Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate RR42_RS32640 RR42_RS32640 4-oxalocrotonate decarboxylase
Query= metacyc::MONOMER-14737 (262 letters) >FitnessBrowser__Cup4G11:RR42_RS32640 Length = 262 Score = 370 bits (950), Expect = e-107 Identities = 180/262 (68%), Positives = 216/262 (82%) Query: 1 MKLDKNTLAQLAEHLENAELKAHDVTKITDDHPDMDWDDAYAIQDLIRARKESRGHKTLG 60 M L ++T QLAEHLE AEL V KITD HP+MDW+DAYAIQD IRARK++RG + G Sbjct: 1 MNLTQDTTRQLAEHLETAELNREPVRKITDTHPEMDWEDAYAIQDAIRARKQARGTRIAG 60 Query: 61 LKCGLTSYAKMKQMGVDTPVFGFVSDYMACAEGSDIKTSELIHPKVEAEICVVTKAPLKG 120 LK GLTS+AKM+QMGV PV+GF++DY AC +G I T+ LIHPKVEAEI V K PLKG Sbjct: 61 LKMGLTSFAKMRQMGVTDPVYGFLTDYGACMDGGAIDTASLIHPKVEAEIAFVLKHPLKG 120 Query: 121 PGCHVGAVMAAIDFVIPGVEIIDSRYRDFKFDLKSVIADNTSASRFVIGGRARRVEDLDL 180 PGCH+G V+AA DFV+P VE+IDSRY +F+FDLKSVIADNTS++RFV+GG R E +DL Sbjct: 121 PGCHIGDVLAATDFVLPAVEVIDSRYENFRFDLKSVIADNTSSARFVVGGTHRSAEGIDL 180 Query: 181 RTLGVVLEKNGQIVAMAAGAAVMGHPAAAIAALANHLGARGQEIPTGSFIMTGGVTEAIA 240 + LGVVLEKNG++VA AAGAAV+GHPA+++A LAN LGARG+E+P G+FIMTGGVTEAIA Sbjct: 181 KNLGVVLEKNGEVVATAAGAAVLGHPASSVAMLANMLGARGRELPAGTFIMTGGVTEAIA 240 Query: 241 VQAGDSVNVRFQDLGTVGMRFV 262 V AGDS+ VR+Q LGTV MRFV Sbjct: 241 VAAGDSITVRYQHLGTVSMRFV 262 Lambda K H 0.320 0.135 0.391 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: 241 Number of extensions: 6 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: 262 Length of database: 262 Length adjustment: 25 Effective length of query: 237 Effective length of database: 237 Effective search space: 56169 Effective search space used: 56169 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: 47 (22.7 bits)
Align candidate RR42_RS32640 RR42_RS32640 (4-oxalocrotonate decarboxylase)
to HMM TIGR03218 (dmpH: 4-oxalocrotonate decarboxylase (EC 4.1.1.77))
# 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/TIGR03218.hmm # target sequence database: /tmp/gapView.13497.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03218 [M=263] Accession: TIGR03218 Description: catechol_dmpH: 4-oxalocrotonate decarboxylase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-141 454.1 0.6 7.6e-141 454.0 0.6 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS32640 RR42_RS32640 4-oxalocrotonate de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS32640 RR42_RS32640 4-oxalocrotonate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 454.0 0.6 7.6e-141 7.6e-141 3 263 .] 1 261 [. 1 261 [. 1.00 Alignments for each domain: == domain 1 score: 454.0 bits; conditional E-value: 7.6e-141 TIGR03218 3 ltltreqiealaehvenaeleareitkitdeyPdldfadaydiqaeirrrklarGakvvGlkaGltska 71 ++lt+++ +laeh+e ael+ + + kitd +P++d++day+iq++ir+rk+arG+++ Glk+Glts+a lcl|FitnessBrowser__Cup4G11:RR42_RS32640 1 MNLTQDTTRQLAEHLETAELNREPVRKITDTHPEMDWEDAYAIQDAIRARKQARGTRIAGLKMGLTSFA 69 689****************************************************************** PP TIGR03218 72 kmkqmGvetpvfGfladyfsvpdggeiktselihPkveaeiafvlkaelkgpgchigdvlaatdfvlpa 140 km+qmGv++pv+Gfl+dy + dgg+i+t lihPkveaeiafvlk++lkgpgchigdvlaatdfvlpa lcl|FitnessBrowser__Cup4G11:RR42_RS32640 70 KMRQMGVTDPVYGFLTDYGACMDGGAIDTASLIHPKVEAEIAFVLKHPLKGPGCHIGDVLAATDFVLPA 138 ********************************************************************* PP TIGR03218 141 vevidsrykdfkfdlksvvadnassarfvtGgraaavedldlrtlGvvleknGevvalgagaavlGhpa 209 vevidsry++f+fdlksv+adn+ssarfv+Gg ++ e++dl++lGvvleknGevva++agaavlGhpa lcl|FitnessBrowser__Cup4G11:RR42_RS32640 139 VEVIDSRYENFRFDLKSVIADNTSSARFVVGGTHRSAEGIDLKNLGVVLEKNGEVVATAAGAAVLGHPA 207 ********************************************************************* PP TIGR03218 210 aavamlanllaergeeiPaGslilsggiteavavaaGdsvtvrvqelgsvslrf 263 ++vamlan+l++rg+e+PaG++i++gg+tea+avaaGds+tvr+q+lg+vs+rf lcl|FitnessBrowser__Cup4G11:RR42_RS32640 208 SSVAMLANMLGARGRELPAGTFIMTGGVTEAIAVAAGDSITVRYQHLGTVSMRF 261 *****************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (262 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: 10.22 // [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