Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate RR42_RS31275 RR42_RS31275 homogentisate 1,2-dioxygenase
Query= reanno::Cup4G11:RR42_RS31275 (449 letters) >FitnessBrowser__Cup4G11:RR42_RS31275 Length = 449 Score = 943 bits (2437), Expect = 0.0 Identities = 449/449 (100%), Positives = 449/449 (100%) Query: 1 MTQTQLNVVNVTGQAPDHGTPGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQIS 60 MTQTQLNVVNVTGQAPDHGTPGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQIS Sbjct: 1 MTQTQLNVVNVTGQAPDHGTPGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQIS 60 Query: 61 GTAFTAPRAHNRRSWCYRIRAAAMHEPFTRVEQSRIVSHFDAVPPSPNQMRWSPPAMPKE 120 GTAFTAPRAHNRRSWCYRIRAAAMHEPFTRVEQSRIVSHFDAVPPSPNQMRWSPPAMPKE Sbjct: 61 GTAFTAPRAHNRRSWCYRIRAAAMHEPFTRVEQSRIVSHFDAVPPSPNQMRWSPPAMPKE 120 Query: 121 PTDFVDGIITMAGNGGPEAMSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATE 180 PTDFVDGIITMAGNGGPEAMSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATE Sbjct: 121 PTDFVDGIITMAGNGGPEAMSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATE 180 Query: 181 MGLLDVEPQEIVVIPRGVRFRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDF 240 MGLLDVEPQEIVVIPRGVRFRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDF Sbjct: 181 MGLLDVEPQEIVVIPRGVRFRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDF 240 Query: 241 LTPHAWYEDREGDFELVAKFQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSIS 300 LTPHAWYEDREGDFELVAKFQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSIS Sbjct: 241 LTPHAWYEDREGDFELVAKFQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSIS 300 Query: 301 FDHPDPSIFLVLQSPSDTPGVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGV 360 FDHPDPSIFLVLQSPSDTPGVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGV Sbjct: 301 FDHPDPSIFLVLQSPSDTPGVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGV 360 Query: 361 YDAKADGFSPGGASLHNCMSGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPT 420 YDAKADGFSPGGASLHNCMSGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPT Sbjct: 361 YDAKADGFSPGGASLHNCMSGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPT 420 Query: 421 PYAAESAQLQDDYYRCWQGLKKHFNPNER 449 PYAAESAQLQDDYYRCWQGLKKHFNPNER Sbjct: 421 PYAAESAQLQDDYYRCWQGLKKHFNPNER 449 Lambda K H 0.320 0.138 0.439 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: 973 Number of extensions: 31 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: 449 Length of database: 449 Length adjustment: 33 Effective length of query: 416 Effective length of database: 416 Effective search space: 173056 Effective search space used: 173056 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: 51 (24.3 bits)
Align candidate RR42_RS31275 RR42_RS31275 (homogentisate 1,2-dioxygenase)
to HMM TIGR01015 (hmgA: homogentisate 1,2-dioxygenase (EC 1.13.11.5))
# 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/TIGR01015.hmm # target sequence database: /tmp/gapView.633.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01015 [M=429] Accession: TIGR01015 Description: hmgA: homogentisate 1,2-dioxygenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.9e-207 672.7 0.0 1.1e-206 672.5 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS31275 RR42_RS31275 homogentisate 1,2-d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS31275 RR42_RS31275 homogentisate 1,2-dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 672.5 0.0 1.1e-206 1.1e-206 3 429 .] 22 444 .. 20 444 .. 0.99 Alignments for each domain: == domain 1 score: 672.5 bits; conditional E-value: 1.1e-206 TIGR01015 3 kylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafee 71 y+sGf nef++ea+pgalPvGqnsPq+apyglyaeq+sG+aftaPra+n+rsw yrir +a+he+f++ lcl|FitnessBrowser__Cup4G11:RR42_RS31275 22 GYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQISGTAFTAPRAHNRRSWCYRIRAAAMHEPFTR 90 59*****************************************************************99 PP TIGR01015 72 lkeseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasmed 140 ++ ++ ++++f+ ++++pnq+rwsp +p+ e +dfv+g+ t+ag+g +++ +G ++hly++n sm+d lcl|FitnessBrowser__Cup4G11:RR42_RS31275 91 VE--QSRIVSHFDAVPPSPNQMRWSPPAMPK-EPTDFVDGIITMAGNGGPEAMSGCGIHLYLANRSMTD 156 99..789999********************5.9************************************ PP TIGR01015 141 evfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfqlPd 208 + fynadG++livpq+G l++ te+G l+veP+ei+viprGvrfrve+ +earGyi+e+yga f+lPd lcl|FitnessBrowser__Cup4G11:RR42_RS31275 157 RFFYNADGEMLIVPQQGRLRLATEMGLLDVEPQEIVVIPRGVRFRVELPdGEARGYICENYGALFRLPD 225 ************************************************9899***************** PP TIGR01015 209 lGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlkk 277 lG iG+nglanprdf +P a++ed+e+ +++++ kfqg+l+ a ++hspldvvawhGny+Pykydl++ lcl|FitnessBrowser__Cup4G11:RR42_RS31275 226 LGVIGSNGLANPRDFLTPHAWYEDREG--DFELVAKFQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRR 292 ***************************..9*************************************** PP TIGR01015 278 fnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikGky 346 fn+i+s+sfdhpdPsif vl +psd++G+ +dfvif Prwl ++tfrPP++hrn+ sefmGli+G y lcl|FitnessBrowser__Cup4G11:RR42_RS31275 293 FNTIGSISFDHPDPSIFLVLQSPSDTPGVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGVY 361 ********************************************************************* PP TIGR01015 347 dakeeGfvpgGaslhnimsahGPdveafekasnael.kPekiddgtlafmfesslslavtklakelekl 414 dak++Gf pgGaslhn+ms hGPd+e+f ka++a+ +P++i+d t+afmfe+ +++ t +a+e+++l lcl|FitnessBrowser__Cup4G11:RR42_RS31275 362 DAKADGFSPGGASLHNCMSGHGPDAETFAKATAADTsQPHRIGD-TMAFMFETPAVIRPTPYAAESAQL 429 *********************************98638******.************************ PP TIGR01015 415 dedyeevwqglkkkf 429 ++dy+ +wqglkk+f lcl|FitnessBrowser__Cup4G11:RR42_RS31275 430 QDDYYRCWQGLKKHF 444 **************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (429 nodes) Target sequences: 1 (449 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: 00:00:00.01 # Mc/sec: 11.82 // [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