Align acylating aldehyde dehydrogenase (EC 1.2.1.10) (characterized)
to candidate WP_003943168.1 C1M55_RS29420 acetaldehyde dehydrogenase (acetylating)
Query= metacyc::MONOMER-11388 (316 letters) >NCBI__GCF_002893965.1:WP_003943168.1 Length = 314 Score = 402 bits (1032), Expect = e-117 Identities = 212/309 (68%), Positives = 243/309 (78%), Gaps = 5/309 (1%) Query: 4 KVKAAIIGSGNIGTDLMIKILRHGQHIEMGAMVGIDPASDGLARGERMGVAITHEGVEGL 63 KVK AIIGSGNIGTDLMIK+LR+ ++EMGAMVGIDPASDGLAR R+ V IT EGVEGL Sbjct: 3 KVKVAIIGSGNIGTDLMIKVLRNSDYLEMGAMVGIDPASDGLARAARLNVPITAEGVEGL 62 Query: 64 TRLPVFNEIDVVFDATSAGAHVKNEALLRERKPGLRMIDLTPAAIAPYCIPVVNGDDHLD 123 LP F+EI++VFDATSA AHV N A L G RMIDLTPAAI PY +P VN D+HLD Sbjct: 63 VGLPNFDEIEIVFDATSAKAHVANNARLAPL--GKRMIDLTPAAIGPYVVPAVNADEHLD 120 Query: 124 ATNVNMVTCGGQATIPMVAAVSRVAKVHYAEIIASISSKSAGPGTRANIDEFTETTSKAI 183 A NVNMVTCGGQATIPMVAAVSRV V YAEI+ASI+SKSAGPGTRANIDEFTETTS+AI Sbjct: 121 APNVNMVTCGGQATIPMVAAVSRVVPVAYAEIVASIASKSAGPGTRANIDEFTETTSEAI 180 Query: 184 EVVGGAAKGKAIIVLNPAEPPLMMRDAVYTLSDFAD---IDQIEESVQRMADAVQAYVPG 240 VGGA +GKAII+LNPAEPPL+MRD V+ L D D D+I +S+++M V AYVPG Sbjct: 181 VAVGGARRGKAIIILNPAEPPLIMRDTVFCLVDAPDPAVHDEIRQSIEKMVGDVSAYVPG 240 Query: 241 YRLKQRVQFDRIEADCPIRIPGVGDRMNGLKTSIFLEVEGAAHYLPAYAGNLDIMTSAAL 300 YRLKQ VQ I AD P+ V + S+FLEVEGAAHYLPAYAGNLDIMTSA + Sbjct: 241 YRLKQEVQITEIPADQPVETLLVDGNRPTHQVSVFLEVEGAAHYLPAYAGNLDIMTSAGM 300 Query: 301 RTAEKLAER 309 + AE++A++ Sbjct: 301 QIAERIAQQ 309 Lambda K H 0.319 0.135 0.379 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: 357 Number of extensions: 10 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: 316 Length of database: 314 Length adjustment: 27 Effective length of query: 289 Effective length of database: 287 Effective search space: 82943 Effective search space used: 82943 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: 48 (23.1 bits)
Align candidate WP_003943168.1 C1M55_RS29420 (acetaldehyde dehydrogenase (acetylating))
to HMM TIGR03215 (acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10))
# 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/TIGR03215.hmm # target sequence database: /tmp/gapView.1560564.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03215 [M=285] Accession: TIGR03215 Description: ac_ald_DH_ac: acetaldehyde dehydrogenase (acetylating) 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-143 462.1 5.7 3.9e-143 461.9 5.7 1.0 1 NCBI__GCF_002893965.1:WP_003943168.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002893965.1:WP_003943168.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 461.9 5.7 3.9e-143 3.9e-143 1 283 [. 3 310 .. 3 312 .. 0.98 Alignments for each domain: == domain 1 score: 461.9 bits; conditional E-value: 3.9e-143 TIGR03215 1 kvkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...didivf 69 kvkvaiiGsGnigtdl+ik+lr s+ le+ ++vGidp+sdGlara++l+v ++aeGv++l+ + +i+ivf NCBI__GCF_002893965.1:WP_003943168.1 3 KVKVAIIGSGNIGTDLMIKVLRnSDYLEMGAMVGIDPASDGLARAARLNVPITAEGVEGLVGLPnfdEIEIVF 75 79********************99*************************************9988889***** PP TIGR03215 70 datsakahaenaklleelgkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsrvakvk 142 datsakah++n+++l+ lgk++idltPaa+GpyvvPavn++e+lda+nvn+vtCgGqatiP+vaavsrv++v+ NCBI__GCF_002893965.1:WP_003943168.1 76 DATSAKAHVANNARLAPLGKRMIDLTPAAIGPYVVPAVNADEHLDAPNVNMVTCGGQATIPMVAAVSRVVPVA 148 ************************************************************************* PP TIGR03215 143 yaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalveead...ee 212 yaeivasiasksaGpgtranideftetts+a+ +vgGa++gkaiiilnPaePpl+mrdtv++lv+++d ++ NCBI__GCF_002893965.1:WP_003943168.1 149 YAEIVASIASKSAGPGTRANIDEFTETTSEAIVAVGGARRGKAIIILNPAEPPLIMRDTVFCLVDAPDpavHD 221 ****************************************************************999977789 PP TIGR03215 213 aieasveemveevqkyvpGyrlkqevvld..................gekvsvlleveGagdylPkyaGnldi 267 +i++s+e+mv +v +yvpGyrlkqev+++ ++vsv+leveGa++ylP+yaGnldi NCBI__GCF_002893965.1:WP_003943168.1 222 EIRQSIEKMVGDVSAYVPGYRLKQEVQITeipadqpvetllvdgnrpTHQVSVFLEVEGAAHYLPAYAGNLDI 294 ****************************99*************9998888*********************** PP TIGR03215 268 ltaaalavaeklaeel 283 +t+a +++ae++a++ NCBI__GCF_002893965.1:WP_003943168.1 295 MTSAGMQIAERIAQQK 310 *************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (314 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 12.55 // [ok]
This GapMind analysis is from Sep 24 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