Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate BPHYT_RS19330 BPHYT_RS19330 glycine dehydrogenase (decarboxylating)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5558
(953 letters)
>FitnessBrowser__BFirm:BPHYT_RS19330
Length = 978
Score = 1274 bits (3297), Expect = 0.0
Identities = 643/955 (67%), Positives = 764/955 (80%), Gaps = 16/955 (1%)
Query: 11 FIARHIGPRASDEQAMLERLGYDSLEALSASVIPESIKGTSVLDMG---DGQSEADALAS 67
F RHIGP A+D+ AMLE LG+ S AL +VIP++I+ T L +G +SEA+ALA+
Sbjct: 26 FAERHIGPDAADQHAMLEALGFASRAALIDAVIPKTIRRTETLPLGPFTQPKSEAEALAA 85
Query: 68 IKAIAAKNQLFKTYIGQGYYNCHTPAPILRNLLENPAWYTAYTPYQPEISQGRLEALLNF 127
++ +A KNQ+F++YIGQGYYN HTP ILRN+LENPAWYTAYTPYQPEISQGRLEALLNF
Sbjct: 86 LRELADKNQVFRSYIGQGYYNAHTPTVILRNVLENPAWYTAYTPYQPEISQGRLEALLNF 145
Query: 128 QTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASVHSHPQTLDVLRTR 187
Q +I DLTGL I+NASLLDEATAAAEAMT +R+ K K SN FF + PQT++V+RTR
Sbjct: 146 QQMIVDLTGLAISNASLLDEATAAAEAMTLLQRVGKPK-SNVFFVADDVLPQTIEVVRTR 204
Query: 188 AEPLGIDVVVGDERELSDVSGFFGALLQYPASNGDLFDYRELTERFHTANALVAVAADLL 247
A P+GI+V VG E ++ + F G LLQYP NGD+ DYR LTE H A V VAADLL
Sbjct: 205 ATPVGIEVKVGPASEAANANAF-GVLLQYPGVNGDVRDYRALTEAIHAAGGHVVVAADLL 263
Query: 248 ALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFG 307
ALT+LTPPGE+GADVA+G+ QRFGVP+GFGGPHAAY + +D FKR MPGRLVGV+VD G
Sbjct: 264 ALTVLTPPGEWGADVAVGNTQRFGVPVGFGGPHAAYLAVRDEFKRQMPGRLVGVTVDAQG 323
Query: 308 KPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLVQIANRIHHLTAI 367
PALRLA+QTREQHIRREKATSN+CTAQ LLA +ASMYAVYHGP GL IA R++ + A+
Sbjct: 324 NPALRLALQTREQHIRREKATSNVCTAQALLAIMASMYAVYHGPHGLKTIALRVNRIAAL 383
Query: 368 LAKGLGALGLSVEQESFFDTLTLRTGAQTAALHDKARAQRINLRVVDAERLGLSLDETTS 427
LA+G LG ++ E+FFDTLT TGA+T AL D A A+RINLR V A ++GLS+DETT+
Sbjct: 384 LAEGAKQLGYTLANETFFDTLTFDTGARTQALLDAATAKRINLRRVSATQVGLSIDETTT 443
Query: 428 QADVEALLRLIGNLMADGKAVPDF----AALAASVQSHIPAELVRQSAILSHPVFNRYHS 483
+ D+ LL + A VP A LAAS + +PA L R SA L+H VFNR+HS
Sbjct: 444 RHDLADLLAVFAQA-AFTNDVPQVDALDAKLAASNTASVPAALERTSAYLTHHVFNRHHS 502
Query: 484 ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAG 543
ETE++RYLR L+DKDLALDR+MIPLGSCTMKLNA SEM+PVTW EFG +HPFAPAEQ+ G
Sbjct: 503 ETEMLRYLRSLSDKDLALDRSMIPLGSCTMKLNATSEMLPVTWPEFGQIHPFAPAEQTVG 562
Query: 544 YQQLTDELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSA 603
Y+++ D+LE ML AATGY AVSLQPNAGSQGEYAGLL I AYH SRGE R++CLIP+SA
Sbjct: 563 YREMIDQLEEMLVAATGYAAVSLQPNAGSQGEYAGLLIIHAYHASRGEAHRNVCLIPASA 622
Query: 604 HGTNPATAHMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI 663
HGTNPA+A MAGM+VVV ACDA+GNVDIEDL+ KA +H + LAA+MITYPSTHGVFE+ +
Sbjct: 623 HGTNPASAQMAGMQVVVVACDAQGNVDIEDLKKKAGQHADKLAAIMITYPSTHGVFEQNV 682
Query: 664 REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI 723
REIC I+H +GGQVY+DGANMNAMVGL APG+FGGDVSHLNLHKTFCIPHGGGGPGVGP+
Sbjct: 683 REICEIVHAHGGQVYVDGANMNAMVGLTAPGQFGGDVSHLNLHKTFCIPHGGGGPGVGPV 742
Query: 724 GVKSHLAPFLPGHASMERKQ-----GAVCAAPFGSASILPITWMYIRMMGGAGLKRASQL 778
V +HLA FLP S ++ GAV AP+GSASILPI+WMYI MMG L A++
Sbjct: 743 AVGAHLAQFLPNQISSGYERAPNGIGAVSGAPYGSASILPISWMYIAMMGAKNLTAATET 802
Query: 779 AILNANYIARRLEEHYPVLYSGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHA 838
AILNANY+A++L HYPVLYSG GLVAHECILDLRP+K++SGI+VDDVAKRL D+GFHA
Sbjct: 803 AILNANYVAKKLAPHYPVLYSGPGGLVAHECILDLRPIKETSGITVDDVAKRLADYGFHA 862
Query: 839 PTMSFPVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGSLDKDDNPLKNAPHTA 898
PTMSFPV GTLM+EPTESESKEELDRF +AMI IREEIRAVE+G D++DNPLK+APHTA
Sbjct: 863 PTMSFPVPGTLMVEPTESESKEELDRFIEAMIAIREEIRAVEDGRSDREDNPLKHAPHTA 922
Query: 899 AEIV-GEWTHPYSREQAVYPVASLIDGKYWPPVGRVDNVFGDRNLVCACPSIESY 952
A ++ +W H Y+RE A YP+ +LI KYWPPVGR DNV+GDRNL C+C I Y
Sbjct: 923 AVVIANDWKHAYARETAAYPLPTLIAKKYWPPVGRADNVYGDRNLFCSCVPIADY 977
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: 2277
Number of extensions: 98
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: 953
Length of database: 978
Length adjustment: 44
Effective length of query: 909
Effective length of database: 934
Effective search space: 849006
Effective search space used: 849006
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 BPHYT_RS19330 BPHYT_RS19330 (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.1831810.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 1476.1 0.3 0 1476.0 0.3 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS19330 BPHYT_RS19330 glycine dehydrogen
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS19330 BPHYT_RS19330 glycine dehydrogenase (decarboxylating)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1476.0 0.3 0 0 1 939 [] 29 971 .. 29 971 .. 0.97
Alignments for each domain:
== domain 1 score: 1476.0 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkle...apakeyealaelkkiasknkkvks 67
rh+Gpd+a+q+ ml++lGf + ali+ ++pk ir + +l l+ p++e eala l+++a+kn++++s
lcl|FitnessBrowser__BFirm:BPHYT_RS19330 29 RHIGPDAADQHAMLEALGFASRAALIDAVIPKTIRRTETLPLGpftQPKSEAEALAALRELADKNQVFRS 98
9*************************************999862226788******************** PP
TIGR00461 68 yiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegta 137
yiG+Gyy++ +p vi+rn+lenp wytaytpyqpeisqGrleallnfq++++dltGl ++nasllde+ta
lcl|FitnessBrowser__BFirm:BPHYT_RS19330 99 YIGQGYYNAHTPTVILRNVLENPAWYTAYTPYQPEISQGRLEALLNFQQMIVDLTGLAISNASLLDEATA 168
********************************************************************** PP
TIGR00461 138 aaeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdG 207
aaeam l +rv k k+n f+va+dv pqt+evv+tra p+giev v+ as+ + + +Gvllqyp+ +G
lcl|FitnessBrowser__BFirm:BPHYT_RS19330 169 AAEAMTLLQRVGKPKSNVFFVADDVLPQTIEVVRTRATPVGIEVKVGPASEAAN-ANAFGVLLQYPGVNG 237
*************************************************99876.578************ PP
TIGR00461 208 eildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeyk 277
++ dy+al+++++ v vaadllalt+ltppg+ Gad+++G +qrfGvp+G+GGphaa++av+de+k
lcl|FitnessBrowser__BFirm:BPHYT_RS19330 238 DVRDYRALTEAIHAAGGHVVVAADLLALTVLTPPGEWGADVAVGNTQRFGVPVGFGGPHAAYLAVRDEFK 307
********************************************************************** PP
TIGR00461 278 rklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniarri 347
r++pGr+vGv+ da+Gn+alrlalqtreqhirr+katsn+ctaq+lla +as+yavyhGp+Glk ia r+
lcl|FitnessBrowser__BFirm:BPHYT_RS19330 308 RQMPGRLVGVTVDAQGNPALRLALQTREQHIRREKATSNVCTAQALLAIMASMYAVYHGPHGLKTIALRV 377
********************************************************************** PP
TIGR00461 348 frltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeeaeinlravvltevgialdetttked 417
r++++la g k+ +y l n+t+fdtlt + g ++ ++l aa ++ inlr v +t+vg+++dettt++d
lcl|FitnessBrowser__BFirm:BPHYT_RS19330 378 NRIAALLAEGAKQLGYTLANETFFDTLTFDTGARTQ-ALLDAATAKRINLRRVSATQVGLSIDETTTRHD 446
********************************9988.8999***************************** PP
TIGR00461 418 vldllkvlagk..dnlglsseelsedvan....sfpaellrddeilrdevfnryhsetellrylhrlesk 481
+ dll v+a n +++ l+ ++a s+pa+l+r++ +l+++vfnr+hsete+lryl +l k
lcl|FitnessBrowser__BFirm:BPHYT_RS19330 447 LADLLAVFAQAafTNDVPQVDALDAKLAAsntaSVPAALERTSAYLTHHVFNRHHSETEMLRYLRSLSDK 516
********97522344556677777766555679************************************ PP
TIGR00461 482 dlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdaislq 551
dlal++smiplGsctmklnat emlp+twpef++ihpfapaeq+ Gy+e+i qle+ lv tG+ a+slq
lcl|FitnessBrowser__BFirm:BPHYT_RS19330 517 DLALDRSMIPLGSCTMKLNATSEMLPVTWPEFGQIHPFAPAEQTVGYREMIDQLEEMLVAATGYAAVSLQ 586
********************************************************************** PP
TIGR00461 552 pnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlkak 621
pn+G+qGeyaGl +i yh srge hrn+clipasahGtnpasa+maG++vv+v+cd +Gn+d++dlk+k
lcl|FitnessBrowser__BFirm:BPHYT_RS19330 587 PNAGSQGEYAGLLIIHAYHASRGEAHRNVCLIPASAHGTNPASAQMAGMQVVVVACDAQGNVDIEDLKKK 656
********************************************************************** PP
TIGR00461 622 aekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhk 691
a +++d+laa+m+typst+Gvfe+ +re+++ivh GGqvy+dGanmna vGlt+pg++G dv+hlnlhk
lcl|FitnessBrowser__BFirm:BPHYT_RS19330 657 AGQHADKLAAIMITYPSTHGVFEQNVREICEIVHAHGGQVYVDGANMNAMVGLTAPGQFGGDVSHLNLHK 726
********************************************************************** PP
TIGR00461 692 tfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGa 761
tf+iphGGGGpg+gp++v +hla flp+ ++ s e + igavs apyGsasilpis+myi+mmGa
lcl|FitnessBrowser__BFirm:BPHYT_RS19330 727 TFCIPHGGGGPGVGPVAVGAHLAQFLPN-QISSG--YERAPNGIGAVSGAPYGSASILPISWMYIAMMGA 793
***************************9.56654..4556789*************************** PP
TIGR00461 762 eGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhap 831
+ l+ a+e ailnany+ak+l +y++l+ g + vahecildlr++ke +gi + dvakrl dyGfhap
lcl|FitnessBrowser__BFirm:BPHYT_RS19330 794 KNLTAATETAILNANYVAKKLAPHYPVLYSGPGGLVAHECILDLRPIKETSGITVDDVAKRLADYGFHAP 863
********************************************************************** PP
TIGR00461 832 tlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadp 901
t+sfpv+Gtlmvepteses+eeldrfi+amiai+eei av G+ + edn+lk aph++ +i+ +w+++
lcl|FitnessBrowser__BFirm:BPHYT_RS19330 864 TMSFPVPGTLMVEPTESESKEELDRFIEAMIAIREEIRAVEDGRSDREDNPLKHAPHTAAVVIANDWKHA 933
********************************************************************** PP
TIGR00461 902 ysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
y+re aayp+p l k+wp v+r d++yGdrnl+csc
lcl|FitnessBrowser__BFirm:BPHYT_RS19330 934 YARETAAYPLPTLIAKKYWPPVGRADNVYGDRNLFCSC 971
************************************** PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (978 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 28.26
//
[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