Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate WP_093428263.1 BM272_RS08005 glycine cleavage system aminomethyltransferase GcvT
Query= reanno::Koxy:BWI76_RS23880 (364 letters) >NCBI__GCF_900112605.1:WP_093428263.1 Length = 366 Score = 377 bits (969), Expect = e-109 Identities = 193/366 (52%), Positives = 247/366 (67%), Gaps = 10/366 (2%) Query: 3 QQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGSRI 62 ++TPL ++H GA++ DF+GW +P+HYGSQ++EHH VR +AGMFDVSHM +VD G Sbjct: 4 KRTPLHDKHVAAGAKLADFYGWELPVHYGSQVEEHHHVRNEAGMFDVSHMNVVDIEGEGA 63 Query: 63 REFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATREKDL 122 +FLRYLLANDVAKL PGKALYS M GGV DDLIVY + + ++R ++N+AT +KD+ Sbjct: 64 TDFLRYLLANDVAKLKTPGKALYSCMCNPEGGVEDDLIVYRMHDTWYRAILNAATHDKDM 123 Query: 123 AWIAQQSESYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFGVQAGDL 182 AW+ Q + + R DL+L+AVQGP+A+E+A + A + +KPF L Sbjct: 124 AWLEQHIAGFACTLCERTDLALVAVQGPKARERALDALGENGAFAAD-LKPFQAAGDDRL 182 Query: 183 FIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEMDE 242 FI TGYTGE G+EI++PNE+ W L AG++P G GARDTLRLEAGM LY EMDE Sbjct: 183 FIGRTGYTGEDGFEISVPNERIAGLWDELEAAGIQPVGFGARDTLRLEAGMALYSHEMDE 242 Query: 243 GVSPLAANMGWTIAWEPTDRDFIGREALEMQREKG-TEQLVGLVMTEKGVLRGGLPVRFS 301 SPL A + WT+A+EP DRDF+GR ALE QRE G + VGLV+ ++GVLR G V + Sbjct: 243 STSPLEAGLAWTVAFEPADRDFLGRAALERQREAGVAREQVGLVLADRGVLRDGQTVHCA 302 Query: 302 DADGNQKEGIITSGTFSPTLGYSIALARVPEGIGET---AVVQIRNREMPVKVTKPVFVR 358 D GI TSGTFSPTLG +IALA VP G E V +RN+ + V KP FVR Sbjct: 303 GGD-----GITTSGTFSPTLGRAIALALVPAGTAEAGGRCEVAVRNKRLSAAVVKPPFVR 357 Query: 359 NGKAVV 364 NG+A V Sbjct: 358 NGQARV 363 Lambda K H 0.320 0.137 0.407 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: 438 Number of extensions: 16 Number of successful extensions: 5 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: 364 Length of database: 366 Length adjustment: 30 Effective length of query: 334 Effective length of database: 336 Effective search space: 112224 Effective search space used: 112224 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: 49 (23.5 bits)
Align candidate WP_093428263.1 BM272_RS08005 (glycine cleavage system aminomethyltransferase GcvT)
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))
# 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/TIGR00528.hmm # target sequence database: /tmp/gapView.2642567.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00528 [M=362] Accession: TIGR00528 Description: gcvT: glycine cleavage system T protein 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-131 423.1 0.0 4.8e-131 422.9 0.0 1.0 1 NCBI__GCF_900112605.1:WP_093428263.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900112605.1:WP_093428263.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 422.9 0.0 4.8e-131 4.8e-131 1 362 [] 3 358 .. 3 358 .. 0.96 Alignments for each domain: == domain 1 score: 422.9 bits; conditional E-value: 4.8e-131 TIGR00528 1 lkrtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDv 73 lkrtpL+d h+ g+kl df GwelPv+y+s++eeh+ vr++aG+fDvshm v+++G+ + +fL++llanDv NCBI__GCF_900112605.1:WP_093428263.1 3 LKRTPLHDKHVAAGAKLADFYGWELPVHYGSQVEEHHHVRNEAGMFDVSHMNVVDIEGEGATDFLRYLLANDV 75 69*********************************************************************** PP TIGR00528 74 daLtk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeislla 145 ++L + Gka+ys ++n++GGv DDlivy+ + ++ ++naat +kD++wl++h+++++ + + +++l+a NCBI__GCF_900112605.1:WP_093428263.1 76 AKLKTpGKALYSCMCNPEGGVEDDLIVYRMHDT-WYRAILNAATHDKDMAWLEQHIAGFACTLCERTDLALVA 147 ***555***********************9998.*************************************** PP TIGR00528 146 lqGPkakt.iledlldkaveg..lkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveay 215 +qGPka++ l+ l ++ + + lk+f + l +i rtGytGedGfei+v+ne+ + lw +l +a NCBI__GCF_900112605.1:WP_093428263.1 148 VQGPKARErALDALGENGAFAadLKPFQAAGDDRL-----FIGRTGYTGEDGFEISVPNERIAGLWDELEAA- 214 ******76266777665543335****99977777.....*****************************999. PP TIGR00528 216 gvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlem 288 g++P+G+garDtLrleagmaLy +e+de+++Pleagl w+v+ e++++df+Gra+le q+e g+ + vGl++ NCBI__GCF_900112605.1:WP_093428263.1 215 GIQPVGFGARDTLRLEAGMALYSHEMDESTSPLEAGLAWTVAFEPADRDFLGRAALERQREAGVAREQVGLVL 287 ************************************************************************* PP TIGR00528 289 lekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361 ++g++r++ v + g Gi tsGt+sPtLg +iala+v+ ++++ G + ev vrnk +++ vvk++fvr NCBI__GCF_900112605.1:WP_093428263.1 288 ADRGVLRDGQTVHCAGG---DGITTSGTFSPTLGRAIALALVPAGTAEAGGRCEVAVRNKRLSAAVVKPPFVR 357 ************99666...8***************************************************9 PP TIGR00528 362 s 362 + NCBI__GCF_900112605.1:WP_093428263.1 358 N 358 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (362 nodes) Target sequences: 1 (366 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: 23.73 // [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