Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate 354110 BT4584 putative aminomethyltransferase (NCBI ptt file)
Query= curated2:B2RI74 (362 letters) >lcl|FitnessBrowser__Btheta:354110 BT4584 putative aminomethyltransferase (NCBI ptt file) Length = 361 Score = 521 bits (1341), Expect = e-152 Identities = 256/362 (70%), Positives = 294/362 (81%), Gaps = 1/362 (0%) Query: 1 MKTTPFTDVHIALGAKMHEFAGYNMPIEYGGIIDEHMNVVNNVGVFDVSHMGEFWVKGPN 60 MKTTPFT+ HIALGAKMHEFAGYNMPIEY GIIDEH+ V N VGVFDVSHMGEFWVKGP Sbjct: 1 MKTTPFTEKHIALGAKMHEFAGYNMPIEYSGIIDEHLTVCNAVGVFDVSHMGEFWVKGPQ 60 Query: 61 ALRFLQKVSSNDASKLAVGQVQYCCFPNNDGGIVDDFLLYRYEEEKYMMVPNAANIAKDW 120 AL FLQKV+SN+ + L G++QY CFPN +GGIVDD L+Y YE EKY++V NAANI KDW Sbjct: 61 ALAFLQKVTSNNVAALVPGKIQYTCFPNEEGGIVDDLLVYCYEPEKYLLVVNAANIEKDW 120 Query: 121 AWCRQQNTMGAILENASDNIAQLAVQGPKATEVMQRLTDIDLNEITYYTFKVGSFAGCPD 180 WC NT GA LEN+SDN+AQLAVQGPKA +Q+LTDIDL+ I YYTF VG FAG + Sbjct: 121 NWCVSHNTEGAELENSSDNMAQLAVQGPKAILALQKLTDIDLSAIPYYTFTVGRFAGKEN 180 Query: 181 VIISATGYTGAGGFELYFYPQYAQKIWDALFEAGKPEGIKPAGLGARDTLRLEMGFCLYG 240 VIIS TGYTGAGGFELYFYP A+ IW A+FEAG+ GIKP GLGARDTLRLEMGFCLYG Sbjct: 181 VIISNTGYTGAGGFELYFYPDAAEAIWKAVFEAGEEFGIKPVGLGARDTLRLEMGFCLYG 240 Query: 241 NDICDTTSPIEAGLGWITKFTDDKMDMPSRKIMEEQKAGGLKRKLVAFELKDKGIPRQHY 300 ND+ D TSPIEAGLGWITKF + K + +R ++E+QK+ G RKLV FE+ D+GIPR Y Sbjct: 241 NDLDDKTSPIEAGLGWITKFVEGK-EFINRPMLEKQKSEGTTRKLVGFEMIDRGIPRHGY 299 Query: 301 EIANAEGQIIGEVTSGTMSPCLKKGIGMGYVATEFSKVGTELGIMVRGRQLKAEIVKPPF 360 E+ N EG+ IG VTSGTMSP K GIGMGYV E++KVGTE+ I +RGR+LKA +VKPPF Sbjct: 300 ELVNEEGEGIGVVTSGTMSPTRKIGIGMGYVKPEYAKVGTEICIDMRGRKLKAIVVKPPF 359 Query: 361 RK 362 RK Sbjct: 360 RK 361 Lambda K H 0.320 0.138 0.420 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: 20 Number of successful extensions: 3 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: 362 Length of database: 361 Length adjustment: 29 Effective length of query: 333 Effective length of database: 332 Effective search space: 110556 Effective search space used: 110556 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 354110 BT4584 (putative aminomethyltransferase (NCBI ptt file))
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.28389.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-122 393.4 0.0 5.1e-122 393.2 0.0 1.0 1 lcl|FitnessBrowser__Btheta:354110 BT4584 putative aminomethyltrans Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:354110 BT4584 putative aminomethyltransferase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 393.2 0.0 5.1e-122 5.1e-122 2 360 .. 2 360 .. 1 361 [] 0.98 Alignments for each domain: == domain 1 score: 393.2 bits; conditional E-value: 5.1e-122 TIGR00528 2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLt 77 k tp+ + h lg+k+ +faG+++P++y+++i+eh v +++G+fDvshmg++ ++G+++l+fLq++++n+v+aL lcl|FitnessBrowser__Btheta:354110 2 KTTPFTEKHIALGAKMHEFAGYNMPIEYSGIIDEHLTVCNAVGVFDVSHMGEFWVKGPQALAFLQKVTSNNVAALV 77 789************************************************************************* PP TIGR00528 78 kGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGPkakt 153 +Gk qy+ + n +GG+vDDl+vy + + ++llvvnaa++ekD +w h +e+++l++ s++++ la+qGPka lcl|FitnessBrowser__Btheta:354110 78 PGKIQYTCFPNEEGGIVDDLLVYCYEPE-KYLLVVNAANIEKDWNWCVSHNTEGAELENSSDNMAQLAVQGPKAIL 152 ***********************99888.9********************************************** PP TIGR00528 154 iledlldkaveglkefffvqeaelalkka.liartGytGedGfeiavanekavelwkklvea...ygvkPiGLgar 225 l++l+d ++++++ ++f + +a+k+ +i+ tGytG Gfe++ ++ a +wk++ ea +g+kP+GLgar lcl|FitnessBrowser__Btheta:354110 153 ALQKLTDIDLSAIPYYTFT-VGRFAGKENvIISNTGYTGAGGFELYFYPDAAEAIWKAVFEAgeeFGIKPVGLGAR 227 ***************9999.889998887699***************************9988889********** PP TIGR00528 226 DtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvl 301 DtLrle g +LyG++ld++++P+eaglgw+ k + ++fi r +le+qk +gt +klvG+em+++gi+r++++++ lcl|FitnessBrowser__Btheta:354110 228 DTLRLEMGFCLYGNDLDDKTSPIEAGLGWITKFV-EGKEFINRPMLEKQKSEGTTRKLVGFEMIDRGIPRHGYELV 302 ******************************9999.999************************************** PP TIGR00528 302 ltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfv 360 +g + +G+vtsGt+sPt ++ i+++yv+ e++k+Gt++ +++r++++k+ vvk++f lcl|FitnessBrowser__Btheta:354110 303 NEEG-EGIGVVTSGTMSPTRKIGIGMGYVKPEYAKVGTEICIDMRGRKLKAIVVKPPFR 360 *999.99*************************************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (362 nodes) Target sequences: 1 (361 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: 9.93 // [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 preprint 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