Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate BWI76_RS04665 BWI76_RS04665 3-isopropylmalate dehydratase small subunit
Query= SwissProt::P04787 (201 letters) >FitnessBrowser__Koxy:BWI76_RS04665 Length = 201 Score = 382 bits (981), Expect = e-111 Identities = 184/200 (92%), Positives = 194/200 (97%) Query: 1 MAEKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPE 60 MAEKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRF D+KG+QPNPE Sbjct: 1 MAEKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFQDDKGEQPNPE 60 Query: 61 FVLNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLL 120 FVLNFPEY+GASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLL Sbjct: 61 FVLNFPEYKGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLL 120 Query: 121 PVTLSDAQVDELFALVKANPGIKFEVDLEAQVVKAGDKTYSFKIDDFRRHCMLNGLDSIG 180 PVTLS+AQVDELF LV + PGIKFEVDLE++VVKAGDK+YSFKID FRRHCMLNGLDSIG Sbjct: 121 PVTLSEAQVDELFKLVHSQPGIKFEVDLESEVVKAGDKSYSFKIDAFRRHCMLNGLDSIG 180 Query: 181 LTLQHEDAIAAYENKQPAFM 200 LTLQHE+AI+AYE KQPAFM Sbjct: 181 LTLQHEEAISAYEQKQPAFM 200 Lambda K H 0.321 0.138 0.416 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: 259 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: 201 Length of database: 201 Length adjustment: 21 Effective length of query: 180 Effective length of database: 180 Effective search space: 32400 Effective search space used: 32400 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: 41 (21.9 bits) S2: 45 (21.9 bits)
Align candidate BWI76_RS04665 BWI76_RS04665 (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.15028.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-102 326.2 0.0 3.5e-102 326.1 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS04665 BWI76_RS04665 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS04665 BWI76_RS04665 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 326.1 0.0 3.5e-102 3.5e-102 2 188 .] 3 189 .. 1 189 [. 0.98 Alignments for each domain: == domain 1 score: 326.1 bits; conditional E-value: 3.5e-102 TIGR00171 2 kefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasi 72 ++f ++tGlvvpld+anvdtdaiipkqfl+k++rtGfg+hlf++wr++d+kG++pnpefvln+p+y+gasi lcl|FitnessBrowser__Koxy:BWI76_RS04665 3 EKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFQDDKGEQPNPEFVLNFPEYKGASI 73 459******************************************************************** PP TIGR00171 73 llarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkl 142 llarenfGcGssrehapwal+dyGfkv+iapsfadify+nsf+n+llp+ lse++v+el++lv+ +g+k+ lcl|FitnessBrowser__Koxy:BWI76_RS04665 74 LLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPVTLSEAQVDELFKLVHsQPGIKF 144 ***************************************************************9889**** PP TIGR00171 143 tvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188 +vdle++ vk+++ k ysf+id+fr+hc+lnGld+igltlq+e++i lcl|FitnessBrowser__Koxy:BWI76_RS04665 145 EVDLESEVVKAGD-KSYSFKIDAFRRHCMLNGLDSIGLTLQHEEAI 189 *************.*****************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (201 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: 5.31 // [ok]
This GapMind analysis is from Apr 09 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