Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate AO353_03510 AO353_03510 glycine cleavage system protein T
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1866 (374 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03510 Length = 374 Score = 717 bits (1851), Expect = 0.0 Identities = 361/374 (96%), Positives = 366/374 (97%) Query: 1 MSTEQLLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI 60 MSTEQLLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI Sbjct: 1 MSTEQLLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI 60 Query: 61 RLTGANAAKALETLVPVDIIDLPVGMQRYAMFTNATGGILDDLMVANLGNDELFLVVNAA 120 RLTGANAAKALETLVPVDIIDLPVGMQRYAMFTN GGILDDLMVANLGNDELFLVVNAA Sbjct: 61 RLTGANAAKALETLVPVDIIDLPVGMQRYAMFTNQNGGILDDLMVANLGNDELFLVVNAA 120 Query: 121 CKDQDLAHLRKHIGDQCTIEPLFEERALLALQGPAAVTVLARLAPEVAKMTFMQFARVKL 180 CKDQDLAHLR+HIGDQC+IEPLFEERALLALQGPAAVTVLARLAPEVAKMTFMQF RV L Sbjct: 121 CKDQDLAHLRQHIGDQCSIEPLFEERALLALQGPAAVTVLARLAPEVAKMTFMQFTRVTL 180 Query: 181 LGVDCFVSRSGYTGEDGFEISVPATNAEALARALLAEAEVAAIGLGARDSLRLEAGLCLY 240 LGVDCFVSRSGYTGEDGFEISVPA +AEALARALLAE EVAAIGLGARDSLRLEAGLCLY Sbjct: 181 LGVDCFVSRSGYTGEDGFEISVPAADAEALARALLAEPEVAAIGLGARDSLRLEAGLCLY 240 Query: 241 GHDMNTDTTPIEASLLWAISKPRRADGARAGGFPGAETVFAQQQAGVSRKRVGLLPQERT 300 GHDMNTDTTPIEASLLWAISKPRRADGARAGGFPGAETVFAQQQ GVSRKRVGLLPQERT Sbjct: 241 GHDMNTDTTPIEASLLWAISKPRRADGARAGGFPGAETVFAQQQNGVSRKRVGLLPQERT 300 Query: 301 PVREGAEIVNEAGDIIGSVCSGGFGPTLGGPLAMGYVDSAYIALDTPVWAIVRGKKVPLL 360 PVREGAEIVNEAG+IIGSVCSGGFGPTLGGPLAMGY+DSAYIALDT VWAIVRGKKVPLL Sbjct: 301 PVREGAEIVNEAGEIIGSVCSGGFGPTLGGPLAMGYLDSAYIALDTQVWAIVRGKKVPLL 360 Query: 361 VSKMPFVPQRYYRG 374 VSKMPFVPQRYYRG Sbjct: 361 VSKMPFVPQRYYRG 374 Lambda K H 0.321 0.138 0.405 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: 626 Number of extensions: 21 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 AO353_03510 AO353_03510 (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.14798.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-111 356.9 0.0 6.3e-111 356.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510 AO353_03510 glycine cleavage sys Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510 AO353_03510 glycine cleavage system protein T # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 356.7 0.0 6.3e-111 6.3e-111 2 361 .. 7 368 .. 6 369 .. 0.96 Alignments for each domain: == domain 1 score: 356.7 bits; conditional E-value: 6.3e-111 TIGR00528 2 krtpLydlhtelggklvdfaGwelPvqyk.slieeheavrtkaGlfDvshmgkvelsGskslkfL 65 +tpL+ lh elg+++v+faG+ +Pvqy ++++eh+ +r++aGlfDvshmg+++l+G ++ k+L lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510 7 LKTPLHALHIELGARMVPFAGYDMPVQYPlGVMKEHQHTRDQAGLFDVSHMGQIRLTGANAAKAL 71 79**************************6488********************************* PP TIGR00528 66 qrllanDvdaLtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehlee 130 + l++ D+ L++G +y+ + n +GG++DDl+v + g+d ++ lvvnaa++++Dl++l++h+ + lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510 72 ETLVPVDIIDLPVGMQRYAMFTNQNGGILDDLMVANLGND-ELFLVVNAACKDQDLAHLRQHIGD 135 ****************************************.999********************* PP TIGR00528 131 evtldtlskeisllalqGPkaktiledlldkaveglkefffvqeaelalkkaliartGytGedGf 195 + +++ l +e +llalqGP a t+l l +v ++ + f + l++ +++++r+GytGedGf lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510 136 QCSIEPLFEERALLALQGPAAVTVLARLAP-EVAKMTFMQFT-RVTLLGVDCFVSRSGYTGEDGF 198 **************************9976.56677655555.88999***************** PP TIGR00528 196 eiavanekavelwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkker 260 ei+v+ +a l+++l++++ v iGLgarD+Lrleag++LyG++++ ++tP+ea+l w+++k r lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510 199 EISVPAADAEALARALLAEPEVAAIGLGARDSLRLEAGLCLYGHDMNTDTTPIEASLLWAISKPR 263 ***************************************************************99 PP TIGR00528 261 .....kksdfiGravleeqkengtekklvGlemlekgiarnelkvlltngekevGivtsGtlsPt 320 + f G +++ q++ng+ +k+vGl e+ r++ +++ ++ +++G v sG + Pt lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510 264 radgaRAGGFPGAETVFAQQQNGVSRKRVGLLPQERTPVREGAEIVN-EAGEIIGSVCSGGFGPT 327 888877889**************************************.555************** PP TIGR00528 321 LgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361 Lg +a++y+d+ + t++ vr+k+v++ v k++fv+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510 328 LGGPLAMGYLDSAYIALDTQVWAIVRGKKVPLLVSKMPFVP 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: 10.84 // [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