Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_012709489.1 NGR_RS26100 acetyl-CoA C-acyltransferase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2982 (397 letters) >NCBI__GCF_000018545.1:WP_012709489.1 Length = 393 Score = 479 bits (1232), Expect = e-140 Identities = 251/395 (63%), Positives = 306/395 (77%), Gaps = 4/395 (1%) Query: 3 MSN-DPIVIVSAVRTPMGGFQGELKSLTAPQLGAAAIKAAVERAGVASDSVDEVLFGCVL 61 MSN DP+VIVSA RTPMG FQG LK LTAP+LGA A+KAA++RAG+ D+VDEV+ G VL Sbjct: 1 MSNRDPVVIVSAARTPMGAFQGGLKDLTAPELGAIALKAALDRAGL--DAVDEVMMGNVL 58 Query: 62 PAGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMES 121 PAGLGQ PARQAALGAGL + T TT++K+CGSGM+A +L HD L++GSA VV GGMES Sbjct: 59 PAGLGQNPARQAALGAGLGQQTPSTTVSKVCGSGMKALMLGHDALISGSASVVGVGGMES 118 Query: 122 MSNAPYLLDRARAGYRMGHGRVQDSMFLDGLEDAYDKGRLMGTFAEDCAETNGFSREAQD 181 M+NAPYLL +AR G+R+GHG V+D MFLDGLEDAY GRLMGT+AED A+ FSR QD Sbjct: 119 MTNAPYLLPKARGGFRLGHGEVKDHMFLDGLEDAYS-GRLMGTYAEDTAQHYQFSRADQD 177 Query: 182 AFAIASTTRAQQAIKDGSFKAEIVPLTVTVGKEQVVISNDEQPPKARLDKIASLKPAFRE 241 AFA+ S RA +A +D SF EIV +T + + DEQP KA KI LKPAFR+ Sbjct: 178 AFALRSLERALKAAEDKSFADEIVAITDGGKRGTANLDRDEQPTKADPAKIPKLKPAFRD 237 Query: 242 GGTVTAANSSSISDGAAALVLMRQSQAQKQGLKPLAVIHGHAAFADTPGLFPVAPIGAIK 301 GG+VTAANSSSISDGAAALVLMR S+A+++GL PLA++ GHA A P F APIGAI Sbjct: 238 GGSVTAANSSSISDGAAALVLMRASEAERRGLTPLAIVAGHAGHAQEPAWFTTAPIGAID 297 Query: 302 KLMKKTGWSLNDVDLVEVNEAFAVVGMAAMTHLEIPHEKLNVHGGACALGHPIGASGARI 361 KL++K GW V L E+NEAFA+V MAA+ L + + +N+HGGACALGHPIGASGARI Sbjct: 298 KLIEKLGWEKGSVGLYEINEAFAIVAMAAIRDLGLSDDIVNIHGGACALGHPIGASGARI 357 Query: 362 LVTLLSALRQKGLKRGVAAICIGGGEATAMAVECL 396 +VTLL A+R G+KRG+A++CIGGGEATA+ +E + Sbjct: 358 VVTLLHAMRANGVKRGIASLCIGGGEATAVGLELM 392 Lambda K H 0.318 0.132 0.376 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: 587 Number of extensions: 21 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: 397 Length of database: 393 Length adjustment: 31 Effective length of query: 366 Effective length of database: 362 Effective search space: 132492 Effective search space used: 132492 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_012709489.1 NGR_RS26100 (acetyl-CoA C-acyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))
# 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/TIGR01930.hmm # target sequence database: /tmp/gapView.1071391.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01930 [M=385] Accession: TIGR01930 Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase 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-121 390.3 3.6 5.1e-121 390.2 3.6 1.0 1 NCBI__GCF_000018545.1:WP_012709489.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000018545.1:WP_012709489.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 390.2 3.6 5.1e-121 5.1e-121 1 384 [. 9 389 .. 9 390 .. 0.98 Alignments for each domain: == domain 1 score: 390.2 bits; conditional E-value: 5.1e-121 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 iv+a+Rtp+g+++g lk+l+a +L+a ++k++l+ragld ++dev++Gnvl+ag ++n+aR+aal agl+++ NCBI__GCF_000018545.1:WP_012709489.1 9 IVSAARTPMGAFQGGLKDLTAPELGAIALKAALDRAGLD--AVDEVMMGNVLPAGLGQNPARQAALGAGLGQQ 79 8*************************************9..6******************************* PP TIGR01930 74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144 +p++tv++vC+Sg++A++l+ +++ +G a+vv +GG+Esm+++p+ll+++ r +++lg+ +++d++ d+ NCBI__GCF_000018545.1:WP_012709489.1 80 TPSTTVSKVCGSGMKALMLGHDALISGSASVVGVGGMESMTNAPYLLPKA--RGGFRLGHGEVKDHMFLDGle 150 ************************************************98..89***********99999999 PP TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214 ++++ mg+ Ae +a++y++sR +qD++alrS ++a kA e++ f+deiv ++ gk + +++De++ + NCBI__GCF_000018545.1:WP_012709489.1 151 dAYSGRLMGTYAEDTAQHYQFSRADQDAFALRSLERALKAAEDKSFADEIVAITDGGKrgTANLDRDEQPT-K 222 988999*************************************************9999988999999998.7 PP TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287 +k+ kLkpaf++ gs vtA+Nss+++DGAaal+lm + a++ gltpla + ++a + +p+ ++++p+ NCBI__GCF_000018545.1:WP_012709489.1 223 ADPAKIPKLKPAFRD-GGS-VTAANSSSISDGAAALVLMRASEAERRGLTPLAIVAGHAGHAQEPAWFTTAPI 293 899**********96.786.***************************************************** PP TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360 Ai k+++k g++ ++ l+EinEAFA +++a++++lg l+++ vN++GGA AlGHP+GasGariv+tll+++ NCBI__GCF_000018545.1:WP_012709489.1 294 GAIDKLIEKLGWEKGSVGLYEINEAFAIVAMAAIRDLG-LSDDIVNIHGGACALGHPIGASGARIVVTLLHAM 365 **************************************.889******************************* PP TIGR01930 361 kergkkyGlatlCvggGqGaAvil 384 + +g+k+G+a+lC+ggG ++Av l NCBI__GCF_000018545.1:WP_012709489.1 366 RANGVKRGIASLCIGGGEATAVGL 389 *********************966 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (393 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 17.22 // [ok]
This GapMind analysis is from Apr 09 2024. 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