIDSFVSLMKELG-LVEVGRTGIVGMIRG 167 Lambda K H 0.318 0.136 0.360 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: 79 Number of extensions: 5 Number of successful extensions: 4 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: 163 Length of database: 171 Length adjustment: 18 Effective length of query: 145 Effective length of database: 153 Effective search space: 22185 Effective search space used: 22185 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 43 (21.2 bits)
Align candidate WP_041551064.1 SARO_RS11380 (acetolactate synthase small subunit)
to HMM TIGR00119 (ilvN: acetolactate synthase, small subunit (EC 2.2.1.6))
# 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/TIGR00119.hmm # target sequence database: /tmp/gapView.876746.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00119 [M=158] Accession: TIGR00119 Description: acolac_sm: acetolactate synthase, small subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-57 178.4 0.2 5.8e-57 178.2 0.2 1.0 1 NCBI__GCF_000013325.1:WP_041551064.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000013325.1:WP_041551064.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 178.2 0.2 5.8e-57 5.8e-57 2 157 .. 10 167 .. 9 168 .. 0.97 Alignments for each domain: == domain 1 score: 178.2 bits; conditional E-value: 5.8e-57 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvge.teekdlsrmtivvegddkvveqiekqleklvdvlkv 73 +hvl+++v+ne+G+L++++Glf++rg+ni+sltv++ t+ +d+sr+tiv++g +++qi+ qle+lv+v kv NCBI__GCF_000013325.1:WP_041551064.1 10 RHVLTITVDNEAGILAKIAGLFTARGYNIDSLTVADiTDGHDVSRITIVTHGPPPIIDQIRAQLERLVPVHKV 82 8*********************************965999********************************* PP TIGR00119 74 ldltes.eivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgike 145 +dlte v+rel+l+kvs +ge+r e +l+++fr++vvD + +s+i el+g +dki++f++l+ke+g++e NCBI__GCF_000013325.1:WP_041551064.1 83 TDLTEVgPFVERELALIKVSGKGENRVEALRLADVFRAKVVDTTTSSFIFELTGAPDKIDSFVSLMKELGLVE 155 ****96379**************************************************************** PP TIGR00119 146 varsGlvalsrg 157 v r+G+v++ rg NCBI__GCF_000013325.1:WP_041551064.1 156 VGRTGIVGMIRG 167 *********998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (171 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: 11.38 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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