Align ethanolamine utilization protein eutD (characterized)
to candidate 16557 b2458 predicted phosphotransacetylase subunit (NCBI)
Query= CharProtDB::CH_024378 (338 letters) >FitnessBrowser__Keio:16557 Length = 338 Score = 659 bits (1701), Expect = 0.0 Identities = 338/338 (100%), Positives = 338/338 (100%) Query: 1 MIIERCRELALRAPARVVFPDALDQRVLKAAQYLHQQGLATPILVANPFELRQFALSHGV 60 MIIERCRELALRAPARVVFPDALDQRVLKAAQYLHQQGLATPILVANPFELRQFALSHGV Sbjct: 1 MIIERCRELALRAPARVVFPDALDQRVLKAAQYLHQQGLATPILVANPFELRQFALSHGV 60 Query: 61 AMDGLQVIDPHGNLAMREEFAHRWLARAGEKTPPDALEKLTDPLMFAAAMVSAGKADVCI 120 AMDGLQVIDPHGNLAMREEFAHRWLARAGEKTPPDALEKLTDPLMFAAAMVSAGKADVCI Sbjct: 61 AMDGLQVIDPHGNLAMREEFAHRWLARAGEKTPPDALEKLTDPLMFAAAMVSAGKADVCI 120 Query: 121 AGNLSSTANVLRAGLRIIGLQPGCKTLSSIFLMLPQYSGPALGFADCSVVPQPTAAQLAD 180 AGNLSSTANVLRAGLRIIGLQPGCKTLSSIFLMLPQYSGPALGFADCSVVPQPTAAQLAD Sbjct: 121 AGNLSSTANVLRAGLRIIGLQPGCKTLSSIFLMLPQYSGPALGFADCSVVPQPTAAQLAD 180 Query: 181 IALASAETWRAITGEEPRVAMLSFSSNGSARHPCVANVQQATEIVRERAPKLVVDGELQF 240 IALASAETWRAITGEEPRVAMLSFSSNGSARHPCVANVQQATEIVRERAPKLVVDGELQF Sbjct: 181 IALASAETWRAITGEEPRVAMLSFSSNGSARHPCVANVQQATEIVRERAPKLVVDGELQF 240 Query: 241 DAAFVPEVAAQKAPASPLQGKANVMVFPSLEAGNIGYKIAQRLGGYRAVGPLIQGLAAPM 300 DAAFVPEVAAQKAPASPLQGKANVMVFPSLEAGNIGYKIAQRLGGYRAVGPLIQGLAAPM Sbjct: 241 DAAFVPEVAAQKAPASPLQGKANVMVFPSLEAGNIGYKIAQRLGGYRAVGPLIQGLAAPM 300 Query: 301 HDLSRGCSVQEIIELALVAAVPRQTEVNRESSLQTLVE 338 HDLSRGCSVQEIIELALVAAVPRQTEVNRESSLQTLVE Sbjct: 301 HDLSRGCSVQEIIELALVAAVPRQTEVNRESSLQTLVE 338 Lambda K H 0.320 0.134 0.387 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: 521 Number of extensions: 10 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: 338 Length of database: 338 Length adjustment: 28 Effective length of query: 310 Effective length of database: 310 Effective search space: 96100 Effective search space used: 96100 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: 49 (23.5 bits)
Align candidate 16557 b2458 (predicted phosphotransacetylase subunit (NCBI))
to HMM TIGR00651 (pta: phosphate acetyltransferase (EC 2.3.1.8))
# 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/TIGR00651.hmm # target sequence database: /tmp/gapView.12174.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00651 [M=304] Accession: TIGR00651 Description: pta: phosphate acetyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-103 330.8 0.0 5.2e-103 330.6 0.0 1.0 1 lcl|FitnessBrowser__Keio:16557 b2458 predicted phosphotransacet Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:16557 b2458 predicted phosphotransacetylase subunit (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 330.6 0.0 5.2e-103 5.2e-103 1 303 [. 17 319 .. 17 320 .. 0.94 Alignments for each domain: == domain 1 score: 330.6 bits; conditional E-value: 5.2e-103 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpd.vskdiekyverlyekrkhkGvt 78 +v+P++ ++rvlkAa+ l ++++a+++l++n e + + + ++ ++v+dp+ +e++++r+ + +k t lcl|FitnessBrowser__Keio:16557 17 VVFPDALDQRVLKAAQYLHQQGLATPILVANPFELRQFAL-SHGVAMDGLQVIDPHgNLAMREEFAHRWLARAGEK--T 92 79******************************99999544.445556666666665156789**************..9 PP TIGR00651 79 ekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee..evlvfaDCavav 155 a e+l+D++++aa +v++g+ad +++G+ s+ta++lr++l+ii+ ++g k+ ss+f+m + l faDC+v++ lcl|FitnessBrowser__Keio:16557 93 PPDALEKLTDPLMFAAAMVSAGKADVCIAGNLSSTANVLRAGLRIIGLQPGCKTLSSIFLMLPQYsgPALGFADCSVVP 171 99***********************************************************87765579********** PP TIGR00651 156 dPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqfDaAlvekvae 234 +P+a +LA+iAl sa++ +++++eep+va+ls+s++gs++ v v++A++i++e++p l++dGelqfDaA+v++va+ lcl|FitnessBrowser__Keio:16557 172 QPTAAQLADIALASAETWRAITGEEPRVAMLSFSSNGSARHPCVANVQQATEIVRERAPKLVVDGELQFDAAFVPEVAA 250 ******************************************************************************* PP TIGR00651 235 kkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvviit 303 +kap s+++gkanv+vFP+L+aGnigYki+qRl++++a+GP++qGla P+ DLsRG+sv++i+ ++++ lcl|FitnessBrowser__Keio:16557 251 QKAPASPLQGKANVMVFPSLEAGNIGYKIAQRLGGYRAVGPLIQGLAAPMHDLSRGCSVQEIIELALVA 319 ***************************************************************998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (338 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: 00:00:00.00 # Mc/sec: 10.66 // [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