Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate AO356_13035 AO356_13035 glycine cleavage system protein T
Query= CharProtDB::CH_000563 (364 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_13035 Length = 360 Score = 392 bits (1006), Expect = e-113 Identities = 198/364 (54%), Positives = 260/364 (71%), Gaps = 6/364 (1%) Query: 1 MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60 M Q+TPLY+ H GA+MVDF GW MPLHYGSQ++EHH VR D G+FDVSHMT++D+ G Sbjct: 1 MGQRTPLYDLHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMTVIDVAGP 60 Query: 61 RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120 + + +L+ LLANDV +L +G ALYS MLN GG++DD+I+Y ED +RLV N++TR++ Sbjct: 61 QAKVWLQRLLANDVDRLQDTGSALYSAMLNERGGIVDDMIIYR-VEDGYRLVFNASTRDQ 119 Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180 DL+W+ + ++ R +L+M+A+QGP+A+ K A L ++ Q ++ +KPF G G Sbjct: 120 DLAWMQAQLGDYDAQLHERPELAMLAIQGPHARQKIAELVTQSRGQIIQQLKPFEGRADG 179 Query: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240 + FIA TGYTGE G EI LP ++A F+ LV AG+ P GLGARDTLRLEAGMNLYGQ++ Sbjct: 180 EWFIARTGYTGEDGLEIVLPAQEAPSFFNDLVGAGISPIGLGARDTLRLEAGMNLYGQDI 239 Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTE-KLVGLVMTEKGVLRNELPVR 299 + +SPLA+NM W+IAWEPA R FIGR ALE + G + KLVGLV+ E+GVLR VR Sbjct: 240 HQDVSPLASNMAWSIAWEPASRQFIGRSALETELASGVQHKLVGLVLEERGVLRAHQVVR 299 Query: 300 FTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRN 359 N EG ITSG+FSPTL SIALARVP + A V+IR + PV+V KP FVR+ Sbjct: 300 I----ANVGEGEITSGSFSPTLSKSIALARVPMATADRAEVEIRGKWYPVRVVKPTFVRH 355 Query: 360 GKAV 363 GK + Sbjct: 356 GKTL 359 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: 15 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 AO356_13035 AO356_13035 (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.6590.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-125 405.2 0.0 1.3e-125 405.0 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13035 AO356_13035 glycine cleavage sys Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13035 AO356_13035 glycine cleavage system protein T # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.0 0.0 1.3e-125 1.3e-125 2 361 .. 3 354 .. 2 355 .. 0.95 Alignments for each domain: == domain 1 score: 405.0 bits; conditional E-value: 1.3e-125 TIGR00528 2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkf 64 +rtpLydlh lg+k+vdf+Gw +P++y+s++eeh+ vr + G+fDvshm+ ++++G+++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13035 3 QRTPLYDLHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMTVIDVAGPQAKVW 65 79************************************************************* PP TIGR00528 65 LqrllanDvdaLtk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlke 126 LqrllanDvd+L G+a+ys++ln GG+vDD+i+y+ ++ ++lv na+t+++Dl+w++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13035 66 LQRLLANDVDRLQDtGSALYSAMLNERGGIVDDMIIYRVEDG--YRLVFNASTRDQDLAWMQA 126 ************988**********************99887..******************* PP TIGR00528 127 hleeevtldtlskeisllalqGPkaktiledlldka....veglkefffvqeaelalkkalia 185 +l + + + e+++la+qGP+a++ + +l+ ++ +++lk+f + ++e +ia lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13035 127 QLGDYDAQLHERPELAMLAIQGPHARQKIAELVTQSrgqiIQQLKPFEGRADGEW-----FIA 184 **9999999999***********99888877777651222566999999988888.....*** PP TIGR00528 186 rtGytGedGfeiavanekavelwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPl 248 rtGytGedG ei+++ ++a +++ lv a g+ PiGLgarDtLrleagm+LyGq+++++++Pl lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13035 185 RTGYTGEDGLEIVLPAQEAPSFFNDLVGA-GISPIGLGARDTLRLEAGMNLYGQDIHQDVSPL 246 *****************************.********************************* PP TIGR00528 249 eaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvlltngekevGi 311 ++++ w +++e++ ++fiGr++le + g+++klvGl++ e+g++r + v+ ++ +G lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13035 247 ASNMAWSIAWEPASRQFIGRSALETELASGVQHKLVGLVLEERGVLRAHQVVRI--ANVGEGE 307 *************************************************99999..55699** PP TIGR00528 312 vtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361 +tsG++sPtL k+iala+v+ +++eve+r+k ++++vvk+ fvr lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13035 308 ITSGSFSPTLSKSIALARVP---MATADRAEVEIRGKWYPVRVVKPTFVR 354 ********************...5567899******************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: 7.71 // [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