Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate AO353_08735 AO353_08735 glycine cleavage system protein T
Query= reanno::Koxy:BWI76_RS23880 (364 letters) >FitnessBrowser__pseudo3_N2E3:AO353_08735 Length = 360 Score = 402 bits (1033), Expect = e-117 Identities = 205/365 (56%), Positives = 268/365 (73%), Gaps = 6/365 (1%) Query: 1 MAQQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGS 60 M Q+TPL++ H GA+MVDF GW MPLHYGSQ++EHH VR D G+FDVSHMT++D G Sbjct: 1 MGQRTPLYDLHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMTVIDVSGP 60 Query: 61 RIREFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATREK 120 + + +L++LLANDV +L G+ALYS ML GGV+DD+IVY L ED +RLVVN+ATR++ Sbjct: 61 QAKAWLQHLLANDVERLHSVGRALYSTMLNERGGVVDDMIVYRL-EDAYRLVVNAATRDQ 119 Query: 121 DLAWIAQQSESYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFGVQAG 180 D+AW+ Q +Y +++ R +L+++A+QGP+A++K A L T ++ ++ +KPF G G Sbjct: 120 DMAWMQAQLGNYQVQLHERRELAMLAIQGPQARQKIAELVTQSRGTLIQQLKPFEGHCDG 179 Query: 181 DLFIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEM 240 D FIA TGYTGE G EIALP +QA F+ L+ AG+ P GLGARDTLRLEAGMNLYGQ++ Sbjct: 180 DWFIARTGYTGEDGLEIALPADQAPGFFNDLVGAGISPIGLGARDTLRLEAGMNLYGQDI 239 Query: 241 DEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGTEQ-LVGLVMTEKGVLRGGLPVR 299 + VSPLA+NM W+IAWEP R FIGR ALE +R G +Q LVGLV+ E+GVLR VR Sbjct: 240 HQDVSPLASNMAWSIAWEPATRQFIGRAALEAERAAGVKQKLVGLVLEERGVLRAHQVVR 299 Query: 300 FSDADGNQKEGIITSGTFSPTLGYSIALARVPEGIGETAVVQIRNREMPVKVTKPVFVRN 359 +D EG ITSG+FSPTL SIALARVP + A V+IR + PV+V KP FVR+ Sbjct: 300 IADVG----EGEITSGSFSPTLSKSIALARVPMATADRAEVEIRGKWYPVRVVKPTFVRH 355 Query: 360 GKAVV 364 GK ++ Sbjct: 356 GKTLI 360 Lambda K H 0.320 0.137 0.407 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: 400 Number of extensions: 10 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 AO353_08735 AO353_08735 (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.26076.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-128 414.3 0.0 2.3e-128 414.1 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735 AO353_08735 glycine cleavage sys Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735 AO353_08735 glycine cleavage system protein T # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 414.1 0.0 2.3e-128 2.3e-128 2 361 .. 3 354 .. 2 355 .. 0.95 Alignments for each domain: == domain 1 score: 414.1 bits; conditional E-value: 2.3e-128 TIGR00528 2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLq 66 +rtpLydlh lg+k+vdf+Gw +P++y+s++eeh+ vr + G+fDvshm+ +++sG+++ + Lq lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735 3 QRTPLYDLHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMTVIDVSGPQAKAWLQ 67 79*************************************************************** PP TIGR00528 67 rllanDvdaLtk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehlee 130 +llanDv++L G+a+ys++ln GGvvDD+ivy+ ++ ++lvvnaat+++D++w++ +l + lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735 68 HLLANDVERLHSvGRALYSTMLNERGGVVDDMIVYRLEDA--YRLVVNAATRDQDMAWMQAQLGN 130 **********877**********************98776..*********************** PP TIGR00528 131 evtldtlskeisllalqGPkaktiledlldkaveg....lkefffvqeaelalkkaliartGytG 191 + ++e+++la+qGP+a++ + +l+ ++ + lk+f + +++ +iartGytG lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735 131 YQVQLHERRELAMLAIQGPQARQKIAELVTQSRGTliqqLKPFEGHCDGDW-----FIARTGYTG 190 9999999**************999999999875553333888887767776.....********* PP TIGR00528 192 edGfeiavanekavelwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvv 256 edG eia++ ++a +++ lv a g+ PiGLgarDtLrleagm+LyGq+++++++Pl++++ w + lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735 191 EDGLEIALPADQAPGFFNDLVGA-GISPIGLGARDTLRLEAGMNLYGQDIHQDVSPLASNMAWSI 254 ***********************.***************************************** PP TIGR00528 257 kkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvlltngekevGivtsGtlsPtL 321 ++e++ ++fiGra+le ++ g+++klvGl++ e+g++r + v+ + + +G +tsG++sPtL lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735 255 AWEPATRQFIGRAALEAERAAGVKQKLVGLVLEERGVLRAHQVVRIA--DVGEGEITSGSFSPTL 317 *****************************************999995..5599************ PP TIGR00528 322 gknialayvdkelekiGtklevevrnklvkikvvkklfvr 361 k+iala+v+ +++eve+r+k ++++vvk+ fvr lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735 318 SKSIALARVP---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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.03 // [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