Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate GFF1433 Psest_1470 succinyldiaminopimelate transaminase
Query= metacyc::MONOMER-6501 (397 letters) >FitnessBrowser__psRCH2:GFF1433 Length = 398 Score = 428 bits (1100), Expect = e-124 Identities = 227/398 (57%), Positives = 271/398 (68%), Gaps = 4/398 (1%) Query: 1 MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60 MN L+ LHPYPFEKLR LLA A PT D I LSIGEPKH +P V QA+A NL L+ Sbjct: 1 MNNALNLLHPYPFEKLRGLLAGAEAPT-DKRHIALSIGEPKHRSPDFVAQALADNLDQLA 59 Query: 61 VYPSTKGEPALRQAISQWLSRRYSIPAP--DPESEVLPVLGSREALFAFAQTVIDPSAGA 118 VYP+T G PALR+ I++W RR+ + A DP VLPV G+REALFAF Q V+D Sbjct: 60 VYPTTLGIPALRETIARWCERRFGLAADALDPARHVLPVNGTREALFAFTQAVVDRETDG 119 Query: 119 LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNP 178 LVV PNPFYQIYEGAALLAGATP+Y+ F VP EVW+R Q++F+CSPGNP Sbjct: 120 LVVSPNPFYQIYEGAALLAGATPHYLPCLEQNGFNPDFAAVPAEVWQRCQILFLCSPGNP 179 Query: 179 AGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLV 238 G ++ LE + L L+D++ FVIAA ECYSE+Y DE PP G L A LGR+ Y V Sbjct: 180 TGALVPLETLKKLIALADQYDFVIAADECYSELYFDEANPPAGLLTACAALGRNDYKRCV 239 Query: 239 AFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCRK 298 F SLSKRSN+PG+RSGFVAGDA +L FLLYRTYHG AM ASIAAW+ R Sbjct: 240 VFHSLSKRSNLPGLRSGFVAGDAEILKAFLLYRTYHGCAMPVQTQLASIAAWNDEIHVRA 299 Query: 299 TAQ-YRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLL 357 + YRAKF+AVL IL V+DV+ P FYLW TP D F EL+ R VTV+PGS L Sbjct: 300 NRELYRAKFDAVLEILAPVMDVQRPDGGFYLWPKTPMDDQQFTCELFAREHVTVVPGSYL 359 Query: 358 AREAHNANPGQGRIRIALVAPLDQCVQAAERIAHFART 395 +RE A+PG GR+R+ALVAPL +C++AA+RI HF T Sbjct: 360 SREVDGASPGAGRVRMALVAPLAECIEAAQRIRHFIET 397 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: 508 Number of extensions: 20 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: 398 Length adjustment: 31 Effective length of query: 366 Effective length of database: 367 Effective search space: 134322 Effective search space used: 134322 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 GFF1433 Psest_1470 (succinyldiaminopimelate transaminase)
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.7168.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-208 677.1 0.0 4e-208 677.0 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF1433 Psest_1470 succinyldiaminopimela Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF1433 Psest_1470 succinyldiaminopimelate transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 677.0 0.0 4e-208 4e-208 1 395 [] 1 395 [. 1 395 [. 1.00 Alignments for each domain: == domain 1 score: 677.0 bits; conditional E-value: 4e-208 TIGR03538 1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPttkGlpelreaia 75 mn++l+ l+pyPfekl+ ll+++ +p+d+++ialsiGePkh++P+fv++al++nl++l+ yPtt G+p+lre+ia lcl|FitnessBrowser__psRCH2:GFF1433 1 MNNALNLLHPYPFEKLRGLLAGAEAPTDKRHIALSIGEPKHRSPDFVAQALADNLDQLAVYPTTLGIPALRETIA 75 9************************************************************************** PP TIGR03538 76 eWlerrfelpag.vdperqvlPvnGtrealfafvqavidraekalvvlPnPfyqiyeGaallagaepyflnctae 149 +W+errf l+a +dp+r+vlPvnGtrealfaf+qav+dr+++ lvv+PnPfyqiyeGaallaga+p++l+c ++ lcl|FitnessBrowser__psRCH2:GFF1433 76 RWCERRFGLAADaLDPARHVLPVNGTREALFAFTQAVVDRETDGLVVSPNPFYQIYEGAALLAGATPHYLPCLEQ 150 *********9999************************************************************** PP TIGR03538 150 ngfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleelkklleladkydfiiasdecyselyldeaeaPvGlle 224 ngf+pdf avp+evW+r+q+lf+csPgnPtGa+++le+lkkl++lad+ydf+ia+decysely+dea++P+Gll lcl|FitnessBrowser__psRCH2:GFF1433 151 NGFNPDFAAVPAEVWQRCQILFLCSPGNPTGALVPLETLKKLIALADQYDFVIAADECYSELYFDEANPPAGLLT 225 *************************************************************************** PP TIGR03538 225 aaaelGrddfkrllvfhslskrsnvPGlrsGfvaGdaellkeflryrtyhGcampiavqlasiaaWedekhvren 299 a+a+lGr+d+kr++vfhslskrsn+PGlrsGfvaGdae+lk+fl yrtyhGcamp+++qlasiaaW+de hvr+n lcl|FitnessBrowser__psRCH2:GFF1433 226 ACAALGRNDYKRCVVFHSLSKRSNLPGLRSGFVAGDAEILKAFLLYRTYHGCAMPVQTQLASIAAWNDEIHVRAN 300 *************************************************************************** PP TIGR03538 300 ralyrekfaavleilgavldlelPdasfylWlkvpdgddeafaralyeeenvkvlpGrylsreaegvnPGegrvr 374 r+lyr+kf+avleil++v+d+++Pd++fylW+k+ + dd++f+ +l+++e+v+v+pG+ylsre++g+ PG+grvr lcl|FitnessBrowser__psRCH2:GFF1433 301 RELYRAKFDAVLEILAPVMDVQRPDGGFYLWPKT-PMDDQQFTCELFAREHVTVVPGSYLSREVDGASPGAGRVR 374 **********************************.5*************************************** PP TIGR03538 375 lalvaeleecveaaerikkll 395 +alva+l+ec+eaa+ri++++ lcl|FitnessBrowser__psRCH2:GFF1433 375 MALVAPLAECIEAAQRIRHFI 395 ******************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (395 nodes) Target sequences: 1 (398 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: 00:00:00.02 # Mc/sec: 7.59 // [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