Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate RR42_RS20070 RR42_RS20070 glycine dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1868
(950 letters)
>FitnessBrowser__Cup4G11:RR42_RS20070
Length = 973
Score = 1251 bits (3236), Expect = 0.0
Identities = 626/957 (65%), Positives = 749/957 (78%), Gaps = 11/957 (1%)
Query: 2 TQINLTTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLED--- 58
T L + F +RHIGP A ++Q ML LG+D+ AL +VIP +I+ + L +
Sbjct: 16 TLAELEARDAFASRHIGPDAAEQQHMLKVLGYDNRAALIDAVIPAAIRRRDGMPLGEFTA 75
Query: 59 GLSEADALALIKSIATKNQLFKTFIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEIS 118
L+E ALA ++ +A+KN++ K+FIGQGYY T TP +LRN+ ENPAWYTAYTPYQPEIS
Sbjct: 76 PLTEEAALAKLRGLASKNRVLKSFIGQGYYNTLTPGVVLRNIFENPAWYTAYTPYQPEIS 135
Query: 119 QGRLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCH 178
QGRLEA+LNFQ +++DLTGL IANAS+LDE TAAAEAMT +R++K+ S F+ +
Sbjct: 136 QGRLEAMLNFQQMVTDLTGLDIANASMLDEGTAAAEAMTLLQRVNKH-ASTTFYVADDVL 194
Query: 179 PQTLDVLRTRAEPLGIDVVVGDERELTDVTPFFGALLQYPASNGDVFDYRELTERFHAAN 238
PQTL+V+RTRA PLGI+V VG E F G LLQYP NGDV DYR + + HAA
Sbjct: 195 PQTLEVVRTRALPLGIEVKVGPAAEAAGAHAF-GVLLQYPGVNGDVADYRAIADAVHAAG 253
Query: 239 ALVAVAADLLALTVLTAPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGR 298
LV AADLLALT++ APGE+GADVA+G++QRFGVPLGFGGPHA Y + KDAFKR MPGR
Sbjct: 254 GLVVAAADLLALTLIAAPGEWGADVAVGNSQRFGVPLGFGGPHAGYMAVKDAFKRSMPGR 313
Query: 299 LVGVSVDRFGNPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQI 358
LVGV++D GN A RLA+QTREQHIRREKATSNICTAQVLLA +ASMYAVYHGP+GL +I
Sbjct: 314 LVGVTIDAQGNKAYRLALQTREQHIRREKATSNICTAQVLLAVMASMYAVYHGPQGLKRI 373
Query: 359 ANRVHHLTAILAKGLSALGLSVEQASFFDTLTVKAGAQTAALHDKAHAQRINLRVVDGER 418
A RVH LTA LA GL LG + A+FFDTLT++ G T ALH A A+ INLR R
Sbjct: 374 AQRVHRLTATLAGGLEQLGYARTNATFFDTLTLETGFNTEALHASATARGINLRHAGATR 433
Query: 419 LGLSLDETTTQADVETLWSLLSDGKALPDFAALAASVQSAIPATLVRQSPILSHPVFNRY 478
+G+SLDET ++ DV L + + GK +P F AL A+ Q A PA L RQS L+HPVFN +
Sbjct: 434 IGISLDETASREDVVALLEIFAHGKPVPGFDALEAAAQDAFPAGLARQSAYLTHPVFNTH 493
Query: 479 HSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQS 538
H+E E++RYLR LADKDLALDRTMIPLGSCTMKLNA SEMIPVTW EF +HPFAP +Q+
Sbjct: 494 HAEHEMLRYLRMLADKDLALDRTMIPLGSCTMKLNATSEMIPVTWPEFSKIHPFAPLDQT 553
Query: 539 AGYQQLTDELEAMLCAATGYDSVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPS 598
GY+++ D+LEAMLCAATGY +VSLQPNAGSQGEYAGLL I AYH SRGE RDICLIPS
Sbjct: 554 VGYREMIDQLEAMLCAATGYAAVSLQPNAGSQGEYAGLLIIHAYHASRGESHRDICLIPS 613
Query: 599 SAHGTNPATAQMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEE 658
SAHGTNPA+AQMAGM+VVV ACD GNVD+EDL KA +H ++LAA+MITYPSTHGVFE+
Sbjct: 614 SAHGTNPASAQMAGMKVVVVACDENGNVDLEDLAKKAEQHSKNLAAIMITYPSTHGVFEQ 673
Query: 659 GIREICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVG 718
G+++IC I+H +GGQVY+DGANMNAMVG APG+FGGDVSHLNLHKTFCIPHGGGGPGVG
Sbjct: 674 GVQQICHIVHKHGGQVYVDGANMNAMVGTAAPGQFGGDVSHLNLHKTFCIPHGGGGPGVG 733
Query: 719 PIGVKSHLAPFLP-----GHAQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRAS 773
P+ V +HLA FLP G+ + ++ G V AAPFGSASILPI+WMYI MMG AGL A+
Sbjct: 734 PVAVGAHLADFLPNQDSVGYRRDDQGIGGVSAAPFGSASILPISWMYIAMMGSAGLTAAT 793
Query: 774 QLAILNANYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGF 833
+ AIL ANY++RRL H+PVLYTG +GLVAHECILD+R L+ ++GIS +DVAKRL+D+GF
Sbjct: 794 ENAILAANYVARRLSPHFPVLYTGQHGLVAHECILDVRALQKTTGISNEDVAKRLMDYGF 853
Query: 834 HAPTMSFPVAGTLMIEPTESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPH 893
HAPTMSFPV GTLMIEPTESE+ ELDRF DAMI IR EI VE+GT D++DNPLKNAPH
Sbjct: 854 HAPTMSFPVPGTLMIEPTESEALHELDRFIDAMIAIRAEIARVEDGTFDREDNPLKNAPH 913
Query: 894 TAKELVGE-WSHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESY 949
TA + + W H Y+R++A YPVA+L KYWPPVGR DNV+GDRNL CAC + Y
Sbjct: 914 TAAVITADVWEHKYTRQEAAYPVAALRTQKYWPPVGRADNVYGDRNLFCACVPMSEY 970
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: 2315
Number of extensions: 89
Number of successful extensions: 8
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: 973
Length adjustment: 44
Effective length of query: 906
Effective length of database: 929
Effective search space: 841674
Effective search space used: 841674
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 RR42_RS20070 RR42_RS20070 (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.7975.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 1461.0 0.4 0 1460.8 0.4 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS20070 RR42_RS20070 glycine dehydrogena
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS20070 RR42_RS20070 glycine dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1460.8 0.4 0 0 1 939 [] 29 964 .. 29 964 .. 0.98
Alignments for each domain:
== domain 1 score: 1460.8 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkl...eapakeyealaelkkiasknkkvk 66
rh+Gpd+aeq++mlk lG+d+ ali+ ++p +ir + + l ap +e +ala+l+ +askn+++k
lcl|FitnessBrowser__Cup4G11:RR42_RS20070 29 RHIGPDAAEQQHMLKVLGYDNRAALIDAVIPAAIRRRDGMPLgefTAPLTEEAALAKLRGLASKNRVLK 97
9***********************************98775522279999******************* PP
TIGR00461 67 syiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldeg 135
s+iG+Gyy+t++p v++rn++enp wytaytpyqpeisqGrlea+lnfq++v+dltGl++anas+ldeg
lcl|FitnessBrowser__Cup4G11:RR42_RS20070 98 SFIGQGYYNTLTPGVVLRNIFENPAWYTAYTPYQPEISQGRLEAMLNFQQMVTDLTGLDIANASMLDEG 166
********************************************************************* PP
TIGR00461 136 taaaeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypa 204
taaaeam l +rv k+ + f+va+dv pqtlevv+tra plgiev v+ a + + +Gvllqyp+
lcl|FitnessBrowser__Cup4G11:RR42_RS20070 167 TAAAEAMTLLQRVNKHASTTFYVADDVLPQTLEVVRTRALPLGIEVKVGPAAEAAG-AHAFGVLLQYPG 234
*************************************************9999765.568********* PP
TIGR00461 205 tdGeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavk 273
+G++ dy+a+ d+++ lv aadllaltl+ +pg+ Gad+++G +qrfGvplG+GGpha ++avk
lcl|FitnessBrowser__Cup4G11:RR42_RS20070 235 VNGDVADYRAIADAVHAAGGLVVAAADLLALTLIAAPGEWGADVAVGNSQRFGVPLGFGGPHAGYMAVK 303
********************************************************************* PP
TIGR00461 274 deykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkn 342
d +kr++pGr+vGv+ da+Gn a rlalqtreqhirr+katsnictaqvlla++as+yavyhGp+Glk+
lcl|FitnessBrowser__Cup4G11:RR42_RS20070 304 DAFKRSMPGRLVGVTIDAQGNKAYRLALQTREQHIRREKATSNICTAQVLLAVMASMYAVYHGPQGLKR 372
********************************************************************* PP
TIGR00461 343 iarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeeaeinlravvltevgialde 411
ia+r++rlt+ la gl++ +y +n+t+fdtlt+e g ++ ++ +a +++inlr +t +gi+lde
lcl|FitnessBrowser__Cup4G11:RR42_RS20070 373 IAQRVHRLTATLAGGLEQLGYARTNATFFDTLTLETGFNTE-ALHASATARGINLRHAGATRIGISLDE 440
************************************98876.89************************* PP
TIGR00461 412 tttkedvldllkvlagkdnlglsseelsedvansfpaellrddeilrdevfnryhsetellrylhrles 480
t+++edv+ ll+++a + + l+ +++fpa l r++ +l+++vfn++h+e e+lryl l
lcl|FitnessBrowser__Cup4G11:RR42_RS20070 441 TASREDVVALLEIFAHGKP-VPGFDALEAAAQDAFPAGLARQSAYLTHPVFNTHHAEHEMLRYLRMLAD 508
**************98553.336799******************************************* PP
TIGR00461 481 kdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdais 549
kdlal+++miplGsctmklnat em+p+twpef++ihpfap +q+ Gy+e+i qle+ l+ tG+ a+s
lcl|FitnessBrowser__Cup4G11:RR42_RS20070 509 KDLALDRTMIPLGSCTMKLNATSEMIPVTWPEFSKIHPFAPLDQTVGYREMIDQLEAMLCAATGYAAVS 577
********************************************************************* PP
TIGR00461 550 lqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdl 618
lqpn+G+qGeyaGl +i yh srge hr+iclip sahGtnpasa+maG+kvv+v+cd++Gn+dl+dl
lcl|FitnessBrowser__Cup4G11:RR42_RS20070 578 LQPNAGSQGEYAGLLIIHAYHASRGESHRDICLIPSSAHGTNPASAQMAGMKVVVVACDENGNVDLEDL 646
********************************************************************* PP
TIGR00461 619 kakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchl 687
+kae+++++laa+m+typst+Gvfe++++++++ivh+ GGqvy+dGanmna vG ++pg++G dv+hl
lcl|FitnessBrowser__Cup4G11:RR42_RS20070 647 AKKAEQHSKNLAAIMITYPSTHGVFEQGVQQICHIVHKHGGQVYVDGANMNAMVGTAAPGQFGGDVSHL 715
********************************************************************* PP
TIGR00461 688 nlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyi 756
nlhktf+iphGGGGpg+gp++v +hla flp+ ++ v + ++ ig vsaap+Gsasilpis+myi
lcl|FitnessBrowser__Cup4G11:RR42_RS20070 716 NLHKTFCIPHGGGGPGVGPVAVGAHLADFLPN---QDSVGYRRDDQGIGGVSAAPFGSASILPISWMYI 781
********************************...889999**************************** PP
TIGR00461 757 kmmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlld 825
+mmG+ Gl+ a+e ail+any+a+rl ++++l++g+++ vahecild+r l++ +gi+++dvakrl+d
lcl|FitnessBrowser__Cup4G11:RR42_RS20070 782 AMMGSAGLTAATENAILAANYVARRLSPHFPVLYTGQHGLVAHECILDVRALQKTTGISNEDVAKRLMD 850
********************************************************************* PP
TIGR00461 826 yGfhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqsli 894
yGfhapt+sfpv+Gtlm+eptese+l+eldrfidamiai++ei v G+++ edn+lknaph++
lcl|FitnessBrowser__Cup4G11:RR42_RS20070 851 YGFHAPTMSFPVPGTLMIEPTESEALHELDRFIDAMIAIRAEIARVEDGTFDREDNPLKNAPHTAAVIT 919
***************************************************************888777 PP
TIGR00461 895 vaewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
+ w + y+r+eaayp++ l+ +k+wp v+r d++yGdrnl+c+c
lcl|FitnessBrowser__Cup4G11:RR42_RS20070 920 ADVWEHKYTRQEAAYPVAALRTQKYWPPVGRADNVYGDRNLFCAC 964
7779999*************************************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (973 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: 13.21
//
[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