Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate AO356_06055 AO356_06055 succinyldiaminopimelate transaminase
Query= metacyc::MONOMER-6501 (397 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_06055 Length = 399 Score = 417 bits (1071), Expect = e-121 Identities = 219/395 (55%), Positives = 268/395 (67%), Gaps = 4/395 (1%) Query: 1 MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60 MN L+ L PYPFEKLRALL P D PI LSIGEPKH +P+ V +A+A+NL ++ Sbjct: 1 MNNALNQLQPYPFEKLRALLGSV-TPNPDKRPIALSIGEPKHRSPSFVAEALASNLEKMA 59 Query: 61 VYPSTKGEPALRQAISQWLSRRYSIPAP--DPESEVLPVLGSREALFAFAQTVIDPSAGA 118 VYP+T G P LR+AI+ W RR+++P DP VLPV G+REALFAF QTV++ A Sbjct: 60 VYPTTLGIPELREAITGWCERRFNVPTGWLDPARHVLPVNGTREALFAFTQTVVNRGDDA 119 Query: 119 LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNP 178 LVV PNPFYQIYEGAA LAGA P+Y+ A F V ++W+R Q++F+CSPGNP Sbjct: 120 LVVSPNPFYQIYEGAAFLAGAKPHYLPCLDANGFNPDFDAVSPDIWKRCQILFLCSPGNP 179 Query: 179 AGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLV 238 G ++ ++ + L L+D H FVIAA ECYSE+Y DE TPP G L A LGR + V Sbjct: 180 TGALIPVDVLKKLIALADEHDFVIAADECYSELYFDEQTPPPGLLSACVELGRKDFKRCV 239 Query: 239 AFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCR- 297 F SLSKRSN+PG+RSGFVAGDA +L FLLYRTYHG AM ASIAAW+ R Sbjct: 240 VFHSLSKRSNLPGLRSGFVAGDADILKGFLLYRTYHGCAMPVQTQLASIAAWNDEVHVRA 299 Query: 298 KTAQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLL 357 A YR KF+AVL IL VLDV+ P SFYLW G D AF R+L+ + VTV+PGS L Sbjct: 300 NRALYREKFDAVLEILSPVLDVQRPDGSFYLWPNVAGDDAAFCRDLFEQEHVTVVPGSYL 359 Query: 358 AREAHNANPGQGRIRIALVAPLDQCVQAAERIAHF 392 +R+ NPG GR+R+ALVAPL +CV+AAERI F Sbjct: 360 SRDVDGVNPGAGRVRMALVAPLAECVEAAERIRAF 394 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: 506 Number of extensions: 25 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: 399 Length adjustment: 31 Effective length of query: 366 Effective length of database: 368 Effective search space: 134688 Effective search space used: 134688 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 AO356_06055 AO356_06055 (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.8069.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-211 687.4 0.0 3e-211 687.3 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 AO356_06055 succinyldiaminopimel Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 AO356_06055 succinyldiaminopimelate transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 687.3 0.0 3e-211 3e-211 1 395 [] 1 395 [. 1 395 [. 1.00 Alignments for each domain: == domain 1 score: 687.3 bits; conditional E-value: 3e-211 TIGR03538 1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPt 63 mn++l++l+pyPfekl++ll +vtp+ d+++ialsiGePkh++P+fv+eal++nle+++ yPt lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 1 MNNALNQLQPYPFEKLRALLGSVTPNPDKRPIALSIGEPKHRSPSFVAEALASNLEKMAVYPT 63 9************************************************************** PP TIGR03538 64 tkGlpelreaiaeWlerrfelpag.vdperqvlPvnGtrealfafvqavidraekalvvlPnP 125 t G+pelreai+ W+errf++p+g +dp+r+vlPvnGtrealfaf+q+v++r ++alvv+PnP lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 64 TLGIPELREAITGWCERRFNVPTGwLDPARHVLPVNGTREALFAFTQTVVNRGDDALVVSPNP 126 *************************************************************** PP TIGR03538 126 fyqiyeGaallagaepyflnctaengfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleel 188 fyqiyeGaa+laga+p++l+c ++ngf+pdfdav+ ++Wkr+q+lf+csPgnPtGa+++++ l lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 127 FYQIYEGAAFLAGAKPHYLPCLDANGFNPDFDAVSPDIWKRCQILFLCSPGNPTGALIPVDVL 189 *************************************************************** PP TIGR03538 189 kklleladkydfiiasdecyselyldeaeaPvGlleaaaelGrddfkrllvfhslskrsnvPG 251 kkl++lad++df+ia+decysely+de+++P Gll+a+ elGr+dfkr++vfhslskrsn+PG lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 190 KKLIALADEHDFVIAADECYSELYFDEQTPPPGLLSACVELGRKDFKRCVVFHSLSKRSNLPG 252 *************************************************************** PP TIGR03538 252 lrsGfvaGdaellkeflryrtyhGcampiavqlasiaaWedekhvrenralyrekfaavleil 314 lrsGfvaGda++lk fl yrtyhGcamp+++qlasiaaW+de hvr+nralyrekf+avleil lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 253 LRSGFVAGDADILKGFLLYRTYHGCAMPVQTQLASIAAWNDEVHVRANRALYREKFDAVLEIL 315 *************************************************************** PP TIGR03538 315 gavldlelPdasfylWlkvpdgddeafaralyeeenvkvlpGrylsreaegvnPGegrvrlal 377 ++vld+++Pd+sfylW++v gdd+af+r+l+e+e+v+v+pG+ylsr+++gvnPG+grvr+al lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 316 SPVLDVQRPDGSFYLWPNV-AGDDAAFCRDLFEQEHVTVVPGSYLSRDVDGVNPGAGRVRMAL 377 *******************.7****************************************** PP TIGR03538 378 vaeleecveaaerikkll 395 va+l+ecveaaeri++++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 378 VAPLAECVEAAERIRAFI 395 ***************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (395 nodes) Target sequences: 1 (399 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: 10.13 // [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