Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate AO356_23165 AO356_23165 myo-inosose-2 dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_23165 (297 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23165 Length = 297 Score = 602 bits (1551), Expect = e-177 Identities = 297/297 (100%), Positives = 297/297 (100%) Query: 1 MPAIRIGINPISWSNDDLPSLGGETPLSTALSEGKAIGYEGFELNGKFPKDAKGVGDVLR 60 MPAIRIGINPISWSNDDLPSLGGETPLSTALSEGKAIGYEGFELNGKFPKDAKGVGDVLR Sbjct: 1 MPAIRIGINPISWSNDDLPSLGGETPLSTALSEGKAIGYEGFELNGKFPKDAKGVGDVLR 60 Query: 61 PYDLALVSGWYSSRLARRSAAEEIDAIASHVELLAQNGANVLVYGEVADSIQGQRIPLVE 120 PYDLALVSGWYSSRLARRSAAEEIDAIASHVELLAQNGANVLVYGEVADSIQGQRIPLVE Sbjct: 61 PYDLALVSGWYSSRLARRSAAEEIDAIASHVELLAQNGANVLVYGEVADSIQGQRIPLVE 120 Query: 121 RPRFHTDEAWQAYADKLTELARFTLSQGVRLAYHHHMGAYVESPADIDKLMALTGSEVGL 180 RPRFHTDEAWQAYADKLTELARFTLSQGVRLAYHHHMGAYVESPADIDKLMALTGSEVGL Sbjct: 121 RPRFHTDEAWQAYADKLTELARFTLSQGVRLAYHHHMGAYVESPADIDKLMALTGSEVGL 180 Query: 181 LFDSGHCYMGGGEPLQVLRKHIERVCHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVP 240 LFDSGHCYMGGGEPLQVLRKHIERVCHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVP Sbjct: 181 LFDSGHCYMGGGEPLQVLRKHIERVCHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVP 240 Query: 241 GDGDIDFAALLDVLLAADYQGWLVVEAEQDPAVAPSYAYAKKGYDTLRALLQERSAS 297 GDGDIDFAALLDVLLAADYQGWLVVEAEQDPAVAPSYAYAKKGYDTLRALLQERSAS Sbjct: 241 GDGDIDFAALLDVLLAADYQGWLVVEAEQDPAVAPSYAYAKKGYDTLRALLQERSAS 297 Lambda K H 0.319 0.137 0.413 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: 454 Number of extensions: 12 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 AO356_23165 AO356_23165 (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.27007.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-119 383.0 0.0 6.2e-119 382.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23165 AO356_23165 myo-inosose-2 dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23165 AO356_23165 myo-inosose-2 dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 382.8 0.0 6.2e-119 6.2e-119 2 289 .. 4 290 .. 3 291 .. 0.99 Alignments for each domain: == domain 1 score: 382.8 bits; conditional E-value: 6.2e-119 TIGR04379 2 vklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglel 64 +++gi+Pi+W+ndDlp+lgg+t+l+++lse +++g++g+El kfpkd++ + ++l+ ++l+l lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23165 4 IRIGINPISWSNDDLPSLGGETPLSTALSEGKAIGYEGFELNGKFPKDAKGVGDVLRPYDLAL 66 89************************************************************* PP TIGR04379 65 vsgwfsallleksveeeieavrehlellkalgakvivvaEvgksiqgdkdtplaerpkl.tee 126 vsgw+s++l+++s++eei+a+++h+ell++ ga+v+v++Ev++siqg+ ++pl erp++ t+e lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23165 67 VSGWYSSRLARRSAAEEIDAIASHVELLAQNGANVLVYGEVADSIQGQ-RIPLVERPRFhTDE 128 ***********************************************9.9******9997899 PP TIGR04379 127 eweelaeklnklgeilkekglklayHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfa 189 w+++a+kl++l+++ ++g++layHhH+g++ve+ ++id+lm+lt+ e vgll+D+GH +++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23165 129 AWQAYADKLTELARFTLSQGVRLAYHHHMGAYVESPADIDKLMALTGSE-VGLLFDSGHCYMG 190 9**********************************************99.************* PP TIGR04379 190 gedplavlekyadRiahvHlKDvRkevleevrkekksFldavlkGvftvPGdGcidfeeilea 252 g++pl+vl+k+++R++hvH+KDvRk v++ +r++ +sF d++++G ftvPGdG+idf+++l+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23165 191 GGEPLQVLRKHIERVCHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVPGDGDIDFAALLDV 253 *************************************************************** PP TIGR04379 253 lkakdYeGWlvvEaEqDPakaepleyakkakkyleel 289 l a+dY+GWlvvEaEqDPa+a++++yakk++++l++l lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23165 254 LLAADYQGWLVVEAEQDPAVAPSYAYAKKGYDTLRAL 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.92 // [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