Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate GFF1185 HP15_1162 aminotransferase, class I and II
Query= metacyc::MONOMER-6501 (397 letters) >FitnessBrowser__Marino:GFF1185 Length = 400 Score = 404 bits (1037), Expect = e-117 Identities = 210/399 (52%), Positives = 266/399 (66%), Gaps = 4/399 (1%) Query: 1 MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60 MNP LD LHPYPFEKL L A P H L PI+L IGEPKH +P V Q IA NL L+ Sbjct: 1 MNPNLDRLHPYPFEKLAKLKAGISVPDH-LRPISLGIGEPKHPSPDFVKQVIANNLDKLA 59 Query: 61 VYPSTKGEPALRQAISQWLSRRYSIPAPD--PESEVLPVLGSREALFAFAQTVIDPSAGA 118 YP+T+G LR+AIS W +RR+++ A + ++PV G+REA+F+ Q V+D + A Sbjct: 60 NYPTTRGTDELREAISGWATRRFNLKAGSLSAANNIVPVNGTREAIFSLVQAVVDATKPA 119 Query: 119 LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNP 178 VV PNPFYQ+YEGAA LAGATP Y+ D + F VP+ +W+ Q++F+CSPGNP Sbjct: 120 TVVSPNPFYQVYEGAAFLAGATPVYIPCDGSNGFIPDFDSVPESIWQECQILFLCSPGNP 179 Query: 179 AGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLV 238 +G V+S E + L+D+H F++A+ ECYSE+Y +E P G LQ +GRD Y V Sbjct: 180 SGAVISREALTRVIALADKHDFIVASDECYSELYPEEGNAPEGLLQTCAAIGRDDYARCV 239 Query: 239 AFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCRK 298 F SLSKRSN+PG+RSGFVAGDA +L +L YRTYHG AM ASIAAWS R+ Sbjct: 240 VFHSLSKRSNLPGLRSGFVAGDANILDGYLKYRTYHGCAMPIHNQLASIAAWSDEDHVRE 299 Query: 299 T-AQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLL 357 A YRAKFEAV+PIL+ V+DV P A FYLW TP D FAREL + V VLPG L Sbjct: 300 NRAAYRAKFEAVVPILREVMDVDFPDAGFYLWPITPMDDETFARELSAQQNVHVLPGRYL 359 Query: 358 AREAHNANPGQGRIRIALVAPLDQCVQAAERIAHFARTS 396 +R NPG+ R+R+ALVAPL++CV+AAERI F + + Sbjct: 360 SRTVDGHNPGENRVRMALVAPLEECVEAAERIVEFVKAN 398 Lambda K H 0.321 0.135 0.412 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: 523 Number of extensions: 26 Number of successful extensions: 4 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: 400 Length adjustment: 31 Effective length of query: 366 Effective length of database: 369 Effective search space: 135054 Effective search space used: 135054 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: 50 (23.9 bits)
Align candidate GFF1185 HP15_1162 (aminotransferase, class I and II)
to HMM TIGR03538 (dapC: succinyldiaminopimelate transaminase (EC 2.6.1.17))
# 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.aa/TIGR03538.hmm # target sequence database: /tmp/gapView.3484.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03538 [M=395] Accession: TIGR03538 Description: DapC_gpp: succinyldiaminopimelate transaminase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-201 653.9 0.0 4.5e-201 653.8 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF1185 HP15_1162 aminotransferase, clas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1185 HP15_1162 aminotransferase, class I and II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 653.8 0.0 4.5e-201 4.5e-201 1 395 [] 1 395 [. 1 395 [. 1.00 Alignments for each domain: == domain 1 score: 653.8 bits; conditional E-value: 4.5e-201 TIGR03538 1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPttkGlpelreaia 75 mnpnl+rl+pyPfekla+l+++++ p +l++i+l iGePkh++P+fv++++++nl++l++yPtt+G++elreai+ lcl|FitnessBrowser__Marino:GFF1185 1 MNPNLDRLHPYPFEKLAKLKAGISVPDHLRPISLGIGEPKHPSPDFVKQVIANNLDKLANYPTTRGTDELREAIS 75 9************************************************************************** PP TIGR03538 76 eWlerrfelpag.vdperqvlPvnGtrealfafvqavidraekalvvlPnPfyqiyeGaallagaepyflnctae 149 W++rrf+l+ag ++++++++PvnGtrea+f++vqav+d ++ a+vv+PnPfyq+yeGaa+laga+p++++c+ + lcl|FitnessBrowser__Marino:GFF1185 76 GWATRRFNLKAGsLSAANNIVPVNGTREAIFSLVQAVVDATKPATVVSPNPFYQVYEGAAFLAGATPVYIPCDGS 150 *************************************************************************** PP TIGR03538 150 ngfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleelkklleladkydfiiasdecyselyldeaeaPvGlle 224 ngf+pdfd+vpe++W+++q+lf+csPgnP+Gav+s e l+++++ladk+dfi+asdecysely +e +aP Gll+ lcl|FitnessBrowser__Marino:GFF1185 151 NGFIPDFDSVPESIWQECQILFLCSPGNPSGAVISREALTRVIALADKHDFIVASDECYSELYPEEGNAPEGLLQ 225 *************************************************************************** PP TIGR03538 225 aaaelGrddfkrllvfhslskrsnvPGlrsGfvaGdaellkeflryrtyhGcampiavqlasiaaWedekhvren 299 ++a++Grdd+ r++vfhslskrsn+PGlrsGfvaGda++l+ +l+yrtyhGcampi+ qlasiaaW+de hvren lcl|FitnessBrowser__Marino:GFF1185 226 TCAAIGRDDYARCVVFHSLSKRSNLPGLRSGFVAGDANILDGYLKYRTYHGCAMPIHNQLASIAAWSDEDHVREN 300 *************************************************************************** PP TIGR03538 300 ralyrekfaavleilgavldlelPdasfylWlkvpdgddeafaralyeeenvkvlpGrylsreaegvnPGegrvr 374 ra+yr+kf+av il +v+d++ Pda+fylW+ + + dde+far+l +++nv+vlpGrylsr ++g nPGe+rvr lcl|FitnessBrowser__Marino:GFF1185 301 RAAYRAKFEAVVPILREVMDVDFPDAGFYLWPIT-PMDDETFARELSAQQNVHVLPGRYLSRTVDGHNPGENRVR 374 **********************************.5*************************************** PP TIGR03538 375 lalvaeleecveaaerikkll 395 +alva+leecveaaeri +++ lcl|FitnessBrowser__Marino:GFF1185 375 MALVAPLEECVEAAERIVEFV 395 *****************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (395 nodes) Target sequences: 1 (400 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.02 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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