Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized)
to candidate 15516 b1394 enoyl-CoA hydratase (NCBI)
Query= curated2:P24162 (257 letters) >FitnessBrowser__Keio:15516 Length = 262 Score = 213 bits (541), Expect = 4e-60 Identities = 114/256 (44%), Positives = 157/256 (61%), Gaps = 10/256 (3%) Query: 10 ISEGLAVITLDRPEVMNALNAAMRHELTAALHRARGE--ARAIVLTGSGRAFCSGQDLGD 67 + +G+ +TL+RPE +N+ N M +L L + + R ++LTG+GR FC+GQDL D Sbjct: 9 VEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAGQDLND 68 Query: 68 ------GAAEGLNLETVLREEYEPLLQAIYSCPLPVLAAVNGAAAGAGANLALAADVVIA 121 G A L + + Y PL++ + P PV+ AVNG AAGAGA LAL D+VIA Sbjct: 69 RNVDPTGPAPDLGMS--VERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIA 126 Query: 122 AQSAAFMQAFTRIGLMPDAGGTWWLPRQVGMARAMGMALFAEKIGAEEAARMGLIWEAVP 181 A+SA F+ AF+++GL+PD GGTW LPR G ARAMG+AL ++ AE+A G+IW+ V Sbjct: 127 ARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQVVD 186 Query: 182 DVDFEHHWRARAAHLARGPSAAFAAVKKAFHAGLSNPLPAQLALEARLQGELGQSADFRE 241 D + A HLA P+ +K+A ++ +N L QL LE Q G+SAD+RE Sbjct: 187 DETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADYRE 246 Query: 242 GVQAFLEKRPPHFTGR 257 GV AFL KR P FTG+ Sbjct: 247 GVSAFLAKRSPQFTGK 262 Lambda K H 0.321 0.133 0.397 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: 157 Number of extensions: 6 Number of successful extensions: 3 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: 257 Length of database: 262 Length adjustment: 24 Effective length of query: 233 Effective length of database: 238 Effective search space: 55454 Effective search space used: 55454 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 (21.9 bits) S2: 47 (22.7 bits)
Align candidate 15516 b1394 (enoyl-CoA hydratase (NCBI))
to HMM TIGR02280 (paaB: phenylacetate degradation probable enoyl-CoA hydratase PaaB (EC 4.2.1.17))
# 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/TIGR02280.hmm # target sequence database: /tmp/gapView.25888.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02280 [M=256] Accession: TIGR02280 Description: PaaB1: phenylacetate degradation probable enoyl-CoA hydratase PaaB 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-149 482.9 0.7 1.3e-149 482.7 0.7 1.0 1 lcl|FitnessBrowser__Keio:15516 b1394 enoyl-CoA hydratase (NCBI) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:15516 b1394 enoyl-CoA hydratase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 482.7 0.7 1.3e-149 1.3e-149 1 256 [] 5 262 .] 5 262 .] 1.00 Alignments for each domain: == domain 1 score: 482.7 bits; conditional E-value: 1.3e-149 TIGR02280 1 illelekgvlrltlnrpdklnsfteemhaelaealerverdd.vrallltGaGrGfcaGqdlsernvtkg.aapdlGet 77 il+++ekgv++ltlnrp++lnsf++emha+lae+l++verdd +r+llltGaGrGfcaGqdl++rnv+++ +apdlG++ lcl|FitnessBrowser__Keio:15516 5 ILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDtIRCLLLTGAGRGFCAGQDLNDRNVDPTgPAPDLGMS 83 89****************************************9**************************999******* PP TIGR02280 78 vekfynplvrrlaalpkpvvvavnGvaaGaGanlalagdivlaaesakfiqafaklGlipdsGGtwllprlvGrarakg 156 ve+fynplvrrla+lpkpv++avnGvaaGaGa+lal+gdiv+aa+sakf++af+klGlipd+GGtwllpr++Grara+g lcl|FitnessBrowser__Keio:15516 84 VERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMG 162 ******************************************************************************* PP TIGR02280 157 lallgekldaetaaewGliwqvvddealadevqalaahlakqptrglalikralqaaetnsldtqldlerdlqrelGrs 235 lallg++l+ae+a+ewG+iwqvvdde+lad++q+la+hla+qpt+gl+lik+a+++aetn+ldtqldlerd+qr +Grs lcl|FitnessBrowser__Keio:15516 163 LALLGNQLSAEQAHEWGMIWQVVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRS 241 ******************************************************************************* PP TIGR02280 236 adyaeGvaafldkrepefkGk 256 ady+eGv+afl+kr+p+f+Gk lcl|FitnessBrowser__Keio:15516 242 ADYREGVSAFLAKRSPQFTGK 262 ********************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5.79 // [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