Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate Pf1N1B4_2236 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)
Query= CharProtDB::CH_003480
(957 letters)
>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236
Length = 957
Score = 1261 bits (3264), Expect = 0.0
Identities = 631/957 (65%), Positives = 754/957 (78%), Gaps = 8/957 (0%)
Query: 4 TLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAPAT 63
+LSQL + F+ RH+GPDAA+QQ ML+++G S L Q VP I+L P +
Sbjct: 6 SLSQLRDPNTFLRRHLGPDAAEQQAMLDSLGLGSRVELIEQTVPPGIRLNRPLDLPPALD 65
Query: 64 EYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVSQGR 123
E AALA+L+ A +N+ +TS IGMGY P VILRN+LENPGWYTAYTPYQPE++QGR
Sbjct: 66 EEAALAKLRGYAEQNQIWTSLIGMGYHGTLTPAVILRNVLENPGWYTAYTPYQPEIAQGR 125
Query: 124 LEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVHPQT 183
LEALLNFQQ+T+DLTGL++A+ASLLDEATAAAEAMA+AKRV+K ++ N FFV + HPQT
Sbjct: 126 LEALLNFQQLTIDLTGLELANASLLDEATAAAEAMALAKRVAKSRS-NLFFVDENCHPQT 184
Query: 184 LDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKIVV 243
+ VVRTRAE FGFE+I+D + HQ VFG LLQ T GE+ D LI L +++ +V
Sbjct: 185 ISVVRTRAEGFGFELIIDAVDNLKQHQ-VFGALLQYPDTHGEVRDLRPLIDHLHAQQALV 243
Query: 244 SVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRIIG 303
VA D+++L+LLT PG+ GAD+VFGS+QRFGVPMGYGGPHAAFFA++DEYKR++PGRIIG
Sbjct: 244 CVATDLLSLLLLTPPGELGADVVFGSSQRFGVPMGYGGPHAAFFASRDEYKRAIPGRIIG 303
Query: 304 VSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRIANR 363
VSKDA GN ALRMA+QTREQHIRREKANSNICT+QVLLANIAS YAVYHGP GLKRIA R
Sbjct: 304 VSKDARGNVALRMALQTREQHIRREKANSNICTAQVLLANIASFYAVYHGPEGLKRIAQR 363
Query: 364 IHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVAD-KAGVLTRAEAAEINLRSDILNAVGI 422
+HRLT ILAAGL++ G+ + ++FDTL +EV + ++ A+AA+INLR +G+
Sbjct: 364 VHRLTCILAAGLERHGITRLNQNFFDTLTLEVGGTQTAIIESAQAAQINLRILGRGQLGL 423
Query: 423 TLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDVAHDSRSIQPAMLRDDEILTHPVFNRY 482
+LDET V +LF+V LG +HGL++D LD + I + R L HPVFN +
Sbjct: 424 SLDETCDETTVAKLFDVFLGADHGLNVDDLDAETLVSG--IPAGLQRSTSYLRHPVFNAH 481
Query: 483 HSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPEQA 542
HSETEM+RY+ LE KDLALNQ+MIPLGSCTMKLNA +EMIPITWP+FA LHPF P EQ
Sbjct: 482 HSETEMLRYLKQLENKDLALNQSMIPLGSCTMKLNATSEMIPITWPQFANLHPFVPKEQV 541
Query: 543 EGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIPA 602
GY MIA+L WL +TG+DA+CMQPNSGAQGEYAGLLAIR YHESR++G RDICLIP+
Sbjct: 542 VGYSLMIAELERWLCAITGFDAICMQPNSGAQGEYAGLLAIRKYHESRHQGARDICLIPS 601
Query: 603 SAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVYEE 662
SAHGTNPASA MAGM+VV+V CD+ GN+DL DL+ KA +AGD L+C+M TYPSTHGVYEE
Sbjct: 602 SAHGTNPASAQMAGMRVVIVECDEGGNVDLDDLKEKATEAGDKLACLMATYPSTHGVYEE 661
Query: 663 TIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGMG 722
I E+CEV+H GGQVY+DGAN+NAQVG+ P IGADVSH+NLHKTFCIPHGGGGPGMG
Sbjct: 662 GISEICEVIHSHGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPHGGGGPGMG 721
Query: 723 PIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKKAS 782
PIGV+AHLAPFV H VV I+G L GAVSAAP+GSASILPISWMYI MMG + L AS
Sbjct: 722 PIGVRAHLAPFVANHPVVPIDGPLPENGAVSAAPWGSASILPISWMYIAMMGPQ-LADAS 780
Query: 783 QVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDYGF 842
+VAIL ANY+A L AFPVLYTGR+ RVAHECILD+RPLK +TGISE D+AKRL+DYGF
Sbjct: 781 EVAILAANYLAQHLAGAFPVLYTGRNERVAHECILDLRPLKAQTGISEEDVAKRLMDYGF 840
Query: 843 HAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNAPH 902
HAPTMSFPV GTLMVEPTESESK ELDRFI AML+IRAEI +V+ G WP EDNPL +PH
Sbjct: 841 HAPTMSFPVPGTLMVEPTESESKAELDRFIGAMLSIRAEITEVQNGNWPAEDNPLKRSPH 900
Query: 903 IQSELVAEWAHPYSREVAVFPAG--VADKYWPTVKRLDDVYGDRNLFCSCVPISEYQ 957
+++ W PYS E AV P A KYWP V R+D+VYGDRNLFC+CVP+ EY+
Sbjct: 901 TLADITGVWERPYSIERAVTPDAHTKAHKYWPVVNRVDNVYGDRNLFCACVPVDEYR 957
Lambda K H
0.319 0.134 0.395
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: 2345
Number of extensions: 84
Number of successful extensions: 7
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: 957
Length adjustment: 44
Effective length of query: 913
Effective length of database: 913
Effective search space: 833569
Effective search space used: 833569
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 Pf1N1B4_2236 (Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2))
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.17418.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 1539.8 0.0 0 1539.6 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 Glycine dehydrogenase [decarboxy
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P pro
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1539.6 0.0 0 0 1 939 [] 19 950 .. 19 950 .. 0.99
Alignments for each domain:
== domain 1 score: 1539.6 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkk 64
rhlGpd+aeq+ ml++lG + +lieq vp+ irl+rpl l+ + e +ala+l+ a++n+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 19 RHLGPDAAEQQAMLDSLGLGSRVELIEQTVPPGIRLNRPLDLPPALDEEAALAKLRGYAEQNQI 82
9*************************************************************** PP
TIGR00461 65 vksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevan 128
+s iG+Gy +t++p vi+rn+lenpgwytaytpyqpei+qGrleallnfq++++dltGle+an
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 83 WTSLIGMGYHGTLTPAVILRNVLENPGWYTAYTPYQPEIAQGRLEALLNFQQLTIDLTGLELAN 146
**************************************************************** PP
TIGR00461 129 aslldegtaaaeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkka 192
asllde+taaaeamal++rv+k+++n f+v++++hpqt++vv+trae +g+e+i+d ++++k++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 147 ASLLDEATAAAEAMALAKRVAKSRSNLFFVDENCHPQTISVVRTRAEGFGFELIIDAVDNLKQH 210
******************************************************9888888776 PP
TIGR00461 193 vdvlGvllqypatdGeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrf 256
+v+G+llqyp t+Ge+ d++ lid+l+ ++alv+va+dll+l lltppg+lGad+v+Gs+qrf
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 211 -QVFGALLQYPDTHGEVRDLRPLIDHLHAQQALVCVATDLLSLLLLTPPGELGADVVFGSSQRF 273
.6************************************************************** PP
TIGR00461 257 GvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnicta 320
Gvp+GyGGphaaffa++deykr +pGri+Gvskda Gn alr+alqtreqhirr+ka+snicta
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 274 GVPMGYGGPHAAFFASRDEYKRAIPGRIIGVSKDARGNVALRMALQTREQHIRREKANSNICTA 337
**************************************************************** PP
TIGR00461 321 qvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaas 384
qvllan+as yavyhGp Glk+ia+r++rlt ilaagl+r++ n+++fdtlt+evg +
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 338 QVLLANIASFYAVYHGPEGLKRIAQRVHRLTCILAAGLERHGITRLNQNFFDTLTLEVGGTQT- 400
***********************************************************8877. PP
TIGR00461 385 evlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvan.sfp 447
++ ++a++a+inlr + +++g++ldet + v +l++v++g d +gl+++ l+ + +p
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 401 AIIESAQAAQINLRILGRGQLGLSLDETCDETTVAKLFDVFLGAD-HGLNVDDLDAETLVsGIP 463
89999**************************************87.********99876537** PP
TIGR00461 448 aellrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwp 511
a l+r+ +lr++vfn +hsete+lryl++le+kdlalnqsmiplGsctmklnat em+pitwp
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 464 AGLQRSTSYLRHPVFNAHHSETEMLRYLKQLENKDLALNQSMIPLGSCTMKLNATSEMIPITWP 527
**************************************************************** PP
TIGR00461 512 efaeihpfapaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrge 575
+fa++hpf p eqv Gy +ia+le wl+ itGfdai++qpnsGaqGeyaGl +ir+yhesr +
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 528 QFANLHPFVPKEQVVGYSLMIAELERWLCAITGFDAICMQPNSGAQGEYAGLLAIRKYHESRHQ 591
**************************************************************** PP
TIGR00461 576 ehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypst 639
+ r+iclip sahGtnpasa+maG++vv v+cd+ Gn+dl dlk+ka +agd+la++m typst
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 592 GARDICLIPSSAHGTNPASAQMAGMRVVIVECDEGGNVDLDDLKEKATEAGDKLACLMATYPST 655
**************************************************************** PP
TIGR00461 640 yGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpg 703
+Gv+ee+i e+++++h+ GGqvy+dGan+naqvGl++p+d+Gadv+h+nlhktf+iphGGGGpg
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 656 HGVYEEGISEICEVIHSHGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPHGGGGPG 719
**************************************************************** PP
TIGR00461 704 mgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkka 767
mgpigv++hlapf+ + + vv ++g + gavsaap+Gsasilpis+myi+mmG++ l a
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 720 MGPIGVRAHLAPFVAN---HPVVPIDGPLPENGAVSAAPWGSASILPISWMYIAMMGPQ-LADA 779
****************...78999**********************************8.99** PP
TIGR00461 768 sevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhap 831
sevail+anyla+ l a+++l++gr+ervahecildlr+lk+++gi+++dvakrl+dyGfhap
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 780 SEVAILAANYLAQHLAGAFPVLYTGRNERVAHECILDLRPLKAQTGISEEDVAKRLMDYGFHAP 843
**************************************************************** PP
TIGR00461 832 tlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqsliv 895
t+sfpv+Gtlmvepteses+ eldrfi am++i++ei +v++G++++edn+lk +ph+l + i+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 844 TMSFPVPGTLMVEPTESESKAELDRFIGAMLSIRAEITEVQNGNWPAEDNPLKRSPHTLAD-IT 906
*********************************************************8875.9* PP
TIGR00461 896 aewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
+ w pys e a+ p + +k +k+wp v+r+d++yGdrnl+c+c
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2236 907 GVWERPYSIERAVTPDAHTKAHKYWPVVNRVDNVYGDRNLFCAC 950
*******************************************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (957 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: 9.80
//
[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