Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate PP_5194 PP_5194 aminomethyltransferase
Query= CharProtDB::CH_000563 (364 letters) >FitnessBrowser__Putida:PP_5194 Length = 360 Score = 393 bits (1009), Expect = e-114 Identities = 205/362 (56%), Positives = 256/362 (70%), Gaps = 6/362 (1%) Query: 1 MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60 M Q+T LY+ H GA+ VDF GW MPLHYGSQ++EHH VR+D G+FDVSHMT++D+ G+ Sbjct: 1 MGQRTLLYDLHLALGAKTVDFGGWDMPLHYGSQVEEHHQVRSDCGVFDVSHMTVIDVDGT 60 Query: 61 RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120 +L+ LLANDVA+L GKALYS +LN GGVIDDLIVY TE +RLV N+ATR K Sbjct: 61 DATVWLQRLLANDVARLDDPGKALYSPLLNEQGGVIDDLIVYR-TETGYRLVTNAATRAK 119 Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180 L W+ F ++ VR DL+++A+QGP A+ K A L + A+ + ++PF GV G Sbjct: 120 VLDWLQLQRAGFSVDFQVRPDLAILAIQGPRAREKVAALLSPARAALIRELRPFEGVADG 179 Query: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240 D FIA TGYTGE G EI P ++A F+ LV AG+ P GLGARDTLRLEAGMNLYGQ++ Sbjct: 180 DWFIARTGYTGEDGLEIIFPGDQAVAFFNDLVGAGIAPSGLGARDTLRLEAGMNLYGQDI 239 Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGT-EKLVGLVMTEKGVLRNELPVR 299 DE +PL +N+GW+IAWEPA+R+FIGR L + EHG EKLVGLV+ E+GVLR VR Sbjct: 240 DENHTPLTSNLGWSIAWEPAERNFIGRVGLLAEIEHGVQEKLVGLVLEERGVLRAHQVVR 299 Query: 300 FTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRN 359 EG ITSG+FSPTL SIALARVP G+ A V+IR + PV+V KP FVR+ Sbjct: 300 VAGI----GEGEITSGSFSPTLSKSIALARVPMATGDRAEVEIRGKWYPVRVVKPTFVRH 355 Query: 360 GK 361 GK Sbjct: 356 GK 357 Lambda K H 0.320 0.136 0.402 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: 407 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: 364 Length of database: 360 Length adjustment: 29 Effective length of query: 335 Effective length of database: 331 Effective search space: 110885 Effective search space used: 110885 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 PP_5194 PP_5194 (aminomethyltransferase)
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.6704.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-123 395.9 0.0 8.8e-123 395.7 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_5194 PP_5194 aminomethyltransferase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_5194 PP_5194 aminomethyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 395.7 0.0 8.8e-123 8.8e-123 2 361 .. 3 354 .. 2 355 .. 0.97 Alignments for each domain: == domain 1 score: 395.7 bits; conditional E-value: 8.8e-123 TIGR00528 2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaL 76 +rt Lydlh lg+k+vdf+Gw +P++y+s++eeh+ vr + G+fDvshm+ +++ G+++ LqrllanDv++L lcl|FitnessBrowser__Putida:PP_5194 3 QRTLLYDLHLALGAKTVDFGGWDMPLHYGSQVEEHHQVRSDCGVFDVSHMTVIDVDGTDATVWLQRLLANDVARL 77 79************************************************************************* PP TIGR00528 77 tk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGP. 149 Gka+ys lln qGGv+DDlivy+++ ++lv+naat+ k l+wl+ + ++++ +++ ++++la+qGP lcl|FitnessBrowser__Putida:PP_5194 78 DDpGKALYSPLLNEQGGVIDDLIVYRTETG--YRLVTNAATRAKVLDWLQLQRAGFSVDFQVRPDLAILAIQGPr 150 877**********************98877..******************999999999999************6 PP TIGR00528 150 ...kaktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiG 221 k +++l ++ + + +l++f +v +++ +iartGytGedG ei+ + ++av +++ lv a g+ P G lcl|FitnessBrowser__Putida:PP_5194 151 areKVAALLSPARAALIRELRPFEGVADGDW-----FIARTGYTGEDGLEIIFPGDQAVAFFNDLVGA-GIAPSG 219 666667899*****************99988.....********************************.****** PP TIGR00528 222 LgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarn 296 LgarDtLrleagm+LyGq++de+ tPl ++lgw +++e+++++fiGr l e+g+++klvGl++ e+g++r lcl|FitnessBrowser__Putida:PP_5194 220 LGARDTLRLEAGMNLYGQDIDENHTPLTSNLGWSIAWEPAERNFIGRVGLLAEIEHGVQEKLVGLVLEERGVLRA 294 *************************************************************************** PP TIGR00528 297 elkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361 + v+ g +G +tsG++sPtL k+iala+v+ G+++eve+r+k ++++vvk+ fvr lcl|FitnessBrowser__Putida:PP_5194 295 HQVVRV-AG-IGEGEITSGSFSPTLSKSIALARVP---MATGDRAEVEIRGKWYPVRVVKPTFVR 354 999999.55.789**********************...889**********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (362 nodes) Target sequences: 1 (360 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.39 // [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:
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