Align L-ribulose-5-phosphate 4-epimerase; EC 5.1.3.4 (characterized)
to candidate BWI76_RS04580 BWI76_RS04580 L-ribulose-5-phosphate 4-epimerase
Query= CharProtDB::CH_001292 (231 letters) >FitnessBrowser__Koxy:BWI76_RS04580 Length = 231 Score = 446 bits (1146), Expect = e-130 Identities = 213/231 (92%), Positives = 222/231 (96%) Query: 1 MLEDLKRQVLEANLALPKHNLVTLTWGNVSAVDRERGVFVIKPSGVDYSVMTADDMVVVS 60 MLEDLKRQVLEANLALPKHNLVTLTWGNVSAVDRERGV VIKPSGVDYSVM A+DMVVVS Sbjct: 1 MLEDLKRQVLEANLALPKHNLVTLTWGNVSAVDRERGVLVIKPSGVDYSVMRAEDMVVVS 60 Query: 61 IETGEVVEGTKKPSSDTPTHRLLYQAFPSIGGIVHTHSRHATIWAQAGQSIPATGTTHAD 120 +ETGEVVEG KKPSSDTPTHRLLYQAFP++GGIVHTHSRHATIWAQAGQSIPATGTTHAD Sbjct: 61 LETGEVVEGQKKPSSDTPTHRLLYQAFPTLGGIVHTHSRHATIWAQAGQSIPATGTTHAD 120 Query: 121 YFYGTIPCTRKMTDAEINGEYEWETGNVIVETFEKQGIDAAQMPGVLVHSHGPFAWGKNA 180 YFYG +PCTR MTD EINGEYEWETG VIVETF ++GID AQMPGVLVHSHGPFAWGKNA Sbjct: 121 YFYGAVPCTRLMTDEEINGEYEWETGAVIVETFREKGIDPAQMPGVLVHSHGPFAWGKNA 180 Query: 181 EDAVHNAIVLEEVAYMGIFCRQLAPQLPDMQQTLLDKHYLRKHGAKAYYGQ 231 EDAVHNAIVLEE+AYMGIFCRQLAPQLP+MQQTLLDKHYLRKHGAKAYYGQ Sbjct: 181 EDAVHNAIVLEEIAYMGIFCRQLAPQLPEMQQTLLDKHYLRKHGAKAYYGQ 231 Lambda K H 0.318 0.133 0.404 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: 339 Number of extensions: 3 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: 231 Length of database: 231 Length adjustment: 23 Effective length of query: 208 Effective length of database: 208 Effective search space: 43264 Effective search space used: 43264 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: 46 (22.3 bits)
Align candidate BWI76_RS04580 BWI76_RS04580 (L-ribulose-5-phosphate 4-epimerase)
to HMM TIGR00760 (araD: L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4))
# 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/TIGR00760.hmm # target sequence database: /tmp/gapView.20893.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00760 [M=228] Accession: TIGR00760 Description: araD: L-ribulose-5-phosphate 4-epimerase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-136 439.4 0.1 1.2e-136 439.2 0.1 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS04580 BWI76_RS04580 L-ribulose-5-phosp Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS04580 BWI76_RS04580 L-ribulose-5-phosphate 4-epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 439.2 0.1 1.2e-136 1.2e-136 1 228 [] 1 231 [] 1 231 [] 1.00 Alignments for each domain: == domain 1 score: 439.2 bits; conditional E-value: 1.2e-136 TIGR00760 1 mleelkkevleanlalpkhklvtftwgnvsaidrekelvvikpsgveydeltaddlvvvdle.gevvegdk 70 mle+lk++vleanlalpkh+lvt+twgnvsa+dre++++vikpsgv+y++++a+d+vvv+le gevveg+k lcl|FitnessBrowser__Koxy:BWI76_RS04580 1 MLEDLKRQVLEANLALPKHNLVTLTWGNVSAVDRERGVLVIKPSGVDYSVMRAEDMVVVSLEtGEVVEGQK 71 9*************************************************************9******** PP TIGR00760 71 kpssdtpthlalykafpeiggivhthsrhatiwaqagkdipalgtthadyfygaipctremteeeikgeye 141 kpssdtpth++ly+afp++ggivhthsrhatiwaqag++ipa+gtthadyfyga+pctr mt+eei+geye lcl|FitnessBrowser__Koxy:BWI76_RS04580 72 KPSSDTPTHRLLYQAFPTLGGIVHTHSRHATIWAQAGQSIPATGTTHADYFYGAVPCTRLMTDEEINGEYE 142 *********************************************************************** PP TIGR00760 142 letgkvivetfeek..dpaqipgvlvhshgpfawgkdaadavhnavvleevakmalkslqlakelkplqke 210 +etg vivetf+ek dpaq+pgvlvhshgpfawgk+a+davhna+vlee+a+m+++++qla++l+++q++ lcl|FitnessBrowser__Koxy:BWI76_RS04580 143 WETGAVIVETFREKgiDPAQMPGVLVHSHGPFAWGKNAEDAVHNAIVLEEIAYMGIFCRQLAPQLPEMQQT 213 **************9******************************************************** PP TIGR00760 211 lldkhylrkhganayygq 228 lldkhylrkhga+ayygq lcl|FitnessBrowser__Koxy:BWI76_RS04580 214 LLDKHYLRKHGAKAYYGQ 231 *****************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (231 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: 6.58 // [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