Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate 6938618 Sama_2721 glycine cleavage system aminomethyltransferase T (RefSeq)
Query= CharProtDB::CH_000563 (364 letters) >FitnessBrowser__SB2B:6938618 Length = 364 Score = 521 bits (1342), Expect = e-152 Identities = 254/361 (70%), Positives = 301/361 (83%) Query: 1 MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60 MA +T L+ +H A+MVDFHGW MPL+YGSQI+EHHAVR DAGMFDVSHMT+VD+ G+ Sbjct: 1 MANKTVLFSKHLESNAKMVDFHGWNMPLNYGSQIEEHHAVRRDAGMFDVSHMTVVDVEGA 60 Query: 61 RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120 R FLR LLAND+AKLT GKALY GMLN GGVIDDLI YY ++ +R+VVNSATREK Sbjct: 61 DARAFLRKLLANDIAKLTVPGKALYGGMLNHDGGVIDDLITYYLSDTQYRVVVNSATREK 120 Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180 DL+WI + A+ F + IT R +L+MIAVQGPNA+AKAAT+F Q AVEGMKPFFG QAG Sbjct: 121 DLAWIGEQAKGFDVTITERPELAMIAVQGPNAKAKAATVFTAEQNAAVEGMKPFFGKQAG 180 Query: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240 LFIATTGYTGEAGYEI +P +A W+AL++AGV+PCGLGARDTLRLEAGMNLYGQ+M Sbjct: 181 SLFIATTGYTGEAGYEIIVPEAEAEALWQALLDAGVQPCGLGARDTLRLEAGMNLYGQDM 240 Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRF 300 DE+++PLAANMGWTIAWEPADRDFIGREALE + G++KLVGLVM EKGVLR+++PV F Sbjct: 241 DESVNPLAANMGWTIAWEPADRDFIGREALEAIKAKGSDKLVGLVMEEKGVLRHDMPVFF 300 Query: 301 TDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNG 360 TDA G +H+G+ITSGTFSPTLGYSIA+ARVP IGETA V++R + + V+V P FVRNG Sbjct: 301 TDANGVEHQGVITSGTFSPTLGYSIAMARVPGAIGETAEVEMRKKRVTVRVIAPSFVRNG 360 Query: 361 K 361 K Sbjct: 361 K 361 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: 477 Number of extensions: 12 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 6938618 Sama_2721 (glycine cleavage system aminomethyltransferase T (RefSeq))
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.810162.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-144 467.9 0.1 1.1e-144 467.7 0.1 1.0 1 FitnessBrowser__SB2B:6938618 Domain annotation for each sequence (and alignments): >> FitnessBrowser__SB2B:6938618 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 467.7 0.1 1.1e-144 1.1e-144 2 362 .] 3 359 .. 2 359 .. 0.98 Alignments for each domain: == domain 1 score: 467.7 bits; conditional E-value: 1.1e-144 TIGR00528 2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLtk.Gka 81 ++t L+ h e +k+vdf+Gw++P++y+s+ieeh+avr +aG+fDvshm+ v+++G ++++fL++llanD+++Lt+ Gka FitnessBrowser__SB2B:6938618 3 NKTVLFSKHLESNAKMVDFHGWNMPLNYGSQIEEHHAVRRDAGMFDVSHMTVVDVEGADARAFLRKLLANDIAKLTVpGKA 83 79**************************************************************************99*** PP TIGR00528 82 qysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGP....kaktiledl 158 +y ++ln +GGv+DDli y+ ++ ++++vvn+at+ekDl+w+ e+++++ +t + e++++a+qGP ka+t++ FitnessBrowser__SB2B:6938618 84 LYGGMLNHDGGVIDDLITYYLSDT-QYRVVVNSATREKDLAWIGEQAKGFDVTITERPELAMIAVQGPnakaKAATVFTAE 163 *********************999.9******************************************9999999****** PP TIGR00528 159 ldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgarDtLrleagmaLyGq 239 +++aveg+k+ff+ q++ l +ia+tGytGe+G+ei+v++ +a lw++l++a gv+P+GLgarDtLrleagm+LyGq FitnessBrowser__SB2B:6938618 164 QNAAVEGMKPFFGKQAGSL-----FIATTGYTGEAGYEIIVPEAEAEALWQALLDA-GVQPCGLGARDTLRLEAGMNLYGQ 238 *******************.....********************************.************************ PP TIGR00528 240 eldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvllt..ngekevGivtsGtls 318 ++de++ Pl+a++gw++++e++++dfiGr++le k++g++k lvGl+m ekg++r++++v++t ng ++ G++tsGt+s FitnessBrowser__SB2B:6938618 239 DMDESVNPLAANMGWTIAWEPADRDFIGREALEAIKAKGSDK-LVGLVMEEKGVLRHDMPVFFTdaNGVEHQGVITSGTFS 318 ***************************************998.********************9666779*********** PP TIGR00528 319 PtLgknialayvdkelekiGtklevevrnklvkikvvkklfvrs 362 PtLg++ia+a+v+ iG+++eve+r+k v ++v+ + fvr+ FitnessBrowser__SB2B:6938618 319 PTLGYSIAMARVP---GAIGETAEVEMRKKRVTVRVIAPSFVRN 359 *************...89***********************986 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 16.68 // [ok]
This GapMind analysis is from Apr 09 2024. 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