Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate 351387 BT1859 3-isopropylmalate dehydratase small subunit (NCBI ptt file)
Query= uniprot:A0A1X9Z766 (195 letters) >FitnessBrowser__Btheta:351387 Length = 200 Score = 241 bits (615), Expect = 6e-69 Identities = 120/191 (62%), Positives = 144/191 (75%), Gaps = 2/191 (1%) Query: 3 KFTKLTSAVVPLNIENIDTDQIIPARFLKATTREG--FGENLFRDWRYENDNQPKADFVM 60 KF +TS VPL +EN+DTDQIIPARFLKATTRE FG+NLFRDWRY D DFV+ Sbjct: 5 KFNIITSTCVPLPLENVDTDQIIPARFLKATTREEKFFGDNLFRDWRYNADGSLNKDFVL 64 Query: 61 NNPTYSGQVLVAGKNFGCGSSREHAAWAIQDAGFDAVISSFFADIFKGNALNNGLLPIQV 120 N+PTYSGQ+LVAGKNFG GSSREHAAWAI GF V+SSFFADI K N LNN +LP+ V Sbjct: 65 NDPTYSGQILVAGKNFGSGSSREHAAWAIAGYGFRVVVSSFFADIHKNNELNNFVLPVVV 124 Query: 121 SDEFLAQIFKAVDNNPKSALEVDLENQTVTIVETGAQESFEINPYKKSCLINGYDDIDFI 180 ++ FL ++F ++ +PK +EV+L QT+T TG E FEIN YKK CL+NG DDIDF+ Sbjct: 125 TEGFLQELFDSIFADPKMEVEVNLPEQTITNKATGKSEHFEINAYKKLCLMNGLDDIDFL 184 Query: 181 LNQKQLIEEFE 191 L+ K IEE+E Sbjct: 185 LSNKNKIEEWE 195 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: 193 Number of extensions: 8 Number of successful extensions: 2 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: 200 Length adjustment: 20 Effective length of query: 175 Effective length of database: 180 Effective search space: 31500 Effective search space used: 31500 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 351387 BT1859 (3-isopropylmalate dehydratase small subunit (NCBI ptt file))
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.616.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-56 175.8 0.2 4.7e-56 175.7 0.2 1.0 1 lcl|FitnessBrowser__Btheta:351387 BT1859 3-isopropylmalate dehydra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:351387 BT1859 3-isopropylmalate dehydratase small subunit (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 175.7 0.2 4.7e-56 4.7e-56 4 188 .] 6 191 .. 1 191 [. 0.93 Alignments for each domain: == domain 1 score: 175.7 bits; conditional E-value: 4.7e-56 TIGR00171 4 fkkltGlvvpldkanvdtdaiipkqflkkikrtG..fgkhlfyewryldekGkepnpefvlnvpqyqgasillare 77 f t +vpl nvdtd+iip +flk+ +r fg +lf +wry +++G + n +fvln p+y g +il+a++ lcl|FitnessBrowser__Btheta:351387 6 FNIITSTCVPLPLENVDTDQIIPARFLKATTREEkfFGDNLFRDWRY-NADG-SLNKDFVLNDPTYSG-QILVAGK 78 667788999*********************9964449**********.8888.89***********97.7****** PP TIGR00171 78 nfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvdleaqkvk 152 nfG Gssreha wa++ yGf+v+++ fadi nn ++n +lp+ ++e ++el+ + ++ ++++v+l++q+++ lcl|FitnessBrowser__Btheta:351387 79 NFGSGSSREHAAWAIAGYGFRVVVSSFFADIHKNNELNNFVLPVVVTEGFLQELFDSIFaDPKMEVEVNLPEQTIT 154 *******************************************************999879999***********8 PP TIGR00171 153 d.segkvysfeidefrkhcllnGldeigltlqkedei 188 + + gk +fei++++k cl+nGld+i + l ++++i lcl|FitnessBrowser__Btheta:351387 155 NkATGKSEHFEINAYKKLCLMNGLDDIDFLLSNKNKI 191 62678************************99988876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (200 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: 6.25 // [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