Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate PP_5192 PP_5192 glycine dehydrogenase
Query= CharProtDB::CH_003480
(957 letters)
>FitnessBrowser__Putida:PP_5192
Length = 957
Score = 1246 bits (3225), Expect = 0.0
Identities = 620/957 (64%), Positives = 751/957 (78%), Gaps = 8/957 (0%)
Query: 4 TLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAPAT 63
+L QL+ F+ RH+GPDA +QQ MLNA+G S N L Q VP DI+L P + A
Sbjct: 6 SLHQLQELNPFLRRHLGPDATEQQAMLNALGIASRNELIEQTVPPDIRLNRPLDLPAALD 65
Query: 64 EYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVSQGR 123
E AALA+L A +N+ +TS IGMGY P VILRN+LENPGWYTAYTPYQPE++QGR
Sbjct: 66 EQAALAKLAGYAEQNQVWTSLIGMGYHGTITPTVILRNVLENPGWYTAYTPYQPEIAQGR 125
Query: 124 LEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVHPQT 183
LEALLNFQQ+ +DLTGL +A+ASLLDEATAAAEAMA+AKRV++ K+ N FF HPQT
Sbjct: 126 LEALLNFQQMVIDLTGLPLANASLLDEATAAAEAMALAKRVARNKS-NAFFADEHCHPQT 184
Query: 184 LDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKIVV 243
L V++TRAE FGFE+IVD + H VFG LLQ T GE+ D LI +L S++ +
Sbjct: 185 LSVLKTRAEGFGFELIVDSVDNLAKHS-VFGALLQYPDTHGEVRDLRPLIDQLHSQQALA 243
Query: 244 SVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRIIG 303
VAAD+++LV+L PG+ GAD+V GS QRFGVPMGYGGPHAA+FA +D+YKR+MPGRIIG
Sbjct: 244 CVAADLLSLVVLAPPGELGADVVLGSTQRFGVPMGYGGPHAAYFACRDDYKRAMPGRIIG 303
Query: 304 VSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRIANR 363
VS+DA GNTALRMA+QTREQHIRREKANSNICT+QVLLANIA YAVYHGP GL+RIA R
Sbjct: 304 VSRDARGNTALRMALQTREQHIRREKANSNICTAQVLLANIAGFYAVYHGPEGLQRIAQR 363
Query: 364 IHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVAD-KAGVLTRAEAAEINLRSDILNAVGI 422
+HRLT ILAAGL+ KG+K + H+FDTL + V +A ++ AEAA INLR +G+
Sbjct: 364 VHRLTFILAAGLEAKGIKRLNQHFFDTLTLNVGGAQAAIIESAEAAHINLRILGRGHLGV 423
Query: 423 TLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDVAHDSRSIQPAMLRDDEILTHPVFNRY 482
+LDET T + V++L ++ LG +HGL+I LD+ + I +++R L HPVFN +
Sbjct: 424 SLDETCTEQTVLRLLDIFLGVDHGLEITALDQLALPEG--IPASLVRRTPFLAHPVFNLH 481
Query: 483 HSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPEQA 542
HSETEM+RY+ LE KDLALNQ+MIPLGSCTMKLNA +EMIPITWP FA+LHPF P QA
Sbjct: 482 HSETEMLRYLKQLENKDLALNQSMIPLGSCTMKLNATSEMIPITWPGFAQLHPFAPAAQA 541
Query: 543 EGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIPA 602
GY+ MI +L WL +TG+DA+CMQPNSGAQGEYAGL+AI YH SR++ R +CLIP+
Sbjct: 542 AGYKAMIDELESWLCAITGFDAICMQPNSGAQGEYAGLMAITRYHCSRHQPMRTLCLIPS 601
Query: 603 SAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVYEE 662
SAHGTNPASA MAGM+VV+V CD +GN+DL DL+AKA AG+ LSC+M+TYPSTHGVYEE
Sbjct: 602 SAHGTNPASAQMAGMEVVIVDCDNDGNVDLADLKAKAHAAGERLSCLMITYPSTHGVYEE 661
Query: 663 TIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGMG 722
IRE+C+VVHQ+GGQVY+DGAN+NAQVG+ P IGADVSH+NLHKTFCIPHGGGGPGMG
Sbjct: 662 GIREICDVVHQYGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPHGGGGPGMG 721
Query: 723 PIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKKAS 782
PIG++AHL PFV H VV + G+ AVSAAP+GSASILPISWMYI MMG + L AS
Sbjct: 722 PIGIRAHLKPFVASHPVVPVPGLDPNNSAVSAAPWGSASILPISWMYIAMMGPQ-LADAS 780
Query: 783 QVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDYGF 842
+VAIL+ANY+AS+L AFPVLY GR+ RVAHECILD+RPLK TGISE D+AKRL+DYGF
Sbjct: 781 EVAILSANYLASQLGAAFPVLYRGRNQRVAHECILDLRPLKALTGISEEDVAKRLMDYGF 840
Query: 843 HAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNAPH 902
HAPTMSFPV GTLMVEPTESESK ELDRF++AMLAIRAEID+V+ G WP E+NPL +APH
Sbjct: 841 HAPTMSFPVPGTLMVEPTESESKAELDRFVEAMLAIRAEIDEVQQGNWPAENNPLKHAPH 900
Query: 903 IQSELVAEWAHPYSREVAVFPAGVA--DKYWPTVKRLDDVYGDRNLFCSCVPISEYQ 957
++++ W PYS E AV P+ KYWP V R+D+VYGDRNLFC+CVP+ Y+
Sbjct: 901 TLADVLGVWDRPYSLEQAVAPSAHVRQHKYWPAVNRVDNVYGDRNLFCACVPVEAYR 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: 2309
Number of extensions: 90
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: 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 PP_5192 PP_5192 (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.14003.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 1540.0 0.0 0 1539.8 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_5192 PP_5192 glycine dehydrogenase
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5192 PP_5192 glycine dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1539.8 0.0 0 0 1 939 [] 19 950 .. 19 950 .. 0.99
Alignments for each domain:
== domain 1 score: 1539.8 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyya 75
rhlGpd++eq+ ml++lG+ + n+lieq vp+dirl+rpl l+a+ e++ala+l a++n++ +s iG+Gy +
lcl|FitnessBrowser__Putida:PP_5192 19 RHLGPDATEQQAMLNALGIASRNELIEQTVPPDIRLNRPLDLPAALDEQAALAKLAGYAEQNQVWTSLIGMGYHG 93
9************************************************************************** PP
TIGR00461 76 tilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvsk 150
ti+p vi+rn+lenpgwytaytpyqpei+qGrleallnfq++v+dltGl++anasllde+taaaeamal++rv++
lcl|FitnessBrowser__Putida:PP_5192 94 TITPTVILRNVLENPGWYTAYTPYQPEIAQGRLEALLNFQQMVIDLTGLPLANASLLDEATAAAEAMALAKRVAR 168
*************************************************************************** PP
TIGR00461 151 kkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkal 225
+k+n+f+ ++++hpqtl+v+ktrae +g+e+ivd ++++ k+ +v+G+llqyp t+Ge+ d++ lid+l+s++al
lcl|FitnessBrowser__Putida:PP_5192 169 NKSNAFFADEHCHPQTLSVLKTRAEGFGFELIVDSVDNLAKH-SVFGALLQYPDTHGEVRDLRPLIDQLHSQQAL 242
*********************************999888775.8******************************* PP
TIGR00461 226 vsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrla 300
+vaadll+l++l ppg+lGad+vlGs+qrfGvp+GyGGphaa+fa++d+ykr +pGri+Gvs+da Gntalr+a
lcl|FitnessBrowser__Putida:PP_5192 243 ACVAADLLSLVVLAPPGELGADVVLGSTQRFGVPMGYGGPHAAYFACRDDYKRAMPGRIIGVSRDARGNTALRMA 317
*************************************************************************** PP
TIGR00461 301 lqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtlt 375
lqtreqhirr+ka+snictaqvllan+a yavyhGp Gl++ia+r++rlt ilaagl+ k+ + n+++fdtlt
lcl|FitnessBrowser__Putida:PP_5192 318 LQTREQHIRREKANSNICTAQVLLANIAGFYAVYHGPEGLQRIAQRVHRLTFILAAGLEAKGIKRLNQHFFDTLT 392
*************************************************************************** PP
TIGR00461 376 vevgekaasevlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelse.dvansfpae 449
++vg a ++ ++ae+a+inlr + +++g++ldet t++ vl ll++++g d +gl++ l++ + + +pa
lcl|FitnessBrowser__Putida:PP_5192 393 LNVGGAQA-AIIESAEAAHINLRILGRGHLGVSLDETCTEQTVLRLLDIFLGVD-HGLEITALDQlALPEGIPAS 465
****8877.8999***************************************88.********9835677***** PP
TIGR00461 450 llrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeq 524
l r +l ++vfn +hsete+lryl++le+kdlalnqsmiplGsctmklnat em+pitwp fa++hpfapa q
lcl|FitnessBrowser__Putida:PP_5192 466 LVRRTPFLAHPVFNLHHSETEMLRYLKQLENKDLALNQSMIPLGSCTMKLNATSEMIPITWPGFAQLHPFAPAAQ 540
*************************************************************************** PP
TIGR00461 525 veGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaG 599
+ Gyk +i +le+wl+ itGfdai++qpnsGaqGeyaGl +i +yh sr + r +clip sahGtnpasa+maG
lcl|FitnessBrowser__Putida:PP_5192 541 AAGYKAMIDELESWLCAITGFDAICMQPNSGAQGEYAGLMAITRYHCSRHQPMRTLCLIPSSAHGTNPASAQMAG 615
*************************************************************************** PP
TIGR00461 600 lkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGl 674
++vv v+cd++Gn+dl dlkaka ag++l+++m+typst+Gv+ee+ire++d+vh++GGqvy+dGan+naqvGl
lcl|FitnessBrowser__Putida:PP_5192 616 MEVVIVDCDNDGNVDLADLKAKAHAAGERLSCLMITYPSTHGVYEEGIREICDVVHQYGGQVYMDGANLNAQVGL 690
*************************************************************************** PP
TIGR00461 675 tspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasil 749
++p+d+Gadv+h+nlhktf+iphGGGGpgmgpig+++hl+pf+ + vv + g + + avsaap+Gsasil
lcl|FitnessBrowser__Putida:PP_5192 691 ARPADIGADVSHMNLHKTFCIPHGGGGPGMGPIGIRAHLKPFVAS---HPVVPVPGLDPNNSAVSAAPWGSASIL 762
********************************************9...77888999999**************** PP
TIGR00461 750 pisymyikmmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrll 824
pis+myi+mmG++ l asevail+anyla++l a+++l++gr++rvahecildlr+lk+ +gi+++dvakrl+
lcl|FitnessBrowser__Putida:PP_5192 763 PISWMYIAMMGPQ-LADASEVAILSANYLASQLGAAFPVLYRGRNQRVAHECILDLRPLKALTGISEEDVAKRLM 836
************8.99*********************************************************** PP
TIGR00461 825 dyGfhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewa 899
dyGfhapt+sfpv+Gtlmvepteses+ eldrf++am+ai++eid+v++G++++e+n+lk aph+l ++ + w
lcl|FitnessBrowser__Putida:PP_5192 837 DYGFHAPTMSFPVPGTLMVEPTESESKAELDRFVEAMLAIRAEIDEVQQGNWPAENNPLKHAPHTLADV-LGVWD 910
****************************************************************99885.589** PP
TIGR00461 900 dpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
pys e+a+ p + ++++k+wp+v+r+d++yGdrnl+c+c
lcl|FitnessBrowser__Putida:PP_5192 911 RPYSLEQAVAPSAHVRQHKYWPAVNRVDNVYGDRNLFCAC 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 0.02s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 10.60
//
[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