Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate HSERO_RS12135 HSERO_RS12135 xylose isomerase
Query= reanno::HerbieS:HSERO_RS12135 (306 letters) >FitnessBrowser__HerbieS:HSERO_RS12135 Length = 306 Score = 621 bits (1601), Expect = 0.0 Identities = 306/306 (100%), Positives = 306/306 (100%) Query: 1 VATPFNVKIGINPISWMNDDLPSLGGETPLEQALSEGAEIGYRGFELGNKFPRQPEALRA 60 VATPFNVKIGINPISWMNDDLPSLGGETPLEQALSEGAEIGYRGFELGNKFPRQPEALRA Sbjct: 1 VATPFNVKIGINPISWMNDDLPSLGGETPLEQALSEGAEIGYRGFELGNKFPRQPEALRA 60 Query: 61 VLGKYQLECVSGWYSGQLATRSVEEEIVAVEAHLNLLAANGAQVMVYGEVADSIQGAPTP 120 VLGKYQLECVSGWYSGQLATRSVEEEIVAVEAHLNLLAANGAQVMVYGEVADSIQGAPTP Sbjct: 61 VLGKYQLECVSGWYSGQLATRSVEEEIVAVEAHLNLLAANGAQVMVYGEVADSIQGAPTP 120 Query: 121 LYQRPRFGSEAAWQGYAQRLDQFARHLLQRGVRLAYHHHMGAYVETPEDLDKLMALTGEE 180 LYQRPRFGSEAAWQGYAQRLDQFARHLLQRGVRLAYHHHMGAYVETPEDLDKLMALTGEE Sbjct: 121 LYQRPRFGSEAAWQGYAQRLDQFARHLLQRGVRLAYHHHMGAYVETPEDLDKLMALTGEE 180 Query: 181 VGLLFDSGHIAFAGGDPLAVLQRHLDRVCHVHCKDVRPAVVKLARNRDWSFLQAVINGAF 240 VGLLFDSGHIAFAGGDPLAVLQRHLDRVCHVHCKDVRPAVVKLARNRDWSFLQAVINGAF Sbjct: 181 VGLLFDSGHIAFAGGDPLAVLQRHLDRVCHVHCKDVRPAVVKLARNRDWSFLQAVINGAF 240 Query: 241 TVPGDGAIDFAPLLQLLYRRGYSGWLVVEAEQDPAVAPSYRYAQMGYRHLSTLVAAIENG 300 TVPGDGAIDFAPLLQLLYRRGYSGWLVVEAEQDPAVAPSYRYAQMGYRHLSTLVAAIENG Sbjct: 241 TVPGDGAIDFAPLLQLLYRRGYSGWLVVEAEQDPAVAPSYRYAQMGYRHLSTLVAAIENG 300 Query: 301 SLQEAA 306 SLQEAA Sbjct: 301 SLQEAA 306 Lambda K H 0.320 0.137 0.417 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: 522 Number of extensions: 11 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: 306 Length of database: 306 Length adjustment: 27 Effective length of query: 279 Effective length of database: 279 Effective search space: 77841 Effective search space used: 77841 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate HSERO_RS12135 HSERO_RS12135 (xylose isomerase)
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.20208.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-130 420.3 0.0 2.7e-130 420.1 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS12135 HSERO_RS12135 xylose isomerase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS12135 HSERO_RS12135 xylose isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 420.1 0.0 2.7e-130 2.7e-130 1 289 [. 6 293 .. 6 294 .. 0.99 Alignments for each domain: == domain 1 score: 420.1 bits; conditional E-value: 2.7e-130 TIGR04379 1 kvklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglelvsgw 68 +vk+gi+Pi+W+ndDlp+lgg+t+leq+lse ae+g++g+Elgnkfp++p++L+a+l +++le+vsgw lcl|FitnessBrowser__HerbieS:HSERO_RS12135 6 NVKIGINPISWMNDDLPSLGGETPLEQALSEGAEIGYRGFELGNKFPRQPEALRAVLGKYQLECVSGW 73 59****************************************************************** PP TIGR04379 69 fsallleksveeeieavrehlellkalgakvivvaEvgksiqgdkdtplaerpkl.teeeweelaekl 135 +s++l+++sveeei av++hl+ll+a ga+v+v++Ev++siqg tpl +rp++ +e+ w+ +a++l lcl|FitnessBrowser__HerbieS:HSERO_RS12135 74 YSGQLATRSVEEEIVAVEAHLNLLAANGAQVMVYGEVADSIQGA-PTPLYQRPRFgSEAAWQGYAQRL 140 *******************************************9.99********77889******** PP TIGR04379 136 nklgeilkekglklayHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfagedplavlekyadR 203 ++++++l ++g++layHhH+g++vet e++d+lm+lt++e vgll+D+GH++fag+dplavl+++ dR lcl|FitnessBrowser__HerbieS:HSERO_RS12135 141 DQFARHLLQRGVRLAYHHHMGAYVETPEDLDKLMALTGEE-VGLLFDSGHIAFAGGDPLAVLQRHLDR 207 **************************************99.*************************** PP TIGR04379 204 iahvHlKDvRkevleevrkekksFldavlkGvftvPGdGcidfeeilealkakdYeGWlvvEaEqDPa 271 ++hvH+KDvR++v++ +r++++sFl+av++G+ftvPGdG+idf+++l+ l +++Y+GWlvvEaEqDPa lcl|FitnessBrowser__HerbieS:HSERO_RS12135 208 VCHVHCKDVRPAVVKLARNRDWSFLQAVINGAFTVPGDGAIDFAPLLQLLYRRGYSGWLVVEAEQDPA 275 ******************************************************************** PP TIGR04379 272 kaepleyakkakkyleel 289 +a++++ya++++++l++l lcl|FitnessBrowser__HerbieS:HSERO_RS12135 276 VAPSYRYAQMGYRHLSTL 293 ***************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (290 nodes) Target sequences: 1 (306 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.76 // [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