Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate WP_043972923.1 V474_RS04400 acetolactate synthase small subunit
Query= BRENDA::P00894 (163 letters) >NCBI__GCF_001046635.1:WP_043972923.1 Length = 172 Score = 126 bits (316), Expect = 2e-34 Identities = 69/159 (43%), Positives = 106/159 (66%), Gaps = 3/159 (1%) Query: 2 RRILSVLLENESGALSRVIGLFSQRGYNIESLTVAP-TDDPTLSRMTIQTVGDEKVLEQI 60 R +L+V ++NE+G L+++ GLF+ RGYNI+SLTVA TD+ +SR+TI T G ++QI Sbjct: 11 RHVLTVTVDNEAGILAKIAGLFTARGYNIDSLTVADITDNHEVSRITIVTHGPPSQIDQI 70 Query: 61 EKQLHKLVDVLRVSELGQ-GAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSL 119 QL +LV V +V +L + G HV RE+ LVK+ G R E R E+FR + +D T Sbjct: 71 HAQLERLVPVHKVVDLTELGPHVARELALVKVAGVGDKRVEALRIAEVFRARPVDTTTES 130 Query: 120 YTVQLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRG 158 + ++ G K+D+F+A +RD+ +VEV R+G+V ++RG Sbjct: 131 FIFEMTGAPDKIDSFVALMRDLG-LVEVGRTGIVAMARG 168 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: 80 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: 172 Length adjustment: 18 Effective length of query: 145 Effective length of database: 154 Effective search space: 22330 Effective search space used: 22330 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_043972923.1 V474_RS04400 (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.140171.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-56 175.3 0.2 5e-56 175.1 0.2 1.0 1 NCBI__GCF_001046635.1:WP_043972923.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001046635.1:WP_043972923.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 175.1 0.2 5e-56 5e-56 2 158 .] 11 169 .. 10 169 .. 0.97 Alignments for each domain: == domain 1 score: 175.1 bits; conditional E-value: 5e-56 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvge.teekdlsrmtivvegddkvveqiekqleklvdvlkv 73 +hvl+v+v+ne+G+L++++Glf++rg+ni+sltv++ t+++++sr+tiv++g ++qi+ qle+lv+v kv NCBI__GCF_001046635.1:WP_043972923.1 11 RHVLTVTVDNEAGILAKIAGLFTARGYNIDSLTVADiTDNHEVSRITIVTHGPPSQIDQIHAQLERLVPVHKV 83 8*********************************9659*********************************** PP TIGR00119 74 ldlte.seivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgike 145 +dlte +v rel+lvkv +g +r e +++e+fr+r vD + +s+i e++g +dki++f++l++++g++e NCBI__GCF_001046635.1:WP_043972923.1 84 VDLTElGPHVARELALVKVAGVGDKRVEALRIAEVFRARPVDTTTESFIFEMTGAPDKIDSFVALMRDLGLVE 156 ****9458***************************************************************** PP TIGR00119 146 varsGlvalsrge 158 v r+G+va++rg+ NCBI__GCF_001046635.1:WP_043972923.1 157 VGRTGIVAMARGP 169 ***********85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (172 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: 8.28 // [ok]
This GapMind analysis is from Jul 26 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