Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate GFF3867 PGA1_78p00310 glycine dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1868
(950 letters)
>FitnessBrowser__Phaeo:GFF3867
Length = 951
Score = 1162 bits (3005), Expect = 0.0
Identities = 564/937 (60%), Positives = 700/937 (74%), Gaps = 7/937 (0%)
Query: 15 RHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGLSEADALALIKSIAT 74
RHIGP + ML +GF++L+ L + +P +I+ T L ++E DAL +K IA
Sbjct: 17 RHIGPSPREMADMLKVIGFNTLDELIDATVPPAIRQTEALDWGPAMTERDALFHMKEIAG 76
Query: 75 KNQLFKTFIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLISD 134
KN++ + IGQGY+GT TP+PILRN+LENPAWYTAYTPYQPEISQGRLEALLNFQT++SD
Sbjct: 77 KNKVLTSLIGQGYHGTTTPAPILRNILENPAWYTAYTPYQPEISQGRLEALLNFQTMVSD 136
Query: 135 LTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHA-FFASVHCHPQTLDVLRTRAEPLG 193
LTGLP+ANASLLDEATAAAEAM R S++K ++A FF +CHPQT+ V++TRAEPLG
Sbjct: 137 LTGLPVANASLLDEATAAAEAMAMAHRGSRSKANNAAFFVDKNCHPQTVAVIKTRAEPLG 196
Query: 194 IDVVVGDERELTDVTPFFGALLQYPASNGDVFDYRELTERFHAANALVAVAADLLALTVL 253
IDVVV + EL D FGA+ QYP ++G V D+ + H + VAAD+L+L +L
Sbjct: 197 IDVVVAEPTEL-DAGAVFGAIFQYPGTHGHVTDFSDQIAALHEHKGIAVVAADILSLALL 255
Query: 254 TAPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFGNPALR 313
+PGE GAD+AIGS QRFGVP+G+GGPHAAY +T D KR MPGR++GVS+D GN A R
Sbjct: 256 KSPGEMGADIAIGSTQRFGVPMGYGGPHAAYMATSDKLKRSMPGRIIGVSIDARGNKAYR 315
Query: 314 LAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIANRVHHLTAILAKGL 373
L++QTREQHIRREKA SN+CTAQ LLA IASMYAVYHGP G+ IA VH TA LA GL
Sbjct: 316 LSLQTREQHIRREKANSNVCTAQALLAVIASMYAVYHGPDGIKAIAQSVHRKTARLAAGL 375
Query: 374 SALGLSVEQASFFDTLTVKAGAQTAALHDKAHAQRINLRVVDGERLGLSLDETTTQADVE 433
G VE FFDT+TV+ G + + A + INLR V ++G+SLDE T +E
Sbjct: 376 EEAGFKVEPEVFFDTITVEVGHLQKTVMEAAVQRGINLRRVGETKVGISLDEQTRPETIE 435
Query: 434 TLWSLLSDGKALPDFAALAASVQSAIPATLVRQSPILSHPVFNRYHSETELMRYLRKLAD 493
+W D +++ Q +P ++R S L+HP+F++ +E E+ RY+R+LAD
Sbjct: 436 AVWGAFGI-----DRKDDSSNKQYRLPEAMLRDSAYLTHPIFHKNRAEAEITRYMRRLAD 490
Query: 494 KDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYQQLTDELEAMLC 553
+DLALDR MIPLGSCTMKLNA EMIPVTW EF LHPF P +Q+ GY Q+ D+L LC
Sbjct: 491 RDLALDRAMIPLGSCTMKLNATIEMIPVTWPEFSNLHPFVPEDQAQGYHQMIDDLNDKLC 550
Query: 554 AATGYDSVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSAHGTNPATAQMAGM 613
TGYD++S QPN+G+QGEYAGLL IR YH SRG+ R++CLIP+SAHGTNPA+AQM G
Sbjct: 551 QITGYDAISQQPNSGAQGEYAGLLTIRNYHASRGQAHRNVCLIPTSAHGTNPASAQMVGW 610
Query: 614 RVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGIREICGIIHDNGGQ 673
+VV D GN+D+ D R KA +H +HLA MITYPSTHGVFE ++E+C I HD+GGQ
Sbjct: 611 KVVPIKADDNGNIDVADFREKAEKHSDHLAGCMITYPSTHGVFETTVQEVCQITHDHGGQ 670
Query: 674 VYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSHLAPFLPGH 733
VYIDGANMNAMVG+ PG GGDVSHLNLHKTFCIPHGGGGPG+GPIGVK+HL LPGH
Sbjct: 671 VYIDGANMNAMVGVSRPGDIGGDVSHLNLHKTFCIPHGGGGPGMGPIGVKAHLTEHLPGH 730
Query: 734 AQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNANYISRRLEEHYPV 793
+ G V AAPFGS SILP++W YI +MGG+GL +A+++AILNANYI+ RL++ YP+
Sbjct: 731 PEYGTAVGPVSAAPFGSPSILPVSWAYILLMGGSGLTQATKVAILNANYIAARLQDAYPI 790
Query: 794 LYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAGTLMIEPTES 853
LYT +G VAHECILD RPL D +G+SVDDVAKRLID GFHAPTMS+PVAGTLM+EPTES
Sbjct: 791 LYTSESGRVAHECILDTRPLNDEAGVSVDDVAKRLIDSGFHAPTMSWPVAGTLMVEPTES 850
Query: 854 ESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTAKELVGEWSHPYSREQAVY 913
E K+ELDRFC+AM+ IR E + + +G +D ++NPLK+APHT ++LVGEW PYSREQA +
Sbjct: 851 EPKDELDRFCEAMLSIRSEAQDIIDGKIDAENNPLKHAPHTVRDLVGEWDRPYSREQACF 910
Query: 914 PVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 950
P +L KYWP V RVDN +GDRNL+C CP +E YA
Sbjct: 911 PPGNLGVDKYWPAVNRVDNAYGDRNLICTCPPMEDYA 947
Lambda K H
0.319 0.135 0.398
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: 2266
Number of extensions: 94
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: 950
Length of database: 951
Length adjustment: 44
Effective length of query: 906
Effective length of database: 907
Effective search space: 821742
Effective search space used: 821742
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 GFF3867 PGA1_78p00310 (glycine dehydrogenase)
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.2728.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 1431.1 0.0 0 1431.0 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF3867 PGA1_78p00310 glycine dehydrogen
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3867 PGA1_78p00310 glycine dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1431.0 0.0 0 0 1 939 [] 17 940 .. 17 940 .. 0.98
Alignments for each domain:
== domain 1 score: 1431.0 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyat 76
rh+Gp++ e+ +mlk +Gf++l++li+ vp++ir++ +l + + +e +al ++k+ia knk+++s iG+Gy +t
lcl|FitnessBrowser__Phaeo:GFF3867 17 RHIGPSPREMADMLKVIGFNTLDELIDATVPPAIRQTEALDWGPAMTERDALFHMKEIAGKNKVLTSLIGQGYHGT 92
9*************************************************************************** PP
TIGR00461 77 ilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvskkk 152
+p i+rn+lenp wytaytpyqpeisqGrleallnfqt+v+dltGl+vanasllde+taaaeama+++r s++k
lcl|FitnessBrowser__Phaeo:GFF3867 93 TTPAPILRNILENPAWYTAYTPYQPEISQGRLEALLNFQTMVSDLTGLPVANASLLDEATAAAEAMAMAHRGSRSK 168
**************************************************************************** PP
TIGR00461 153 an..kfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkalv 226
an +f+v+k++hpqt+ v+ktraeplgi+v+v + +++ +a v+G++ qyp+t+G++ d+ + i +l+++k +
lcl|FitnessBrowser__Phaeo:GFF3867 169 ANnaAFFVDKNCHPQTVAVIKTRAEPLGIDVVVAEPTEL-DAGAVFGAIFQYPGTHGHVTDFSDQIAALHEHKGIA 243
65337****************************999886.6789******************************** PP
TIGR00461 227 svaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalq 302
vaad+l+l+ll++pg++Gadi++Gs+qrfGvp+GyGGphaa++a+ d++kr++pGri+Gvs da Gn a rl+lq
lcl|FitnessBrowser__Phaeo:GFF3867 244 VVAADILSLALLKSPGEMGADIAIGSTQRFGVPMGYGGPHAAYMATSDKLKRSMPGRIIGVSIDARGNKAYRLSLQ 319
**************************************************************************** PP
TIGR00461 303 treqhirrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvev 378
treqhirr+ka+sn+ctaq+lla++as+yavyhGp G+k ia+ ++r t+ laagl++ +++++ + +fdt+tvev
lcl|FitnessBrowser__Phaeo:GFF3867 320 TREQHIRREKANSNVCTAQALLAVIASMYAVYHGPDGIKAIAQSVHRKTARLAAGLEEAGFKVEPEVFFDTITVEV 395
**************************************************************************** PP
TIGR00461 379 gekaasevlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvansfpaellrdd 454
g+ +v++aa +++inlr v t+vgi+lde t e ++ ++ + ++ + s++ + +p+++lrd+
lcl|FitnessBrowser__Phaeo:GFF3867 396 GHLQK-TVMEAAVQRGINLRRVGETKVGISLDEQTRPETIEAVWGAFGIDR------KDDSSNKQYRLPEAMLRDS 464
*9776.7999999*********************************99943......44455666689******** PP
TIGR00461 455 eilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGyke 530
+l++++f++ +e+e+ ry+ rl +dlal+++miplGsctmklnat+em+p+twpef+++hpf p +q++Gy++
lcl|FitnessBrowser__Phaeo:GFF3867 465 AYLTHPIFHKNRAEAEITRYMRRLADRDLALDRAMIPLGSCTMKLNATIEMIPVTWPEFSNLHPFVPEDQAQGYHQ 540
**************************************************************************** PP
TIGR00461 531 liaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvk 606
+i +l+++l++itG+dais qpnsGaqGeyaGl ir+yh srg+ hrn+clip+sahGtnpasa+m+G kvvp+k
lcl|FitnessBrowser__Phaeo:GFF3867 541 MIDDLNDKLCQITGYDAISQQPNSGAQGEYAGLLTIRNYHASRGQAHRNVCLIPTSAHGTNPASAQMVGWKVVPIK 616
**************************************************************************** PP
TIGR00461 607 cdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGa 682
d++Gnid+ d+++kaek++d+la m+typst+Gvfe+t++ev++i h GGqvy+dGanmna vG+++pgd+G
lcl|FitnessBrowser__Phaeo:GFF3867 617 ADDNGNIDVADFREKAEKHSDHLAGCMITYPSTHGVFETTVQEVCQITHDHGGQVYIDGANMNAMVGVSRPGDIGG 692
**************************************************************************** PP
TIGR00461 683 dvchlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikm 758
dv+hlnlhktf+iphGGGGpgmgpigvk+hl+ +lp++ +++g vsaap+Gs silp+s++yi +
lcl|FitnessBrowser__Phaeo:GFF3867 693 DVSHLNLHKTFCIPHGGGGPGMGPIGVKAHLTEHLPGHP--------EYGTAVGPVSAAPFGSPSILPVSWAYILL 760
*************************************54........3457899********************** PP
TIGR00461 759 mGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptls 834
mG Gl++a++vailnany+a+rl+day+il++++++rvahecild r+l ++ag+++ dvakrl+d Gfhapt+s
lcl|FitnessBrowser__Phaeo:GFF3867 761 MGGSGLTQATKVAILNANYIAARLQDAYPILYTSESGRVAHECILDTRPLNDEAGVSVDDVAKRLIDSGFHAPTMS 836
**************************************************************************** PP
TIGR00461 835 fpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaayp 910
+pvaGtlmveptese ++eldrf++am++i+ e++ + G+i++e+n+lk aph++++l v+ew pysre+a++p
lcl|FitnessBrowser__Phaeo:GFF3867 837 WPVAGTLMVEPTESEPKDELDRFCEAMLSIRSEAQDIIDGKIDAENNPLKHAPHTVRDL-VGEWDRPYSREQACFP 911
******************************************************99985.79************** PP
TIGR00461 911 apvlkyfkfwptvarlddtyGdrnlvcsc 939
+ l k+wp+v+r+d++yGdrnl+c+c
lcl|FitnessBrowser__Phaeo:GFF3867 912 PGNLGVDKYWPAVNRVDNAYGDRNLICTC 940
****************************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (951 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 13.04
//
[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