Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate WP_011765018.1 AZO_RS06490 glycine dehydrogenase (aminomethyl-transferring)
Query= reanno::Koxy:BWI76_RS23870
(957 letters)
>NCBI__GCF_000061505.1:WP_011765018.1
Length = 959
Score = 1209 bits (3127), Expect = 0.0
Identities = 611/963 (63%), Positives = 741/963 (76%), Gaps = 17/963 (1%)
Query: 1 MTQTLGQLENRDAFIERHIGPDALQQQEMLKTVGADSLNALIGQIVPQDIQLATPPQVGE 60
++ L QLE RDAFI RH+GP+ + M T+G ++ LI Q VP I+L +
Sbjct: 6 LSAPLAQLEQRDAFIHRHLGPNPDEIARMCATIGVPDIDTLIAQTVPASIRLPQALPLAG 65
Query: 61 ATTEFAALAELKAIAGRNKRFKSYIGMGYTAVQLPPVIQRNMLENPGWYTAYTPYQPEVS 120
E AL L+ +A RN KS IGMGY P VI RN++ENPGWYTAYTPYQ E++
Sbjct: 66 PRPEHEALELLRGLAERNAVKKSMIGMGYYGTHTPAVILRNVMENPGWYTAYTPYQAEIA 125
Query: 121 QGRLESLLNFQQVTLDLTGLDIASASLLDEATAAAEAMAMAKRVSKLKNANRFFVAADVH 180
QGRLE+LLNFQQ+ +DLTGL++A+ASLLDEATAAAEAMAMA+RVSK K+ N FFV A
Sbjct: 126 QGRLEALLNFQQMVIDLTGLELANASLLDEATAAAEAMAMARRVSKSKS-NAFFVDAACF 184
Query: 181 PQTLDVVRTRAETFGFDVIVDDAEKALDHQDVFGVLLQQVGTTGEVHDYSKLIADLKARK 240
PQTLDVVRTRAE FGF++++ DA +A +H DVFG LLQ G V D +IA LK R
Sbjct: 185 PQTLDVVRTRAEYFGFNLVLGDAAEAAEH-DVFGALLQYPNVHGTVGDLGAVIAALKGRG 243
Query: 241 VIVSVAADFMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEFKRSMPGR 300
I ++A D MALVLL +PG GADI GSAQRFGVPMG+GGPHAAFFA ++ + RSMPGR
Sbjct: 244 AITALATDLMALVLLKSPGAMGADIALGSAQRFGVPMGFGGPHAAFFATREAYVRSMPGR 303
Query: 301 IIGVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVFHGPAGLKRI 360
IIGVS+DA G TALRM +QTREQHIRREKANSNICTSQVLLAN+A YAV+HGP GL+ I
Sbjct: 304 IIGVSRDARGKTALRMTLQTREQHIRREKANSNICTSQVLLANMAGFYAVYHGPQGLRTI 363
Query: 361 ASRIHRLTDILADGLQKKGLKLRHAHYFDTLCVEVADKAA-VLARAEALRINLRSDIHHA 419
A+RIHRL +L GL+ G +R + YFDTL V+ ++AA +L+ A+ NLR H
Sbjct: 364 AARIHRLAALLDAGLRAAGFAVRSSAYFDTLEVDADERAAAILSAADQAGFNLRDAGHGR 423
Query: 420 VGITLDEATTREDVLNLFRAILGDDHGLDIDTLDKDVALDSRSIPASMLRDDAILTHPVF 479
+G+++DE TTR D+ + A G + +D++TL AL PA +LRDDAIL HPVF
Sbjct: 424 IGLSVDETTTRADIAAVL-ACFGAN--VDLETLTPASAL-----PAGLLRDDAILAHPVF 475
Query: 480 NRYHSETEMMRYMHALERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPV 539
N +H+E EM+RY+ L+ +DLAL+ +MI LGSCTMKLNA +EMIP+TWP FA LHPF P
Sbjct: 476 NTHHTEHEMLRYLKKLQNRDLALDHSMISLGSCTMKLNATSEMIPVTWPAFANLHPFAPP 535
Query: 540 DQAEGYHQMIAQLSDWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICL 599
Q +GY MI L+D+L +TG+DA+CMQPNSGAQGEYAGL+AIR YH SR E HRD+CL
Sbjct: 536 AQTQGYMAMIDGLADYLKAVTGFDAICMQPNSGAQGEYAGLVAIRRYHASRGEAHRDVCL 595
Query: 600 IPSSAHGTNPASAQMAGMQVVVVACDKNGNIDLADLRAKAEQHAANLSCIMVTYPSTHGV 659
IP SAHGTNPA+AQM GM+VVVV CD +GN+DL +L++KA Q+A L+ +M+TYPSTHGV
Sbjct: 596 IPRSAHGTNPATAQMCGMEVVVVDCDGSGNVDLENLQSKAAQYADRLAAMMITYPSTHGV 655
Query: 660 YEETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGP 719
+EE IRE+C VH GGQVY+DGAN+NAQVG+TSP IGADVSH+NLHKTFCIPHGGGGP
Sbjct: 656 FEENIREICAAVHAHGGQVYMDGANLNAQVGLTSPAIIGADVSHMNLHKTFCIPHGGGGP 715
Query: 720 GMGPIGVKSHLAQFVPGHSVV---QIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAE 776
GMGPIG+K+HLA F+ H+V E + QGAVSAAPFGSASILPISWMYI MMG E
Sbjct: 716 GMGPIGLKAHLAPFMADHAVAATGDAERVNKGQGAVSAAPFGSASILPISWMYITMMGGE 775
Query: 777 GLKQASQMAILNANYIATRLKDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKR 836
GLK+A+++AILNANY+A+RL +PVLYTG GRVAHECILDIRP+K TGISE+DIAKR
Sbjct: 776 GLKRATEVAILNANYLASRLAPHYPVLYTGSRGRVAHECILDIRPIKAATGISEVDIAKR 835
Query: 837 LIDFGFHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRGEIDRVKAGEWPLEDNP 896
L+D+GFHAPTMSFPVAGT+MVEPTESE ELDRFI+AM+AIRGEI R++ GEWP +DNP
Sbjct: 836 LMDYGFHAPTMSFPVAGTIMVEPTESEDLAELDRFIEAMVAIRGEILRIERGEWPADDNP 895
Query: 897 LVNAPHTQGELVSA-WNHPYARELAVFPAG--LNNKYWPTVKRLDDVYGDRNLFCSCVPM 953
L NAPHTQGE+ +A W PY+RE AVFP +NK+WP+V R+DDVYGDRNLFC+CVPM
Sbjct: 896 LRNAPHTQGEIAAAQWERPYSREQAVFPLPWVADNKFWPSVNRIDDVYGDRNLFCACVPM 955
Query: 954 SEY 956
Y
Sbjct: 956 EAY 958
Lambda K H
0.320 0.135 0.399
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: 2172
Number of extensions: 83
Number of successful extensions: 9
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: 959
Length adjustment: 44
Effective length of query: 913
Effective length of database: 915
Effective search space: 835395
Effective search space used: 835395
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 WP_011765018.1 AZO_RS06490 (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.29286.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 1488.9 0.0 0 1488.7 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011765018.1 AZO_RS06490 glycine dehydrogenas
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000061505.1:WP_011765018.1 AZO_RS06490 glycine dehydrogenase (aminomethyl-transferring)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1488.7 0.0 0 0 1 939 [] 22 952 .. 22 952 .. 0.99
Alignments for each domain:
== domain 1 score: 1488.7 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyi 69
rhlGp++ e +m t+G+ d++ li q vp +irl+++l l p e+eal+ l+ +a++n + ks i
lcl|NCBI__GCF_000061505.1:WP_011765018.1 22 RHLGPNPDEIARMCATIGVPDIDTLIAQTVPASIRLPQALPLAGPRPEHEALELLRGLAERNAVKKSMI 90
9******************************************************************** PP
TIGR00461 70 GkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaa 138
G+Gyy+t +p vi+rn++enpgwytaytpyq+ei+qGrleallnfq++v+dltGle+anasllde+taa
lcl|NCBI__GCF_000061505.1:WP_011765018.1 91 GMGYYGTHTPAVILRNVMENPGWYTAYTPYQAEIAQGRLEALLNFQQMVIDLTGLELANASLLDEATAA 159
********************************************************************* PP
TIGR00461 139 aeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdG 207
aeama++ rvsk+k+n+f+v+ + pqtl+vv+trae +g++++ +da + + dv+G+llqyp +G
lcl|NCBI__GCF_000061505.1:WP_011765018.1 160 AEAMAMARRVSKSKSNAFFVDAACFPQTLDVVRTRAEYFGFNLVLGDAAEAAE-HDVFGALLQYPNVHG 227
************************************************99876.59************* PP
TIGR00461 208 eildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdey 276
++ d+ a+i +lk r a+ ++a+dl+al+ll++pg +Gadi+lGsaqrfGvp+G+GGphaaffa+++ y
lcl|NCBI__GCF_000061505.1:WP_011765018.1 228 TVGDLGAVIAALKGRGAITALATDLMALVLLKSPGAMGADIALGSAQRFGVPMGFGGPHAAFFATREAY 296
********************************************************************* PP
TIGR00461 277 krklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniar 345
r++pGri+Gvs+da G+talr++lqtreqhirr+ka+snict+qvllan+a yavyhGp+Gl+ ia
lcl|NCBI__GCF_000061505.1:WP_011765018.1 297 VRSMPGRIIGVSRDARGKTALRMTLQTREQHIRREKANSNICTSQVLLANMAGFYAVYHGPQGLRTIAA 365
********************************************************************* PP
TIGR00461 346 rifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeeaeinlravvltevgialdettt 414
ri+rl+++l agl+ ++ +r + yfdtl v+ e+aa ++l aa++a+ nlr + +g+++dettt
lcl|NCBI__GCF_000061505.1:WP_011765018.1 366 RIHRLAALLDAGLRAAGFAVRSSAYFDTLEVDADERAA-AILSAADQAGFNLRDAGHGRIGLSVDETTT 433
********************************888877.9***************************** PP
TIGR00461 415 kedvldllkvlagkdnlglsseelsedvansfpaellrddeilrdevfnryhsetellrylhrleskdl 483
++d+ +l + + + ++ e+l+ a+++pa llrdd il ++vfn++h+e e+lryl++l+++dl
lcl|NCBI__GCF_000061505.1:WP_011765018.1 434 RADIAAVLACFGA-N---VDLETLTP--ASALPAGLLRDDAILAHPVFNTHHTEHEMLRYLKKLQNRDL 496
**********988.3...67888875..678************************************** PP
TIGR00461 484 alnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdaislqp 552
al++smi lGsctmklnat em+p+twp fa++hpfap+ q++Gy +i l+++l +tGfdai++qp
lcl|NCBI__GCF_000061505.1:WP_011765018.1 497 ALDHSMISLGSCTMKLNATSEMIPVTWPAFANLHPFAPPAQTQGYMAMIDGLADYLKAVTGFDAICMQP 565
********************************************************************* PP
TIGR00461 553 nsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlkak 621
nsGaqGeyaGl +ir+yh srge hr++clip sahGtnpa+a+m+G++vv+v+cd+ Gn+dl++l++k
lcl|NCBI__GCF_000061505.1:WP_011765018.1 566 NSGAQGEYAGLVAIRRYHASRGEAHRDVCLIPRSAHGTNPATAQMCGMEVVVVDCDGSGNVDLENLQSK 634
********************************************************************* PP
TIGR00461 622 aekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlh 690
a +++d+laa+m+typst+Gvfee ire++ vh GGqvy+dGan+naqvGltsp+ +Gadv+h+nlh
lcl|NCBI__GCF_000061505.1:WP_011765018.1 635 AAQYADRLAAMMITYPSTHGVFEENIREICAAVHAHGGQVYMDGANLNAQVGLTSPAIIGADVSHMNLH 703
********************************************************************* PP
TIGR00461 691 ktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmm 759
ktf+iphGGGGpgmgpig+k+hlapf+ + + + + e +k +gavsaap+Gsasilpis+myi mm
lcl|NCBI__GCF_000061505.1:WP_011765018.1 704 KTFCIPHGGGGPGMGPIGLKAHLAPFMADHAVAATGDAERVNKGQGAVSAAPFGSASILPISWMYITMM 772
********************************************************************* PP
TIGR00461 760 GaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGf 828
G eGlk+a+evailnanyla+rl +y++l++g+ +rvahecild+r++k+ +gi+++d+akrl+dyGf
lcl|NCBI__GCF_000061505.1:WP_011765018.1 773 GGEGLKRATEVAILNANYLASRLAPHYPVLYTGSRGRVAHECILDIRPIKAATGISEVDIAKRLMDYGF 841
********************************************************************* PP
TIGR00461 829 haptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivae 897
hapt+sfpvaGt+mveptese+l eldrfi+am+ai+ ei + Ge++++dn+l+naph+ + +a+
lcl|NCBI__GCF_000061505.1:WP_011765018.1 842 HAPTMSFPVAGTIMVEPTESEDLAELDRFIEAMVAIRGEILRIERGEWPADDNPLRNAPHTQGEIAAAQ 910
************************************************************988888999 PP
TIGR00461 898 wadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
w pysre+a++p+p++ +kfwp+v+r+dd+yGdrnl+c+c
lcl|NCBI__GCF_000061505.1:WP_011765018.1 911 WERPYSREQAVFPLPWVADNKFWPSVNRIDDVYGDRNLFCAC 952
99***************************************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (959 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: 00:00:00.06
# Mc/sec: 13.64
//
[ok]
This GapMind analysis is from Sep 24 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