Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate WP_066328411.1 BLR17_RS00955 3-isopropylmalate dehydratase small subunit
Query= uniprot:A0A1X9Z766 (195 letters) >NCBI__GCF_900100165.1:WP_066328411.1 Length = 198 Score = 265 bits (677), Expect = 4e-76 Identities = 125/190 (65%), Positives = 155/190 (81%) Query: 3 KFTKLTSAVVPLNIENIDTDQIIPARFLKATTREGFGENLFRDWRYENDNQPKADFVMNN 62 KF LTS+ VPL IEN+DTDQIIPARFLKAT REGFG+NLFRDWRY D+ PKADFV+NN Sbjct: 5 KFNILTSSAVPLPIENVDTDQIIPARFLKATKREGFGDNLFRDWRYNGDDTPKADFVLNN 64 Query: 63 PTYSGQVLVAGKNFGCGSSREHAAWAIQDAGFDAVISSFFADIFKGNALNNGLLPIQVSD 122 PTYSG++LV GKNFG GSSREHAAWA+ D GF AV+SSFFADIFKGN LN G+LP+QVS Sbjct: 65 PTYSGKILVGGKNFGSGSSREHAAWAVYDYGFRAVVSSFFADIFKGNCLNIGVLPVQVSP 124 Query: 123 EFLAQIFKAVDNNPKSALEVDLENQTVTIVETGAQESFEINPYKKSCLINGYDDIDFILN 182 EF +IF A++ +P + LE++L QT+T+ TG +ESF+IN YKK+ ++NG+DDID++ + Sbjct: 125 EFSDKIFAAIEADPNTELEINLPEQTITLKATGEKESFDINGYKKNNMLNGFDDIDYLQS 184 Query: 183 QKQLIEEFEE 192 K+ I F E Sbjct: 185 VKEEIVSFAE 194 Lambda K H 0.318 0.135 0.393 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: 194 Number of extensions: 5 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: 195 Length of database: 198 Length adjustment: 20 Effective length of query: 175 Effective length of database: 178 Effective search space: 31150 Effective search space used: 31150 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: 45 (21.9 bits)
Align candidate WP_066328411.1 BLR17_RS00955 (3-isopropylmalate dehydratase small subunit)
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))
# 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/TIGR00171.hmm # target sequence database: /tmp/gapView.2967270.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00171 [M=188] Accession: TIGR00171 Description: leuD: 3-isopropylmalate dehydratase, 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-57 179.8 0.1 3.3e-57 179.4 0.1 1.0 1 NCBI__GCF_900100165.1:WP_066328411.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100165.1:WP_066328411.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 179.4 0.1 3.3e-57 3.3e-57 3 181 .. 5 182 .. 3 189 .. 0.93 Alignments for each domain: == domain 1 score: 179.4 bits; conditional E-value: 3.3e-57 TIGR00171 3 efkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasilla 75 +f lt +vpl nvdtd+iip +flk+ kr Gfg +lf +wry ++ p+++fvln p+y g +il+ NCBI__GCF_900100165.1:WP_066328411.1 5 KFNILTSSAVPLPIENVDTDQIIPARFLKATKREGFGDNLFRDWRYNGDD--TPKADFVLNNPTYSG-KILVG 74 57788999**************************************6444..499**********97.7**** PP TIGR00171 76 renfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvdle 147 ++nfG Gssreha wa+ dyGf+ +++ fadif +n+++ g+lp+++s e ++++a ++ ++ ++l+++l+ NCBI__GCF_900100165.1:WP_066328411.1 75 GKNFGSGSSREHAAWAVYDYGFRAVVSSFFADIFKGNCLNIGVLPVQVSPEFSDKIFAAIEaDPNTELEINLP 147 ************************************************************98999******** PP TIGR00171 148 aqkvk.dsegkvysfeidefrkhcllnGldeiglt 181 +q+++ ++ g++ sf+i+ ++k+ +lnG+d+i NCBI__GCF_900100165.1:WP_066328411.1 148 EQTITlKATGEKESFDINGYKKNNMLNGFDDIDYL 182 ***9735778**********************854 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (198 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: 15.93 // [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