Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate 14473 b0335 predicted propionyl-CoA synthetase with ATPase domain (NCBI)
Query= BRENDA::P77495 (628 letters) >FitnessBrowser__Keio:14473 Length = 628 Score = 1279 bits (3309), Expect = 0.0 Identities = 628/628 (100%), Positives = 628/628 (100%) Query: 1 MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDR 60 MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDR Sbjct: 1 MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDR 60 Query: 61 WLEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAE 120 WLEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAE Sbjct: 61 WLEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAE 120 Query: 121 AHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDD 180 AHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDD Sbjct: 121 AHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDD 180 Query: 181 AISQAQHQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYT 240 AISQAQHQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYT Sbjct: 181 AISQAQHQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYT 240 Query: 241 SGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAG 300 SGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAG Sbjct: 241 SGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAG 300 Query: 301 MATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLY 360 MATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLY Sbjct: 301 MATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLY 360 Query: 361 LAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYN 420 LAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYN Sbjct: 361 LAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYN 420 Query: 421 VQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRPVYATFDWG 480 VQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRPVYATFDWG Sbjct: 421 VQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRPVYATFDWG 480 Query: 481 IRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVAF 540 IRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVAF Sbjct: 481 IRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVAF 540 Query: 541 VIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQA 600 VIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQA Sbjct: 541 VIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQA 600 Query: 601 ICEGRDPGDLTTIDDPASLDQIRQAMEE 628 ICEGRDPGDLTTIDDPASLDQIRQAMEE Sbjct: 601 ICEGRDPGDLTTIDDPASLDQIRQAMEE 628 Lambda K H 0.320 0.136 0.422 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: 1440 Number of extensions: 33 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: 628 Length of database: 628 Length adjustment: 38 Effective length of query: 590 Effective length of database: 590 Effective search space: 348100 Effective search space used: 348100 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: 54 (25.4 bits)
Align candidate 14473 b0335 (predicted propionyl-CoA synthetase with ATPase domain (NCBI))
to HMM TIGR02316 (prpE: propionate--CoA ligase (EC 6.2.1.17))
# 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/TIGR02316.hmm # target sequence database: /tmp/gapView.13106.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02316 [M=628] Accession: TIGR02316 Description: propion_prpE: propionate--CoA ligase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1308.6 0.3 0 1308.4 0.3 1.0 1 lcl|FitnessBrowser__Keio:14473 b0335 predicted propionyl-CoA sy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:14473 b0335 predicted propionyl-CoA synthetase with ATPase domain (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1308.4 0.3 0 0 1 628 [] 1 628 [] 1 628 [] 1.00 Alignments for each domain: == domain 1 score: 1308.4 bits; conditional E-value: 0 TIGR02316 1 mayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrgeqlalvavssetg 79 m+++e+yqrsi+epe+fwaeqarridwqtpf+++ld+sn+pfarwf++grtnlc+na+dr+lek++e+lal+avsset+ lcl|FitnessBrowser__Keio:14473 1 MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDRWLEKQPEALALIAVSSETE 79 79***************************************************************************** PP TIGR02316 80 eertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacarigaihsvvfggfashslaariddatpkl 158 eert+t+rqlh+evna+as+lr+lgv+rgdrvl+y+pmiaea+++llacarigaihsvvfggfashs+aaridda+p+l lcl|FitnessBrowser__Keio:14473 80 EERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAEAHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVL 158 ******************************************************************************* PP TIGR02316 159 ivsadagarggkvieykklldaaiaeaqhkpahvllvdrglaklrrvpgrdvdyaalrrqhedadvevewlesnepsyi 237 ivsadagarggk+i+ykklld+ai++aqh+p+hvllvdrglak++rv+grdvd+a+lr+qh++a+v+v+wlesne+s+i lcl|FitnessBrowser__Keio:14473 159 IVSADAGARGGKIIPYKKLLDDAISQAQHQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCI 237 ******************************************************************************* PP TIGR02316 238 lytsgttgkpkgvqrdvggyavalaasmdaifgakagdvlfsasdvgwvvghsyivyapllaglatvlyeglptrpdgg 316 lytsgttgkpkgvqrdvggyavala+smd+ifg+kag+v+f+asd+gwvvghsyivyapllag+at++yeglpt+pd+g lcl|FitnessBrowser__Keio:14473 238 LYTSGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAGMATIVYEGLPTWPDCG 316 ******************************************************************************* PP TIGR02316 317 vwwsivekyrvsvmfsaptairvlkkqdaallrkhdlsslevlflagepldeptarwisdalgkpvidnywqtetgwpv 395 vww+iveky+vs+mfsaptairvlkk+++a++rkhdlsslevl+lagepldepta+w+s++l++pvidnywqte+gwp+ lcl|FitnessBrowser__Keio:14473 317 VWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLYLAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPI 395 ******************************************************************************* PP TIGR02316 396 laiarglddkpvklgspglpvygyrldvldeatgedvgpnekgllvvaaplppgclstvwgddarflktyfsafkrlly 474 +aiargldd+p++lgspg+p+ygy++++l+e+tge++g+nekg+lvv++plppgc++t+wgdd+rf+kty+s+f+r++y lcl|FitnessBrowser__Keio:14473 396 MAIARGLDDRPTRLGSPGVPMYGYNVQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRPVY 474 ******************************************************************************* PP TIGR02316 475 ssldwgirdedgytfilgrtddvinvaghrlgtreieesvsshaavaevavvgvkdelkgqvavafailkeadsvedad 553 +++dwgird+dgy+filgrtddvinvaghrlgtreiees+ssh++vaevavvgvkd+lkgqvavaf+i+ke+ds+ed+d lcl|FitnessBrowser__Keio:14473 475 ATFDWGIRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVAFVIPKESDSLEDRD 553 ******************************************************************************* PP TIGR02316 554 dahalekelmalvesqlgavarparvyvvaalpktrsgkllrraiqavaegrdpgdlttiddpaaleqvrealee 628 +ah++ek++malv+sq+g+++rpa+v++v++lpktrsgk+lrr+iqa++egrdpgdlttiddpa+l+q+r+a+ee lcl|FitnessBrowser__Keio:14473 554 VAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQAICEGRDPGDLTTIDDPASLDQIRQAMEE 628 *************************************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (628 nodes) Target sequences: 1 (628 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 9.88 // [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