Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate PfGW456L13_904 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)
Query= CharProtDB::CH_003480
(957 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904
Length = 957
Score = 1253 bits (3242), Expect = 0.0
Identities = 631/957 (65%), Positives = 752/957 (78%), Gaps = 8/957 (0%)
Query: 4 TLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAPAT 63
+LSQL + AF+ RH+GPDAA+QQ ML+++G S L Q VP I+L P +
Sbjct: 6 SLSQLRDPNAFLRRHLGPDAAEQQAMLDSLGLGSRVDLIEQTVPPGIRLNRPLDLPPALD 65
Query: 64 EYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVSQGR 123
E AALA+L+ A +N+ +TS IGMGY P VILRN+LENPGWYTAYTPYQPE++QGR
Sbjct: 66 EEAALAKLRGYAEQNQVWTSLIGMGYHGTLTPAVILRNVLENPGWYTAYTPYQPEIAQGR 125
Query: 124 LEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVHPQT 183
LEALLNFQQ+T+DLTGL++A+ASLLDEATAAAEAMA+AKRV+K K+ N FFV + HPQT
Sbjct: 126 LEALLNFQQLTIDLTGLELANASLLDEATAAAEAMALAKRVAKSKS-NLFFVDENCHPQT 184
Query: 184 LDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKIVV 243
+ VV+TRAE FGF++IVD + HQ VFG LLQ T GEIHD LI L +++ +
Sbjct: 185 ISVVQTRAEGFGFDLIVDTVDNLKRHQ-VFGALLQYPDTHGEIHDLRPLIDHLHAQQALA 243
Query: 244 SVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRIIG 303
VA D+++L+LLT PG+ GAD+VFGS+QRFGVPMGYGGPHAAFFA++DEYKR++PGRIIG
Sbjct: 244 CVATDLLSLLLLTPPGELGADVVFGSSQRFGVPMGYGGPHAAFFASRDEYKRAIPGRIIG 303
Query: 304 VSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRIANR 363
VSKDA GNTALRMA+QTREQHIRREKANSNICT+QVLLANIAS YAVYHGP GLKRIA R
Sbjct: 304 VSKDARGNTALRMALQTREQHIRREKANSNICTAQVLLANIASFYAVYHGPEGLKRIAQR 363
Query: 364 IHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVAD-KAGVLTRAEAAEINLRSDILNAVGI 422
+HRLT ILA GL++ G+ + H+FDTL +EV + ++ A AA+INLR +G+
Sbjct: 364 VHRLTCILATGLERNGIVRVNRHFFDTLTLEVGGTQTAIIESARAAQINLRILGRGQLGL 423
Query: 423 TLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDVAHDSRSIQPAMLRDDEILTHPVFNRY 482
+LDET V +LF+V LG +HGL ID LD +V I + R L HPVF+ +
Sbjct: 424 SLDETCDEGTVAKLFDVFLGADHGLSIDDLDAEVLPGG--IPQGLARTSPYLRHPVFSAH 481
Query: 483 HSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPEQA 542
HSETEM+RY+ LE KDLALNQ+MIPLGSCTMKLNA +EMIPITWP+FA LHPF P EQA
Sbjct: 482 HSETEMLRYLKQLENKDLALNQSMIPLGSCTMKLNATSEMIPITWPQFANLHPFVPKEQA 541
Query: 543 EGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIPA 602
GY MI +L WL +TG+DA+CMQPNSGAQGEYAGLLAIR YHESR +G RDICLIP+
Sbjct: 542 AGYGLMIEELERWLCAITGFDAICMQPNSGAQGEYAGLLAIRKYHESRQQGGRDICLIPS 601
Query: 603 SAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVYEE 662
SAHGTNPASA MAGM+VV+V CD+ GN+DL DL+ KA QA + L+C+M TYPSTHGVYEE
Sbjct: 602 SAHGTNPASAQMAGMRVVIVECDEAGNVDLDDLKEKAAQAAEKLACLMATYPSTHGVYEE 661
Query: 663 TIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGMG 722
I E+CEV+HQ GGQVY+DGAN+NAQVG+ P IGADVSH+NLHKTFCIPHGGGGPGMG
Sbjct: 662 GISEICEVIHQHGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPHGGGGPGMG 721
Query: 723 PIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKKAS 782
PIGV+AHLAPFV H VV I+G + GAVSAAP+GSASILPISWMYI MMG + L AS
Sbjct: 722 PIGVRAHLAPFVANHPVVPIDGPHPQNGAVSAAPWGSASILPISWMYIAMMGPQ-LADAS 780
Query: 783 QVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDYGF 842
+VAIL ANY+A L AFPVLYTGR+ RVAHECILD+RPLK TGI+E D+AKRL+DYGF
Sbjct: 781 EVAILAANYLARHLSGAFPVLYTGRNERVAHECILDLRPLKALTGITEEDVAKRLMDYGF 840
Query: 843 HAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNAPH 902
HAPTMSFPV GTLMVEPTESESK ELDRFI AML+IRAEI++V+ G WP E+NPL APH
Sbjct: 841 HAPTMSFPVPGTLMVEPTESESKAELDRFIGAMLSIRAEINEVQNGNWPAEENPLKGAPH 900
Query: 903 IQSELVAEWAHPYSREVAVFPAG--VADKYWPTVKRLDDVYGDRNLFCSCVPISEYQ 957
+++ W PYS AV P A KYWP V R+D+VYGDRNLFC+CVP+ +Y+
Sbjct: 901 TLADITGVWERPYSIVQAVTPDAHTKAHKYWPVVNRVDNVYGDRNLFCACVPVDDYR 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: 2325
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 PfGW456L13_904 (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.2594.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 1533.2 0.0 0 1533.1 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 Glycine dehydrogenase [decarboxy
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 Glycine dehydrogenase [decarboxylating] (glycine cleavage syst
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1533.1 0.0 0 0 1 939 [] 19 950 .. 19 950 .. 0.99
Alignments for each domain:
== domain 1 score: 1533.1 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelk 56
rhlGpd+aeq+ ml++lG + +lieq vp+ irl+rpl l+ + e +ala+l+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 19 RHLGPDAAEQQAMLDSLGLGSRVDLIEQTVPPGIRLNRPLDLPPALDEEAALAKLR 74
9******************************************************* PP
TIGR00461 57 kiasknkkvksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleall 112
a++n++ +s iG+Gy +t++p vi+rn+lenpgwytaytpyqpei+qGrleall
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 75 GYAEQNQVWTSLIGMGYHGTLTPAVILRNVLENPGWYTAYTPYQPEIAQGRLEALL 130
******************************************************** PP
TIGR00461 113 nfqtvvldltGlevanaslldegtaaaeamalsfrvskkkankfvvakdvhpqtle 168
nfq++++dltGle+anasllde+taaaeamal++rv+k+k+n f+v++++hpqt++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 131 NFQQLTIDLTGLELANASLLDEATAAAEAMALAKRVAKSKSNLFFVDENCHPQTIS 186
******************************************************** PP
TIGR00461 169 vvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrka 224
vv+trae +g+++ivd ++++k++ +v+G+llqyp t+Gei+d++ lid+l+ ++a
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 187 VVQTRAEGFGFDLIVDTVDNLKRH-QVFGALLQYPDTHGEIHDLRPLIDHLHAQQA 241
**************9999888776.6****************************** PP
TIGR00461 225 lvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrkl 280
l +va+dll+l lltppg+lGad+v+Gs+qrfGvp+GyGGphaaffa++deykr +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 242 LACVATDLLSLLLLTPPGELGADVVFGSSQRFGVPMGYGGPHAAFFASRDEYKRAI 297
******************************************************** PP
TIGR00461 281 pGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhG 336
pGri+Gvskda Gntalr+alqtreqhirr+ka+snictaqvllan+as yavyhG
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 298 PGRIIGVSKDARGNTALRMALQTREQHIRREKANSNICTAQVLLANIASFYAVYHG 353
******************************************************** PP
TIGR00461 337 pkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaee 392
p Glk+ia+r++rlt ila+gl+r++ n ++fdtlt+evg + ++ ++a++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 354 PEGLKRIAQRVHRLTCILATGLERNGIVRVNRHFFDTLTLEVGGTQT-AIIESARA 408
*******************************************8877.89999*** PP
TIGR00461 393 aeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvan.sfp 447
a+inlr + +++g++ldet + v +l++v++g d +gls++ l+ +v +p
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 409 AQINLRILGRGQLGLSLDETCDEGTVAKLFDVFLGAD-HGLSIDDLDAEVLPgGIP 463
***********************************87.***********98769** PP
TIGR00461 448 aellrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnata 503
+ l r++ +lr++vf +hsete+lryl++le+kdlalnqsmiplGsctmklnat
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 464 QGLARTSPYLRHPVFSAHHSETEMLRYLKQLENKDLALNQSMIPLGSCTMKLNATS 519
******************************************************** PP
TIGR00461 504 emlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdaislqpnsGaqGe 559
em+pitwp+fa++hpf p eq+ Gy +i +le wl+ itGfdai++qpnsGaqGe
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 520 EMIPITWPQFANLHPFVPKEQAAGYGLMIEELERWLCAITGFDAICMQPNSGAQGE 575
******************************************************** PP
TIGR00461 560 yaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidl 615
yaGl +ir+yhesr+++ r+iclip sahGtnpasa+maG++vv v+cd+ Gn+dl
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 576 YAGLLAIRKYHESRQQGGRDICLIPSSAHGTNPASAQMAGMRVVIVECDEAGNVDL 631
******************************************************** PP
TIGR00461 616 vdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaq 671
dlk+ka +a+++la++m typst+Gv+ee+i e+++++h+ GGqvy+dGan+naq
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 632 DDLKEKAAQAAEKLACLMATYPSTHGVYEEGISEICEVIHQHGGQVYMDGANLNAQ 687
******************************************************** PP
TIGR00461 672 vGltspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvve 727
vGl++p+d+Gadv+h+nlhktf+iphGGGGpgmgpigv++hlapf+ + + vv
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 688 VGLARPADIGADVSHMNLHKTFCIPHGGGGPGMGPIGVRAHLAPFVAN---HPVVP 740
************************************************...78899 PP
TIGR00461 728 legesksigavsaapyGsasilpisymyikmmGaeGlkkasevailnanylakrlk 783
++g + + gavsaap+Gsasilpis+myi+mmG++ l asevail+anyla+ l
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 741 IDGPHPQNGAVSAAPWGSASILPISWMYIAMMGPQ-LADASEVAILAANYLARHLS 795
**********************************8.99****************** PP
TIGR00461 784 daykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaG 839
a+++l++gr+ervahecildlr+lk+ +gi ++dvakrl+dyGfhapt+sfpv+G
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 796 GAFPVLYTGRNERVAHECILDLRPLKALTGITEEDVAKRLMDYGFHAPTMSFPVPG 851
******************************************************** PP
TIGR00461 840 tlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqsliv 895
tlmvepteses+ eldrfi am++i++ei++v++G++++e+n+lk aph+l + i+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 852 TLMVEPTESESKAELDRFIGAMLSIRAEINEVQNGNWPAEENPLKGAPHTLAD-IT 906
*************************************************8875.9* PP
TIGR00461 896 aewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
+ w pys +a+ p + +k +k+wp v+r+d++yGdrnl+c+c
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_904 907 GVWERPYSIVQAVTPDAHTKAHKYWPVVNRVDNVYGDRNLFCAC 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 0.04s 00:00:00.10 Elapsed: 00:00:00.10
# Mc/sec: 8.90
//
[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