Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate AO356_18160 AO356_18160 glycine cleavage system protein T
Query= reanno::pseudo6_N2E2:Pf6N2E2_5556 (374 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_18160 Length = 374 Score = 723 bits (1866), Expect = 0.0 Identities = 361/374 (96%), Positives = 371/374 (99%) Query: 1 MSTEQLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI 60 MSTEQLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI Sbjct: 1 MSTEQLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI 60 Query: 61 RLTGAGAAKALETLVPVDIIDLPVGMQRYAMFTNENGGILDDLMVANLGNDELFLVVNAA 120 RL+GAGAAKALETLVPVDIIDLPVGMQRYAMFTN+NGGILDDLMVANLGNDELFLVVNAA Sbjct: 61 RLSGAGAAKALETLVPVDIIDLPVGMQRYAMFTNDNGGILDDLMVANLGNDELFLVVNAA 120 Query: 121 CKDQDLAHLRAHIGAQCSIEPLFEARALLALQGPAAVTVLARLAPDVAKMTFMQFQRVTL 180 CKDQDLAHLRAHIG QC+IEPLFEARALLALQGPAAVTVLARLAPDVAKMTFMQFQRVTL Sbjct: 121 CKDQDLAHLRAHIGDQCNIEPLFEARALLALQGPAAVTVLARLAPDVAKMTFMQFQRVTL 180 Query: 181 LGMDCYVSRSGYTGEDGFEISVPAAEAEKLARALLAEPEVAAIGLGARDSLRLEAGLCLY 240 LG+DC+VSRSGYTGEDGFEISVPAA+AEKLARALLAEPEVAAIGLGARDSLRLEAGLCLY Sbjct: 181 LGVDCFVSRSGYTGEDGFEISVPAADAEKLARALLAEPEVAAIGLGARDSLRLEAGLCLY 240 Query: 241 GHDMNTETTPIEASLLWAISKVRRADGARAGGFPGAETVFAQQQGGVKRKRVGLLPQERT 300 GHDMNTETTPIEASLLWAISKVRRADG RAGGFPGAE+VFAQQQGGVKRKRVGLLPQERT Sbjct: 241 GHDMNTETTPIEASLLWAISKVRRADGGRAGGFPGAESVFAQQQGGVKRKRVGLLPQERT 300 Query: 301 PVREGAEIVNEAGEIIGTVCSGGFGPTLGGPLAMGYLDSAYVALDTPVWAIVRGKKVPLL 360 PVREGAEIVN+AGEIIG+VCSGGFGPTLG PLAMGYLDSAYVALDTPVWAIVRGK+VPLL Sbjct: 301 PVREGAEIVNDAGEIIGSVCSGGFGPTLGAPLAMGYLDSAYVALDTPVWAIVRGKRVPLL 360 Query: 361 VSKMPFVPQRYYRG 374 VSKMPFVPQRYYRG Sbjct: 361 VSKMPFVPQRYYRG 374 Lambda K H 0.321 0.138 0.406 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: 669 Number of extensions: 29 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: 374 Length of database: 374 Length adjustment: 30 Effective length of query: 344 Effective length of database: 344 Effective search space: 118336 Effective search space used: 118336 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: 50 (23.9 bits)
Align candidate AO356_18160 AO356_18160 (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.11509.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-109 351.4 0.0 3e-109 351.2 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18160 AO356_18160 glycine cleavage sys Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18160 AO356_18160 glycine cleavage system protein T # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 351.2 0.0 3e-109 3e-109 2 361 .. 7 368 .. 6 369 .. 0.97 Alignments for each domain: == domain 1 score: 351.2 bits; conditional E-value: 3e-109 TIGR00528 2 krtpLydlhtelggklvdfaGwelPvqyk.slieeheavrtkaGlfDvshmgkvelsGskslk 63 +tpL+ lh elg+++v+faG+ +Pvqy ++++eh+ +r++aGlfDvshmg+++lsG + k lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18160 7 LKTPLHALHLELGARMVPFAGYDMPVQYPlGVMKEHQHTRDQAGLFDVSHMGQIRLSGAGAAK 69 79**************************6488******************************* PP TIGR00528 64 fLqrllanDvdaLtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlke 126 +L+ l++ D+ L++G +y+ + n +GG++DDl+v + g+d ++ lvvnaa++++Dl++l+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18160 70 ALETLVPVDIIDLPVGMQRYAMFTNDNGGILDDLMVANLGND-ELFLVVNAACKDQDLAHLRA 131 ******************************************.999***************** PP TIGR00528 127 hleeevtldtlskeisllalqGPkaktiledlldkaveglkefffvqeaelalkkaliartGy 189 h+ ++ +++ l + +llalqGP a t+l l +v ++ f+ q+ l++ +++++r+Gy lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18160 132 HIGDQCNIEPLFEARALLALQGPAAVTVLARLAP-DVAKM-TFMQFQRVTLLGVDCFVSRSGY 192 *****************************99875.66676.47777899************** PP TIGR00528 190 tGedGfeiavanekavelwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleagl 252 tGedGfei+v+ +a +l+++l++++ v iGLgarD+Lrleag++LyG++++ e+tP+ea+l lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18160 193 TGEDGFEISVPAADAEKLARALLAEPEVAAIGLGARDSLRLEAGLCLYGHDMNTETTPIEASL 255 *************************************************************** PP TIGR00528 253 gwvvkker.....kksdfiGravleeqkengtekklvGlemlekgiarnelkvlltngekevG 310 w+++k r + f G + + q++ g+++k+vGl e+ r++ +++ ++ +++G lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18160 256 LWAISKVRradggRAGGFPGAESVFAQQQGGVKRKRVGLLPQERTPVREGAEIVN-DAGEIIG 317 *****998888888899**************************************.777**** PP TIGR00528 311 ivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361 v sG + PtLg +a++y+d+ + t + vr+k v++ v k++fv+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18160 318 SVCSGGFGPTLGAPLAMGYLDSAYVALDTPVWAIVRGKRVPLLVSKMPFVP 368 *************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (362 nodes) Target sequences: 1 (374 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: 8.70 // [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