Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate BPHYT_RS17360 BPHYT_RS17360 phenylacetate-CoA ligase
Query= BRENDA::B4E7B5 (432 letters) >FitnessBrowser__BFirm:BPHYT_RS17360 Length = 434 Score = 802 bits (2071), Expect = 0.0 Identities = 395/431 (91%), Positives = 416/431 (96%) Query: 1 MTTPLPLEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADL 60 MTT LPL+PIETASRDEL ALQLERLKWSL HAY++SPVYR KFDEAGVHP ++KTLADL Sbjct: 1 MTTALPLDPIETASRDELAALQLERLKWSLNHAYENSPVYRHKFDEAGVHPSEVKTLADL 60 Query: 61 SRFPFTTKGDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARS 120 +RFPFTTK DLRDSYPFGMFAVPQ++ISRIHASSGTTGKPTVVGYTA DIDTWANLVARS Sbjct: 61 ARFPFTTKKDLRDSYPFGMFAVPQEQISRIHASSGTTGKPTVVGYTARDIDTWANLVARS 120 Query: 121 IRAAGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDI 180 +RAAGA+RGDKVH+SYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDI Sbjct: 121 VRAAGAKRGDKVHISYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDI 180 Query: 181 IMVTPSYMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLS 240 IMVTPSYMLSIADE+ERQG+DP SLRIGIFGAEPWTNDMR AIE+RMGIDAVDIYGLS Sbjct: 181 IMVTPSYMLSIADELERQGVDPANCSLRIGIFGAEPWTNDMRQAIEKRMGIDAVDIYGLS 240 Query: 241 EVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIR 300 EVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPI+R Sbjct: 241 EVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIVR 300 Query: 301 YRTRDLTRLLPGTARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIV 360 YRTRDLTRLLPG+ARTMRRMEKITGRSDDMMIVRGVNVFPTQIEE LLKQRALAPHYQIV Sbjct: 301 YRTRDLTRLLPGSARTMRRMEKITGRSDDMMIVRGVNVFPTQIEELLLKQRALAPHYQIV 360 Query: 361 LTKEGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSV 420 LTKEGPLDVLTLNVEPCPE+APDTAA+ AKQALAYDIK+LIGV+AV+NVL VNGIERSV Sbjct: 361 LTKEGPLDVLTLNVEPCPESAPDTAALSTAKQALAYDIKALIGVSAVVNVLAVNGIERSV 420 Query: 421 GKARRVVDKRK 431 GKARRVVDKRK Sbjct: 421 GKARRVVDKRK 431 Lambda K H 0.319 0.137 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: 773 Number of extensions: 12 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: 432 Length of database: 434 Length adjustment: 32 Effective length of query: 400 Effective length of database: 402 Effective search space: 160800 Effective search space used: 160800 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 (21.7 bits) S2: 51 (24.3 bits)
Align candidate BPHYT_RS17360 BPHYT_RS17360 (phenylacetate-CoA ligase)
to HMM TIGR02155 (paaF: phenylacetate-CoA ligase (EC 6.2.1.30))
# 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/TIGR02155.hmm # target sequence database: /tmp/gapView.31180.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02155 [M=422] Accession: TIGR02155 Description: PA_CoA_ligase: phenylacetate-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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-219 713.1 0.0 5.1e-219 712.9 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS17360 BPHYT_RS17360 phenylacetate-CoA Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS17360 BPHYT_RS17360 phenylacetate-CoA ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 712.9 0.0 5.1e-219 5.1e-219 1 422 [] 11 430 .. 11 430 .. 0.99 Alignments for each domain: == domain 1 score: 712.9 bits; conditional E-value: 5.1e-219 TIGR02155 1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdll 70 e++s+del alqlerlk+s+++ayen p+yr++fd+agv+p+++k+l+dla+fp+t+k+dlrd ypf+++ lcl|FitnessBrowser__BFirm:BPHYT_RS17360 11 ETASRDELAALQLERLKWSLNHAYENSPVYRHKFDEAGVHPSEVKTLADLARFPFTTKKDLRDSYPFGMF 80 89******************************************************************** PP TIGR02155 71 avprekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyG 140 avp+e++ r+hassGttGkptvv+yt++d+dtw+++vars+raaG ++gd++h++yGyGlftGGlG+hyG lcl|FitnessBrowser__BFirm:BPHYT_RS17360 81 AVPQEQISRIHASSGTTGKPTVVGYTARDIDTWANLVARSVRAAGAKRGDKVHISYGYGLFTGGLGAHYG 150 ********************************************************************** PP TIGR02155 141 aeklGatvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwtea 210 ae+ G tv+p+ GGqtekqvqliqdf+pdii+vtpsy+l++++el+r+g+dp+++sl+++i+Gaepwt++ lcl|FitnessBrowser__BFirm:BPHYT_RS17360 151 AERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMVTPSYMLSIADELERQGVDPANCSLRIGIFGAEPWTND 220 ********************************************************************** PP TIGR02155 211 mrkelearlgikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvftt 280 mr+++e+r+gi+a+diyGlsev+GpGva ecvetkdG++iwedhfypeiidpetgevlpdGe Gelvft+ lcl|FitnessBrowser__BFirm:BPHYT_RS17360 221 MRQAIEKRMGIDAVDIYGLSEVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTS 290 ********************************************************************** PP TIGR02155 281 ltkealpviryrtrdltrllpgtartmrrmdkikGrsddllilrGvnvfptqleevllkldklsphyqle 350 ltkealp++ryrtrdltrllpg+artmrrm+ki+Grsdd++i+rGvnvfptq+ee+llk+ l+phyq+ lcl|FitnessBrowser__BFirm:BPHYT_RS17360 291 LTKEALPIVRYRTRDLTRLLPGSARTMRRMEKITGRSDDMMIVRGVNVFPTQIEELLLKQRALAPHYQIV 360 ********************************************************************** PP TIGR02155 351 ltreGaldeltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgslerseGkakrvvd 420 lt+eG ld ltl+ve +esa + s+ ++ + +ika +gvs+ v++ + +ers Gka+rvvd lcl|FitnessBrowser__BFirm:BPHYT_RS17360 361 LTKEGPLDVLTLNVEPCPESAPDT--AALSTAKQALAYDIKALIGVSAVVNVLAVNGIERSVGKARRVVD 428 *******************99877..445567999*********************************** PP TIGR02155 421 kr 422 kr lcl|FitnessBrowser__BFirm:BPHYT_RS17360 429 KR 430 *8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (422 nodes) Target sequences: 1 (434 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: 00:00:00.01 # Mc/sec: 11.85 // [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