Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate BWI76_RS23880 BWI76_RS23880 glycine cleavage system protein T
Query= reanno::Koxy:BWI76_RS23880 (364 letters) >lcl|FitnessBrowser__Koxy:BWI76_RS23880 BWI76_RS23880 glycine cleavage system protein T Length = 364 Score = 729 bits (1883), Expect = 0.0 Identities = 364/364 (100%), Positives = 364/364 (100%) Query: 1 MAQQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGS 60 MAQQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGS Sbjct: 1 MAQQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGS 60 Query: 61 RIREFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATREK 120 RIREFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATREK Sbjct: 61 RIREFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATREK 120 Query: 121 DLAWIAQQSESYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFGVQAG 180 DLAWIAQQSESYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFGVQAG Sbjct: 121 DLAWIAQQSESYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFGVQAG 180 Query: 181 DLFIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEM 240 DLFIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEM Sbjct: 181 DLFIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEM 240 Query: 241 DEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGTEQLVGLVMTEKGVLRGGLPVRF 300 DEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGTEQLVGLVMTEKGVLRGGLPVRF Sbjct: 241 DEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGTEQLVGLVMTEKGVLRGGLPVRF 300 Query: 301 SDADGNQKEGIITSGTFSPTLGYSIALARVPEGIGETAVVQIRNREMPVKVTKPVFVRNG 360 SDADGNQKEGIITSGTFSPTLGYSIALARVPEGIGETAVVQIRNREMPVKVTKPVFVRNG Sbjct: 301 SDADGNQKEGIITSGTFSPTLGYSIALARVPEGIGETAVVQIRNREMPVKVTKPVFVRNG 360 Query: 361 KAVV 364 KAVV Sbjct: 361 KAVV 364 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: 672 Number of extensions: 13 Number of successful extensions: 1 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: 364 Length adjustment: 29 Effective length of query: 335 Effective length of database: 335 Effective search space: 112225 Effective search space used: 112225 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 BWI76_RS23880 BWI76_RS23880 (glycine cleavage system protein T)
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.4515.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-162 525.9 0.0 2.6e-162 525.8 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS23880 BWI76_RS23880 glycine cleavage s Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS23880 BWI76_RS23880 glycine cleavage system protein T # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 525.8 0.0 2.6e-162 2.6e-162 1 362 [] 2 359 .. 2 359 .. 0.99 Alignments for each domain: == domain 1 score: 525.8 bits; conditional E-value: 2.6e-162 TIGR00528 1 lkrtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllan 71 +++tpL+++ht +g+++vdf+Gw++P++y+s+i+eh+avr +aG+fDvshm++v+ Gs+ ++fL++llan lcl|FitnessBrowser__Koxy:BWI76_RS23880 2 AQQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGSRIREFLRYLLAN 72 68********************************************************************* PP TIGR00528 72 DvdaLtk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskei 141 Dv++Lt+ Gka+ys++l a+GGv+DDlivy +ed f+lvvn+at+ekDl+w+ ++ e + ++t+++++ lcl|FitnessBrowser__Koxy:BWI76_RS23880 73 DVAKLTVpGKALYSGMLTASGGVIDDLIVYFLSED-YFRLVVNSATREKDLAWIAQQSESYGLEITVRDDL 142 ******99***************************.*********************************** PP TIGR00528 142 sllalqGP....kaktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelw 208 sl+a+qGP ka+t++ d++++aveg+k+ff+vq+++l +ia+tGytGe+G+eia++ne+av++w lcl|FitnessBrowser__Koxy:BWI76_RS23880 143 SLIAVQGPrakeKAATLFTDAQRQAVEGMKPFFGVQAGDL-----FIATTGYTGEAGYEIALPNEQAVDFW 208 ********9999999*************************.....************************** PP TIGR00528 209 kklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengt 279 + l++a gvkP+GLgarDtLrleagm+LyGqe+de ++Pl+a++gw++++e++++dfiGr++le q+e+gt lcl|FitnessBrowser__Koxy:BWI76_RS23880 209 RGLLDA-GVKPCGLGARDTLRLEAGMNLYGQEMDEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGT 278 ******.**************************************************************** PP TIGR00528 280 ekklvGlemlekgiarnelkvllt..ngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnk 348 e+ lvGl+m+ekg++r +l+v+++ +g++++Gi+tsGt+sPtLg++iala+v+ e+iG+++ v++rn+ lcl|FitnessBrowser__Koxy:BWI76_RS23880 279 EQ-LVGLVMTEKGVLRGGLPVRFSdaDGNQKEGIITSGTFSPTLGYSIALARVP---EGIGETAVVQIRNR 345 *9.*******************997789**************************...99************ PP TIGR00528 349 lvkikvvkklfvrs 362 ++++kv+k++fvr+ lcl|FitnessBrowser__Koxy:BWI76_RS23880 346 EMPVKVTKPVFVRN 359 ************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (362 nodes) Target sequences: 1 (364 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 6.60 // [ok]
This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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