Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate AO353_21340 AO353_21340 myo-inosose-2 dehydratase
Query= reanno::pseudo3_N2E3:AO353_21340 (297 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21340 Length = 297 Score = 605 bits (1561), Expect = e-178 Identities = 297/297 (100%), Positives = 297/297 (100%) Query: 1 MPAIRIGINPISWSNDDLPALGGETPLSTALSEGKEIGYEGFELNGKFPKDAKGVGDVLR 60 MPAIRIGINPISWSNDDLPALGGETPLSTALSEGKEIGYEGFELNGKFPKDAKGVGDVLR Sbjct: 1 MPAIRIGINPISWSNDDLPALGGETPLSTALSEGKEIGYEGFELNGKFPKDAKGVGDVLR 60 Query: 61 PYDLALVSGWYSSRLARRSVAEEIEAIGSHVELLAKNGAKVLVYGEVADSIQGQRIPLVE 120 PYDLALVSGWYSSRLARRSVAEEIEAIGSHVELLAKNGAKVLVYGEVADSIQGQRIPLVE Sbjct: 61 PYDLALVSGWYSSRLARRSVAEEIEAIGSHVELLAKNGAKVLVYGEVADSIQGQRIPLVE 120 Query: 121 RPRFHTEQAWQEYADKLNELARFTLSQGVRLAYHHHMGAYVESPADIDKLMSLTGSEVGL 180 RPRFHTEQAWQEYADKLNELARFTLSQGVRLAYHHHMGAYVESPADIDKLMSLTGSEVGL Sbjct: 121 RPRFHTEQAWQEYADKLNELARFTLSQGVRLAYHHHMGAYVESPADIDKLMSLTGSEVGL 180 Query: 181 LFDSGHCYMGGGEPLEVLRKHIGRICHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVP 240 LFDSGHCYMGGGEPLEVLRKHIGRICHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVP Sbjct: 181 LFDSGHCYMGGGEPLEVLRKHIGRICHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVP 240 Query: 241 GDGDIDFAALLDVLLAADYHGWLVVEAEQDPAVAPSYVYAKKGYETLRALLDQRTGQ 297 GDGDIDFAALLDVLLAADYHGWLVVEAEQDPAVAPSYVYAKKGYETLRALLDQRTGQ Sbjct: 241 GDGDIDFAALLDVLLAADYHGWLVVEAEQDPAVAPSYVYAKKGYETLRALLDQRTGQ 297 Lambda K H 0.319 0.138 0.420 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: 455 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: 297 Length of database: 297 Length adjustment: 26 Effective length of query: 271 Effective length of database: 271 Effective search space: 73441 Effective search space used: 73441 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate AO353_21340 AO353_21340 (myo-inosose-2 dehydratase)
to HMM TIGR04379 (iolE: myo-inosose-2 dehydratase (EC 4.2.1.44))
# 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.carbon/TIGR04379.hmm # target sequence database: /tmp/gapView.6786.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04379 [M=290] Accession: TIGR04379 Description: myo_inos_iolE: myo-inosose-2 dehydratase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-118 381.9 0.0 1.3e-118 381.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_21340 AO353_21340 myo-inosose-2 dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_21340 AO353_21340 myo-inosose-2 dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 381.7 0.0 1.3e-118 1.3e-118 2 289 .. 4 290 .. 3 291 .. 0.99 Alignments for each domain: == domain 1 score: 381.7 bits; conditional E-value: 1.3e-118 TIGR04379 2 vklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglelvs 66 +++gi+Pi+W+ndDlp lgg+t+l+++lse +e+g++g+El kfpkd++ + ++l+ ++l+lvs lcl|FitnessBrowser__pseudo3_N2E3:AO353_21340 4 IRIGINPISWSNDDLPALGGETPLSTALSEGKEIGYEGFELNGKFPKDAKGVGDVLRPYDLALVS 68 89*************************************************************** PP TIGR04379 67 gwfsallleksveeeieavrehlellkalgakvivvaEvgksiqgdkdtplaerpkl.teeewee 130 gw+s++l+++sv+eeiea+ +h+ell++ gakv+v++Ev++siqg+ ++pl erp++ te+ w+e lcl|FitnessBrowser__pseudo3_N2E3:AO353_21340 69 GWYSSRLARRSVAEEIEAIGSHVELLAKNGAKVLVYGEVADSIQGQ-RIPLVERPRFhTEQAWQE 132 *********************************************9.9******99977889*** PP TIGR04379 131 laeklnklgeilkekglklayHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfagedpla 195 +a+kln+l+++ ++g++layHhH+g++ve+ ++id+lm+lt+ e vgll+D+GH +++g++pl+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_21340 133 YADKLNELARFTLSQGVRLAYHHHMGAYVESPADIDKLMSLTGSE-VGLLFDSGHCYMGGGEPLE 196 *******************************************99.******************* PP TIGR04379 196 vlekyadRiahvHlKDvRkevleevrkekksFldavlkGvftvPGdGcidfeeilealkakdYeG 260 vl+k++ Ri+hvH+KDvRk v++ +r++ +sF d++++G ftvPGdG+idf+++l+ l a+dY+G lcl|FitnessBrowser__pseudo3_N2E3:AO353_21340 197 VLRKHIGRICHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVPGDGDIDFAALLDVLLAADYHG 261 ***************************************************************** PP TIGR04379 261 WlvvEaEqDPakaepleyakkakkyleel 289 WlvvEaEqDPa+a+++ yakk++++l++l lcl|FitnessBrowser__pseudo3_N2E3:AO353_21340 262 WLVVEAEQDPAVAPSYVYAKKGYETLRAL 290 *************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (290 nodes) Target sequences: 1 (297 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: 10.08 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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