Align Probable acetolactate synthase small subunit; EC 2.2.1.6; Acetohydroxy-acid synthase small subunit; AHAS; ALS (uncharacterized)
to candidate WP_092348743.1 BLU87_RS11920 acetolactate synthase small subunit
Query= curated2:Q57625 (172 letters) >NCBI__GCF_900107645.1:WP_092348743.1 Length = 156 Score = 91.3 bits (225), Expect = 7e-24 Identities = 55/158 (34%), Positives = 93/158 (58%), Gaps = 6/158 (3%) Query: 8 RHVISALVLNKPGVLQRISGLFTRRGFNISSITVGITENPQISRVTIVVNGDDKI-LEQV 66 R I A L+ PGVL ++S L ++ +N+ ++TV + P +SR+TI + DD+ + Q+ Sbjct: 3 RRAILAFTLDNPGVLNKVSMLIRKKMYNVDTLTVCRSRIPGVSRMTITLREDDQTRVTQI 62 Query: 67 IKQLNKLIDVIKVSELEEKKSVQRELCLIKIYAPTESAKSQVIQYTSIFRGNVVDLSPES 126 IKQL K +VI EL+ S RE+ ++K+ E + + +T + +++ E Sbjct: 63 IKQLEKFTEVISAKELDTDHSYWREVAIVKL----EVDVAHLQDFTERYNFEILEQKGED 118 Query: 127 L-IVEITGSEDKINAFIDLVKPLGIKEMARTGITALAR 163 + I++I GS +I+AF+D V I E+ARTG+TAL + Sbjct: 119 VHILQIVGSTRRIDAFLDEVGQEHIIEIARTGVTALEK 156 Lambda K H 0.318 0.136 0.363 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: 78 Number of extensions: 5 Number of successful extensions: 3 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: 172 Length of database: 156 Length adjustment: 18 Effective length of query: 154 Effective length of database: 138 Effective search space: 21252 Effective search space used: 21252 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_092348743.1 BLU87_RS11920 (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.30106.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-34 104.9 2.7 2.3e-34 104.7 2.7 1.0 1 lcl|NCBI__GCF_900107645.1:WP_092348743.1 BLU87_RS11920 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900107645.1:WP_092348743.1 BLU87_RS11920 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 104.7 2.7 2.3e-34 2.3e-34 2 155 .. 3 155 .. 2 156 .] 0.90 Alignments for each domain: == domain 1 score: 104.7 bits; conditional E-value: 2.3e-34 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkv.veqiekqleklvd 69 ++ + + ++pGvL++vs l++++ +n+++ltv+++ +++srmti+++ dd++ v qi+kqlek + lcl|NCBI__GCF_900107645.1:WP_092348743.1 3 RRAILAFTLDNPGVLNKVSMLIRKKMYNVDTLTVCRSRIPGVSRMTITLREDDQTrVTQIIKQLEKFTE 71 55566666788**************************************9997644************* PP TIGR00119 70 vlkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDv.sedslivelsgkedkisaflkl 137 v+ ++l+ +++ re+++vk+++ ++++ te + ++++ ed i++++g+ +i+afl+ lcl|NCBI__GCF_900107645.1:WP_092348743.1 72 VISAKELDTDHSYWREVAIVKLEVDVAHLQDF---TERYNFEILEQkGEDVHILQIVGSTRRIDAFLDE 137 ***********************999887775...66677788875268899***************** PP TIGR00119 138 lkefgikevarsGlvals 155 + + i e+ar+G++al lcl|NCBI__GCF_900107645.1:WP_092348743.1 138 VGQEHIIEIARTGVTALE 155 ****************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (156 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: 5.10 // [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