Align Acetolactate synthase small subunit; Short=AHAS; Short=ALS; EC 2.2.1.6 (characterized, see rationale)
to candidate WP_035235674.1 Q366_RS01715 acetolactate synthase small subunit
Query= uniprot:A0A154R0Y7 (82 letters) >NCBI__GCF_000745975.1:WP_035235674.1 Length = 161 Score = 65.5 bits (158), Expect = 2e-16 Identities = 29/71 (40%), Positives = 51/71 (71%) Query: 3 HTLSILLQNEAGALVRVAGLFAARGYNIDTLTVAATHDPAVSRLTLSLQCDEAALGQILQ 62 +TL++L++NE G R+ GLFA+RGYNI+T+ A T +P +SR+T++ L Q ++ Sbjct: 6 YTLTMLVENEPGVTARITGLFASRGYNIETICGAPTANPKMSRITITTHTHPKMLEQCMK 65 Query: 63 QTRKLVDVLQV 73 Q ++LV+V+++ Sbjct: 66 QIKRLVNVIKL 76 Lambda K H 0.321 0.130 0.356 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: 32 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: 82 Length of database: 161 Length adjustment: 12 Effective length of query: 70 Effective length of database: 149 Effective search space: 10430 Effective search space used: 10430 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: 40 (21.5 bits) S2: 40 (20.0 bits)
Align candidate WP_035235674.1 Q366_RS01715 (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.18634.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-52 162.1 0.0 6e-52 161.9 0.0 1.0 1 lcl|NCBI__GCF_000745975.1:WP_035235674.1 Q366_RS01715 acetolactate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745975.1:WP_035235674.1 Q366_RS01715 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 161.9 0.0 6e-52 6e-52 2 157 .. 5 160 .. 4 161 .] 0.99 Alignments for each domain: == domain 1 score: 161.9 bits; conditional E-value: 6e-52 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdv 70 + +l++lvenepGv +r++Glfa rg+nie++ + t ++++sr+ti+++++ k++eq kq+++lv+v lcl|NCBI__GCF_000745975.1:WP_035235674.1 5 RYTLTMLVENEPGVTARITGLFASRGYNIETICGAPTANPKMSRITITTHTHPKMLEQCMKQIKRLVNV 73 6789***************************************************************** PP TIGR00119 71 lkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllk 139 +k +d+t ++ vkre++l+ v+al+e+r+ei +l++ f g ++D + +i ++ g+ed i+ +l+ l lcl|NCBI__GCF_000745975.1:WP_035235674.1 74 IKLRDMTGEKAVKREMALICVKALPENRDEIRSLIQEFNGTMMDEGSQHFIFDVCGDEDTIDMLLEKLS 142 ********************************************************************* PP TIGR00119 140 efgikevarsGlvalsrg 157 +fgik +arsG++al r+ lcl|NCBI__GCF_000745975.1:WP_035235674.1 143 PFGIKKLARSGVLALYRE 160 ***************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (161 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: 7.25 // [ok]
This GapMind analysis is from Apr 10 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