Align Glycine dehydrogenase (decarboxylating), mitochondrial; Glycine cleavage system P protein; Glycine decarboxylase; Glycine dehydrogenase (aminomethyl-transferring); EC 1.4.4.2 (characterized)
to candidate CA265_RS25185 CA265_RS25185 glycine dehydrogenase (aminomethyl-transferring)
Query= SwissProt::P26969
(1057 letters)
>FitnessBrowser__Pedo557:CA265_RS25185
Length = 958
Score = 1117 bits (2889), Expect = 0.0
Identities = 565/958 (58%), Positives = 695/958 (72%), Gaps = 13/958 (1%)
Query: 96 DTFPRRHNSATPDEQTKMAESVGFDTLDSLVDATVPKSIRLKEMKFNKFDGGLTEGQMIE 155
+ F RH + + +M ++VG +++D L++ TVP +IRLK+ +E + +
Sbjct: 9 EDFQNRHIAPNEADTAEMLQTVGVNSIDELIEQTVPTAIRLKQPL--NLPAAKSETEYLG 66
Query: 156 HMKDLASKNKVFKSFIGMGYYNTHVPPVILRNIMENPAWYTQYTPYQAEISQGRLESLLN 215
+K + NKVFKSFIG GYY+T P VILRN+ ENP WYTQYTPYQAEI+QGRL++LLN
Sbjct: 67 ALKQTSLLNKVFKSFIGQGYYDTITPGVILRNVFENPGWYTQYTPYQAEIAQGRLQALLN 126
Query: 216 FQTMITDLTGLPMSNASLLDEGTAAAEAMSMCNNIQKGK-KKTFIIASNCHPQTIDICQT 274
FQTM+ DLTG+ ++NASLLDEGTAAAEAM M +++K + K F +++ PQTIDI +T
Sbjct: 127 FQTMVIDLTGMEIANASLLDEGTAAAEAMFMQYSLRKNQGAKKFFVSALLFPQTIDILKT 186
Query: 275 RADGFELKVVVKDLKDIDYKSGDVCGVLVQYPGTEGEVLDYGEFIKKAHANEVKVVMASD 334
RA+ + +++V+ D + D G +VQYP GEV DY +F H +K+ + +D
Sbjct: 187 RANPYGIELVIGSHLDF-VATEDFFGAIVQYPAGNGEVFDYKDFASALHNQNIKLTVVAD 245
Query: 335 LLALTVLKPPGEFGADIVVGSAQRFGVPMGYGGPHAAFLATSQEYKRMMPGRIIGVSVDS 394
+L+LT+L PPGE+GAD+VVG+ QR G+PMG+GGPHAAF AT +EYKR +PGRIIGV++DS
Sbjct: 246 ILSLTLLTPPGEWGADVVVGTTQRLGIPMGFGGPHAAFFATKEEYKRNIPGRIIGVTIDS 305
Query: 395 SGKQALRMAMQTREQHIRRDKATSNICTAQALLANMAAMYAVYHGPEGLKAIAQRVHGLA 454
G ALRMA+QTREQHIRRDKATSNICTAQALLA MA YA YHGP+GLKAIA+R HGLA
Sbjct: 306 HGDYALRMALQTREQHIRRDKATSNICTAQALLAIMAGFYAAYHGPKGLKAIAERTHGLA 365
Query: 455 GVFALGLKKLGLEVQDLGFFDTVKVKTSNAKA-IADAAIKSEINLRVVDGNTITAAFDET 513
A LK LG E + +FDT++ + K I I +EINL V GN T +FDET
Sbjct: 366 ISLASTLKGLGFEQLNSAYFDTIRFDLGDLKGGIHSGCIDNEINLNYV-GNVATISFDET 424
Query: 514 TTLEDVDKLFKVFAGGKPVSFTAASLAPEFQNAIPSGLVRESPYLTHPIFNTYQTEHELL 573
+T EDV + K+FA K ++ +A + IPS L R S YLTHPIFN + +EHE+L
Sbjct: 425 STFEDVALIAKIFAKVKAIAADQVEVAENVETVIPSALQRTSAYLTHPIFNAHHSEHEML 484
Query: 574 RYIHRLQSKDLSLCHSMIPLGSCTMKLNATTEMMPVTWPSFTDLHPFAPTEQAQGYQEMF 633
RYI L++KDLSLCHSMI LGSCTMKLNAT EM+PVTW F +HPFAP +Q GY +F
Sbjct: 485 RYIKSLEAKDLSLCHSMIALGSCTMKLNATAEMIPVTWSHFGRIHPFAPADQVLGYYSVF 544
Query: 634 NNLGDLLCTITGFDSFSLQPNAGAAGEYAGLMVIRAYHLSRGDHHRNVCIIPASAHGTNP 693
N L L ITGF + SLQPNAGA GEYAGLMVIRAYH RGD HRNV +IPASAHGTNP
Sbjct: 545 NELDKWLSEITGFAAMSLQPNAGAQGEYAGLMVIRAYHQDRGDFHRNVALIPASAHGTNP 604
Query: 694 ASAAMVGMKIVTIGTDAKGNINIEELKKAAEKHKDNLSAFMVTYPSTHGVYEEGIDDICK 753
ASAAM MKIV + + GNI++E+LK AE HKDNLS MVTYPSTHGV+EE I +IC+
Sbjct: 605 ASAAMADMKIVVVKSLENGNIDVEDLKAKAELHKDNLSCLMVTYPSTHGVFEESIIEICE 664
Query: 754 IIHDNGGQVYMDGANMNAQVGLTSPGWIGADVCHLNLHKTFCIPHGGGGPGMGPIGVKKH 813
IH NGGQVYMDGANMNAQVGLTSP IGADVCHLNLHKTFCIPHGGGGPGMGPIGV KH
Sbjct: 665 TIHANGGQVYMDGANMNAQVGLTSPANIGADVCHLNLHKTFCIPHGGGGPGMGPIGVAKH 724
Query: 814 LAPFLPSHPVVPTGGIPAPENPQPLGSISAAPWGSALILPISYTYIAMMGSQGLTDASKI 873
L P+LP H VV + + + ++S+APWGSA IL IS+ YIAMMG++GLT+A+K
Sbjct: 725 LVPYLPGHAVVDI------DKGKSISAVSSAPWGSASILIISHAYIAMMGAEGLTNATKY 778
Query: 874 AILNANYMAKRLESYYPVLFRGVNGTVAHEFIIDLRGFKNTAGIEPEDVAKRLMDYGFHG 933
AILNANYM RLE +YPVL+ G G AHE I+D R FK GIE D+AKRLMDYGFH
Sbjct: 779 AILNANYMKARLEQHYPVLYSGAQGRCAHEMILDCRSFK-AFGIEVTDIAKRLMDYGFHA 837
Query: 934 PTMSWPVAGTLMIEPTESESKAELDRFCDALISIRKEIAEVEKGNADVHNNVLKGAPHPP 993
PT+S+PVAGTLM+EPTESE K ELDRFCDALI+I+ EI VE G D +N LK APH
Sbjct: 838 PTVSFPVAGTLMVEPTESEPKHELDRFCDALIAIKNEITAVENGTLDKVDNPLKNAPHTV 897
Query: 994 SLLMADAWTKPYSREYAAFPAAWLRGAKFWPTTGRVDNVYGDRNLVCTLLPASQAVEE 1051
S++ A+ W YSR+ AAFP ++ KFWP+ GRV++ +GDR L+C P +EE
Sbjct: 898 SVITANEWDHAYSRQTAAFPLPYVLARKFWPSVGRVNDSHGDRALICACPPIESYLEE 955
Lambda K H
0.317 0.133 0.393
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: 2371
Number of extensions: 85
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: 1057
Length of database: 958
Length adjustment: 45
Effective length of query: 1012
Effective length of database: 913
Effective search space: 923956
Effective search space used: 923956
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)
Align candidate CA265_RS25185 CA265_RS25185 (glycine dehydrogenase (aminomethyl-transferring))
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.8623.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 1434.7 1.2 0 1434.5 1.2 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS25185 CA265_RS25185 glycine dehydrogen
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS25185 CA265_RS25185 glycine dehydrogenase (aminomethyl-transferring)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1434.5 1.2 0 0 1 939 [] 14 946 .. 14 946 .. 0.99
Alignments for each domain:
== domain 1 score: 1434.5 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksy 68
rh+ p+ea+ +ml+t+G++++++lieq vp +irl++pl+l+a+++e e l lk+ + nk++ks+
lcl|FitnessBrowser__Pedo557:CA265_RS25185 14 RHIAPNEADTAEMLQTVGVNSIDELIEQTVPTAIRLKQPLNLPAAKSETEYLGALKQTSLLNKVFKSF 81
9******************************************************************* PP
TIGR00461 69 iGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegt 136
iG+Gyy+ti+p vi+rn++enpgwyt ytpyq+ei+qGrl+allnfqt+v+dltG+e+anaslldegt
lcl|FitnessBrowser__Pedo557:CA265_RS25185 82 IGQGYYDTITPGVILRNVFENPGWYTQYTPYQAEIAQGRLQALLNFQTMVIDLTGMEIANASLLDEGT 149
******************************************************************** PP
TIGR00461 137 aaaeamalsfrvskkk.ankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqyp 203
aaaeam + +++ k++ a+kf+v+ + pqt++++ktra+p+gie++++ + ++ + d +G+++qyp
lcl|FitnessBrowser__Pedo557:CA265_RS25185 150 AAAEAMFMQYSLRKNQgAKKFFVSALLFPQTIDILKTRANPYGIELVIGSHLDFVATEDFFGAIVQYP 217
**************9999************************************************** PP
TIGR00461 204 atdGeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffa 271
a +Ge++dyk++ ++l+++++ ++v ad+l+ltlltppg+ Gad+v+G++qr+G+p+G+GGphaaffa
lcl|FitnessBrowser__Pedo557:CA265_RS25185 218 AGNGEVFDYKDFASALHNQNIKLTVVADILSLTLLTPPGEWGADVVVGTTQRLGIPMGFGGPHAAFFA 285
******************************************************************** PP
TIGR00461 272 vkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhGpkG 339
+k+eykr++pGri+Gv+ d++G+ alr+alqtreqhirrdkatsnictaq+lla +a ya yhGpkG
lcl|FitnessBrowser__Pedo557:CA265_RS25185 286 TKEEYKRNIPGRIIGVTIDSHGDYALRMALQTREQHIRRDKATSNICTAQALLAIMAGFYAAYHGPKG 353
******************************************************************** PP
TIGR00461 340 lkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeeaeinlravvltevgi 407
lk ia+r + l+ la +lk ++e n+ yfdt++ ++g+ + + + einl v + +i
lcl|FitnessBrowser__Pedo557:CA265_RS25185 354 LKAIAERTHGLAISLASTLKGLGFEQLNSAYFDTIRFDLGDLKG-GIHSGCIDNEINLNY-VGNVATI 419
*****************************************998.89999999****975.567889* PP
TIGR00461 408 aldetttkedvldllkvlagkdnlglsseelsedvansfpaellrddeilrdevfnryhsetellryl 475
++det t edv + k++a + + ++ e+ e+v++ +p++l+r++ +l++++fn +hse e+lry+
lcl|FitnessBrowser__Pedo557:CA265_RS25185 420 SFDETSTFEDVALIAKIFAKVKAIAADQVEVAENVETVIPSALQRTSAYLTHPIFNAHHSEHEMLRYI 487
********************999999999*************************************** PP
TIGR00461 476 hrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveit 543
++le+kdl+l +smi lGsctmklnataem+p+tw +f++ihpfapa+qv Gy ++ +l+kwl+eit
lcl|FitnessBrowser__Pedo557:CA265_RS25185 488 KSLEAKDLSLCHSMIALGSCTMKLNATAEMIPVTWSHFGRIHPFAPADQVLGYYSVFNELDKWLSEIT 555
******************************************************************** PP
TIGR00461 544 GfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeG 611
Gf a+slqpn+GaqGeyaGl vir yh+ rg+ hrn+ lipasahGtnpasaama +k+v+vk +++G
lcl|FitnessBrowser__Pedo557:CA265_RS25185 556 GFAAMSLQPNAGAQGEYAGLMVIRAYHQDRGDFHRNVALIPASAHGTNPASAAMADMKIVVVKSLENG 623
******************************************************************** PP
TIGR00461 612 nidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgd 679
nid++dlkakae + d+l+++mvtypst+Gvfee+i e+++ +h GGqvy+dGanmnaqvGltsp++
lcl|FitnessBrowser__Pedo557:CA265_RS25185 624 NIDVEDLKAKAELHKDNLSCLMVTYPSTHGVFEESIIEICETIHANGGQVYMDGANMNAQVGLTSPAN 691
******************************************************************** PP
TIGR00461 680 lGadvchlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsas 747
+Gadvchlnlhktf+iphGGGGpgmgpigv hl+p+lp++ +v++ + ksi avs+ap+Gsas
lcl|FitnessBrowser__Pedo557:CA265_RS25185 692 IGADVCHLNLHKTFCIPHGGGGPGMGPIGVAKHLVPYLPGHAVVDI----DKGKSISAVSSAPWGSAS 755
****************************************777665....35689************* PP
TIGR00461 748 ilpisymyikmmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagie 815
il is++yi+mmGaeGl+ a++ ailnany+ +rl+++y++l+ g ++r+ahe+ild r +k+ gie
lcl|FitnessBrowser__Pedo557:CA265_RS25185 756 ILIISHAYIAMMGAEGLTNATKYAILNANYMKARLEQHYPVLYSGAQGRCAHEMILDCRSFKAF-GIE 822
**************************************************************99.*** PP
TIGR00461 816 aldvakrlldyGfhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednil 883
+ d+akrl+dyGfhapt+sfpvaGtlmveptese ++eldrf+da+iaik+ei av +G++++ dn+l
lcl|FitnessBrowser__Pedo557:CA265_RS25185 823 VTDIAKRLMDYGFHAPTVSFPVAGTLMVEPTESEPKHELDRFCDALIAIKNEITAVENGTLDKVDNPL 890
******************************************************************** PP
TIGR00461 884 knaphslqslivaewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
knaph++ + ew ++ysr+ aa+p+p++ kfwp+v+r++d +Gdr l+c+c
lcl|FitnessBrowser__Pedo557:CA265_RS25185 891 KNAPHTVSVITANEWDHAYSRQTAAFPLPYVLARKFWPSVGRVNDSHGDRALICAC 946
******99999999*****************************************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (958 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: 00:00:00.07
# Mc/sec: 12.63
//
[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