Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate Dsui_2737 Dsui_2737 glycine dehydrogenase, decarboxylating
Query= reanno::Koxy:BWI76_RS23870
(957 letters)
>FitnessBrowser__PS:Dsui_2737
Length = 966
Score = 1229 bits (3179), Expect = 0.0
Identities = 615/965 (63%), Positives = 755/965 (78%), Gaps = 13/965 (1%)
Query: 1 MTQTLGQLENRDAFIERHIGPDALQQQEMLKTVGADSLNALIGQIVPQDIQLATPPQVGE 60
+ Q+L LE +D FI RHIGP A + +ML +GA SL+ L+ Q VP I+ +
Sbjct: 5 LPQSLSALEQKDEFIARHIGPCASEMSQMLAAIGAASLDQLVDQTVPAAIRFPADLPLPA 64
Query: 61 ATTEFAALAELKAIAGRNKRFKSYIGMGYTAVQLPPVIQRNMLENPGWYTAYTPYQPEVS 120
E ALA+LKA+AGRN KS IG GY P VI RN+LENPGWYTAYTPYQ E++
Sbjct: 65 PRREHEALADLKALAGRNVVKKSLIGQGYHETLTPKVILRNVLENPGWYTAYTPYQAEIA 124
Query: 121 QGRLESLLNFQQVTLDLTGLDIASASLLDEATAAAEAMAMAKRVSKLKNANRFFVAADVH 180
QGRLE+LLN+QQV +DLTGL++A+ASLLDEATAAAEAM MA+RVSK +NRFFV A
Sbjct: 125 QGRLEALLNYQQVIIDLTGLELANASLLDEATAAAEAMTMARRVSK-SGSNRFFVDAACF 183
Query: 181 PQTLDVVRTRAETFGFDVIVDDAEKALDHQDVFGVLLQQVGTTGEVHDYSKLIADLKARK 240
PQT+DVV+TRA FGF++I E+A +VFG LLQ GEV D + IA LKA+
Sbjct: 184 PQTIDVVKTRAAYFGFELIFGPVEEAAT-VEVFGALLQYPNDKGEVQDLTATIAALKAKG 242
Query: 241 VIVSVAADFMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEFKRSMPGR 300
+ +VA D MALVLL +PG GAD+ GS+QRFG+PMG+GGPHAAFFA KDE KRS+ GR
Sbjct: 243 AVTAVACDLMALVLLKSPGAMGADMALGSSQRFGIPMGFGGPHAAFFACKDEHKRSVAGR 302
Query: 301 IIGVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVFHGPAGLKRI 360
IIGVS DA GN ALRMA+QTREQHIRREKANSNICTSQVLLAN+A +YAV+HGP GLK I
Sbjct: 303 IIGVSVDARGNKALRMALQTREQHIRREKANSNICTSQVLLANMAGMYAVYHGPEGLKTI 362
Query: 361 ASRIHRLTDILADGLQKKGLKLRHAHYFDTLCVEVADKA-AVLARAEALRINLRSDIHHA 419
A RIHRL ILA GL K G+K +A YFDTL +++ KA V A+ NLR
Sbjct: 363 ARRIHRLAAILATGLAKAGIKQLNACYFDTLQLDLGAKALTVYQAAQNAGYNLRLIEGGR 422
Query: 420 VGITLDEATTREDVLNLFRAILGDDHGLDIDTLDKDVALDSRSIPASMLRDDAILTHPVF 479
+GI L+E TTREDV L + I G +DI+ LD VA ++PA +LR DAIL+HPVF
Sbjct: 423 LGIALNEKTTREDVATLLQLIAGVK--VDIEALDAQVAAADPALPAELLRTDAILSHPVF 480
Query: 480 NRYHSETEMMRYMHALERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPV 539
N +H+E EM+RY+ L+ KDLAL+ +MI LGSCTMKLNA +EMIP+TWPEF ++HPF P+
Sbjct: 481 NTHHTEHEMLRYLKKLQNKDLALDHSMISLGSCTMKLNATSEMIPVTWPEFGDIHPFAPL 540
Query: 540 DQAEGYHQMIAQLSDWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICL 599
DQA+GY +MI QL++WL +TG+DAVCMQPNSGAQGEYAGL+AIR Y E+ +G RDICL
Sbjct: 541 DQAQGYLEMIEQLAEWLKTVTGFDAVCMQPNSGAQGEYAGLVAIRRYQEANGQGQRDICL 600
Query: 600 IPSSAHGTNPASAQMAGMQVVVVACDKNGNIDLADLRAKAEQHAANLSCIMVTYPSTHGV 659
IP SAHGTNPA+AQMAG+QVVVV CD NGN+D+ADL+AKAEQHAA LSC+M+TYPSTHGV
Sbjct: 601 IPKSAHGTNPATAQMAGLQVVVVDCDDNGNVDVADLKAKAEQHAAKLSCLMLTYPSTHGV 660
Query: 660 YEETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGP 719
+EE ++++C++VH GGQVY+DGAN+NAQVG+T+PGFIGADVSH+NLHKTF IPHGGGGP
Sbjct: 661 FEEAVKDICDIVHANGGQVYMDGANLNAQVGLTAPGFIGADVSHMNLHKTFAIPHGGGGP 720
Query: 720 GMGPIGVKSHLAQFVPGHSVVQIEGMLTR----QGAVSAAPFGSASILPISWMYIRMMGA 775
GMGPIG+K+HLA ++ H+ VQ G R QGAVSAAPFGSASILPISWMYI M+G
Sbjct: 721 GMGPIGLKAHLAPYMADHA-VQATGPAERKHKGQGAVSAAPFGSASILPISWMYIAMLGG 779
Query: 776 EGLKQASQMAILNANYIATRLKDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAK 835
+G+K A+Q+AILNANY+A RL++ +PVLY G++GRVAHECILDIRP+K TGI+E+DIAK
Sbjct: 780 KGVKTATQVAILNANYVAARLQEHYPVLYRGKNGRVAHECILDIRPIKAATGIAEIDIAK 839
Query: 836 RLIDFGFHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRGEIDRVKAGEWPLEDN 895
RL+D+GFHAPT+SFPVAGT+MVEPTESESK ELDRFIDA++AIR EI +V+AG+WP ++N
Sbjct: 840 RLMDYGFHAPTVSFPVAGTIMVEPTESESKAELDRFIDALIAIRNEIRKVEAGQWPADNN 899
Query: 896 PLVNAPHTQGELV-SAWNHPYARELAVFPAG--LNNKYWPTVKRLDDVYGDRNLFCSCVP 952
PL +APHTQ +L W+ PY+R+ A +P NK+WP+V R+DDVYGDRNLFC+C P
Sbjct: 900 PLKHAPHTQKDLADEVWSRPYSRQEACYPLAWVAENKFWPSVNRIDDVYGDRNLFCACAP 959
Query: 953 MSEYQ 957
+ +YQ
Sbjct: 960 VEDYQ 964
Lambda K H
0.320 0.135 0.399
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: 2189
Number of extensions: 92
Number of successful extensions: 10
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: 957
Length of database: 966
Length adjustment: 44
Effective length of query: 913
Effective length of database: 922
Effective search space: 841786
Effective search space used: 841786
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: 57 (26.6 bits)
Align candidate Dsui_2737 Dsui_2737 (glycine dehydrogenase, decarboxylating)
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))
# 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/TIGR00461.hmm
# target sequence database: /tmp/gapView.25562.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR00461 [M=939]
Accession: TIGR00461
Description: gcvP: glycine dehydrogenase
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1503.2 0.5 0 1503.0 0.5 1.0 1 lcl|FitnessBrowser__PS:Dsui_2737 Dsui_2737 glycine dehydrogenase,
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2737 Dsui_2737 glycine dehydrogenase, decarboxylating
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1503.0 0.5 0 0 1 939 [] 21 957 .. 21 957 .. 0.99
Alignments for each domain:
== domain 1 score: 1503.0 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyati 77
rh+Gp ++e+ +ml ++G+ +l++l++q vp +ir++ l l+ap +e+eala+lk++a +n + ks iG+Gy +t+
lcl|FitnessBrowser__PS:Dsui_2737 21 RHIGPCASEMSQMLAAIGAASLDQLVDQTVPAAIRFPADLPLPAPRREHEALADLKALAGRNVVKKSLIGQGYHETL 97
9**************************************************************************** PP
TIGR00461 78 lppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvskkkan 154
+p vi+rn+lenpgwytaytpyq+ei+qGrlealln+q+v++dltGle+anasllde+taaaeam ++ rvsk+ +n
lcl|FitnessBrowser__PS:Dsui_2737 98 TPKVILRNVLENPGWYTAYTPYQAEIAQGRLEALLNYQQVIIDLTGLELANASLLDEATAAAEAMTMARRVSKSGSN 174
***************************************************************************** PP
TIGR00461 155 kfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkalvsvaad 231
+f+v+ + pqt++vvktra +g+e+i + +++ +v+v+G+llqyp +Ge+ d++a i +lk + a+ +va+d
lcl|FitnessBrowser__PS:Dsui_2737 175 RFFVDAACFPQTIDVVKTRAAYFGFELIFGPVEEA-ATVEVFGALLQYPNDKGEVQDLTATIAALKAKGAVTAVACD 250
******************************99886.6799************************************* PP
TIGR00461 232 llaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhi 308
l+al+ll++pg +Gad++lGs+qrfG+p+G+GGphaaffa+kde+kr++ Gri+Gvs da Gn alr+alqtreqhi
lcl|FitnessBrowser__PS:Dsui_2737 251 LMALVLLKSPGAMGADMALGSSQRFGIPMGFGGPHAAFFACKDEHKRSVAGRIIGVSVDARGNKALRMALQTREQHI 327
***************************************************************************** PP
TIGR00461 309 rrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaase 385
rr+ka+snict+qvllan+a +yavyhGp Glk iarri+rl++ila+gl + + + n+ yfdtl++++g ka +
lcl|FitnessBrowser__PS:Dsui_2737 328 RREKANSNICTSQVLLANMAGMYAVYHGPEGLKTIARRIHRLAAILATGLAKAGIKQLNACYFDTLQLDLGAKAL-T 403
************************************************************************988.8 PP
TIGR00461 386 vlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvan...sfpaellrddeilrd 459
v +aa++a+ nlr + + +gial+e tt+edv ll+++ag +++e l+ +va ++paellr+d il +
lcl|FitnessBrowser__PS:Dsui_2737 404 VYQAAQNAGYNLRLIEGGRLGIALNEKTTREDVATLLQLIAGV---KVDIEALDAQVAAadpALPAELLRTDAILSH 477
******************************************4...59********9987889************** PP
TIGR00461 460 evfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqle 536
+vfn++h+e e+lryl++l++kdlal++smi lGsctmklnat em+p+twpef++ihpfap +q++Gy e+i ql+
lcl|FitnessBrowser__PS:Dsui_2737 478 PVFNTHHTEHEMLRYLKKLQNKDLALDHSMISLGSCTMKLNATSEMIPVTWPEFGDIHPFAPLDQAQGYLEMIEQLA 554
***************************************************************************** PP
TIGR00461 537 kwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGni 613
+wl +tGfda+++qpnsGaqGeyaGl +ir+y+e++g+++r+iclip+sahGtnpa+a+maGl+vv+v+cd++Gn+
lcl|FitnessBrowser__PS:Dsui_2737 555 EWLKTVTGFDAVCMQPNSGAQGEYAGLVAIRRYQEANGQGQRDICLIPKSAHGTNPATAQMAGLQVVVVDCDDNGNV 631
***************************************************************************** PP
TIGR00461 614 dlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlh 690
d+ dlkakae+++ +l+++m+typst+Gvfee++++++divh GGqvy+dGan+naqvGlt+pg++Gadv+h+nlh
lcl|FitnessBrowser__PS:Dsui_2737 632 DVADLKAKAEQHAAKLSCLMLTYPSTHGVFEEAVKDICDIVHANGGQVYMDGANLNAQVGLTAPGFIGADVSHMNLH 708
***************************************************************************** PP
TIGR00461 691 ktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkka 767
ktf+iphGGGGpgmgpig+k+hlap++ + ++ + e ++k +gavsaap+Gsasilpis+myi+m+G +G+k a
lcl|FitnessBrowser__PS:Dsui_2737 709 KTFAIPHGGGGPGMGPIGLKAHLAPYMADHAVQATGPAERKHKGQGAVSAAPFGSASILPISWMYIAMLGGKGVKTA 785
***************************************************************************** PP
TIGR00461 768 sevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmve 844
++vailnany+a+rl+++y++l++g+++rvahecild+r++k+ +gi ++d+akrl+dyGfhapt+sfpvaGt+mve
lcl|FitnessBrowser__PS:Dsui_2737 786 TQVAILNANYVAARLQEHYPVLYRGKNGRVAHECILDIRPIKAATGIAEIDIAKRLMDYGFHAPTVSFPVAGTIMVE 862
***************************************************************************** PP
TIGR00461 845 ptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaaypapvlkyfkfwp 921
pteses+ eldrfida+iai++ei +v aG++++++n+lk aph+ ++l w pysr+ea+yp++++ ++kfwp
lcl|FitnessBrowser__PS:Dsui_2737 863 PTESESKAELDRFIDALIAIRNEIRKVEAGQWPADNNPLKHAPHTQKDLADEVWSRPYSRQEACYPLAWVAENKFWP 939
********************************************999999999************************ PP
TIGR00461 922 tvarlddtyGdrnlvcsc 939
+v+r+dd+yGdrnl+c+c
lcl|FitnessBrowser__PS:Dsui_2737 940 SVNRIDDVYGDRNLFCAC 957
*****************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (966 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: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.09
# Mc/sec: 9.77
//
[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