Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate WP_004304844.1 C665_RS07885 glycine dehydrogenase (aminomethyl-transferring)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1868
(950 letters)
>NCBI__GCF_000310185.1:WP_004304844.1
Length = 960
Score = 1346 bits (3483), Expect = 0.0
Identities = 670/949 (70%), Positives = 763/949 (80%), Gaps = 3/949 (0%)
Query: 2 TQINLTTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGLS 61
T L ++F+ RH+GP A + +AML+ LG DSL+ L VIP SI + L L +G S
Sbjct: 11 TLAQLEQRDDFVGRHVGPDAAETRAMLDVLGLDSLDQLIDKVIPASILSAAPLALPEGRS 70
Query: 62 EADALALIKSIATKNQLFKTFIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQGR 121
E + LAL+++IA N++ ++FIG GY+ T TP+ ILRN+LENPAWYTAYTPYQPEISQGR
Sbjct: 71 EPETLALLRAIAGTNRVLRSFIGTGYHDTFTPTVILRNVLENPAWYTAYTPYQPEISQGR 130
Query: 122 LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQT 181
LEALLNFQT+++DLTGL IANASLLDEATAAAEAM FC+RLSK+K S AFF S CHPQT
Sbjct: 131 LEALLNFQTMVTDLTGLEIANASLLDEATAAAEAMAFCQRLSKSK-SKAFFVSRDCHPQT 189
Query: 182 LDVLRTRAEPLGIDVVVGDERELTDVTPFFGALLQYPASNGDVFDYRELTERFHAANALV 241
++V+RTRAEPLG +V+VGD FG LLQYPAS G+V D+ + H ALV
Sbjct: 190 IEVVRTRAEPLGFEVIVGDAATELAAHEVFGVLLQYPASTGEVVDHAAIVAAAHDRKALV 249
Query: 242 AVAADLLALTVLTAPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVG 301
VAADLLALT+L PGEFGADVAIGS QRFG+P+GFGGPHAAYF+T+D KR MPGR+VG
Sbjct: 250 VVAADLLALTLLKPPGEFGADVAIGSTQRFGIPMGFGGPHAAYFATRDEHKRVMPGRVVG 309
Query: 302 VSVDRFGNPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIANR 361
VS+D GN A RLAMQTREQHIRREKATSNICTAQ LLA +ASMYA YHGP GLT IA R
Sbjct: 310 VSIDSHGNKAYRLAMQTREQHIRREKATSNICTAQALLAIMASMYACYHGPAGLTTIARR 369
Query: 362 VHHLTAILAKGLSALGLSVEQASFFDTLTVKAGAQTAALHDKAHAQRINLRVVDGERLGL 421
VH LTA LA GL LG+ V +FFDT+TV+ A AA+H A A +NLR +D +G+
Sbjct: 370 VHRLTATLAAGLRRLGIDVPTTAFFDTITVRV-ADAAAVHAAARAAGMNLREIDAGTVGI 428
Query: 422 SLDETTTQADVETLWSLLSDGKALPDFAALAASVQSAIPATLVRQSPILSHPVFNRYHSE 481
+LDETT +ADVE LW++ G A PDF A+ + VQ A+PA +R S L+HPVF+ Y SE
Sbjct: 429 ALDETTRRADVEALWAVFGSGVAAPDFDAVESLVQEALPAAQLRSSAFLTHPVFSAYQSE 488
Query: 482 TELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGY 541
T ++RYLR LADKDLALDRTMIPLGSCTMKLNA +EMIPVTW EFG LHPFAPA+Q+ GY
Sbjct: 489 TRMLRYLRSLADKDLALDRTMIPLGSCTMKLNATTEMIPVTWPEFGGLHPFAPADQTQGY 548
Query: 542 QQLTDELEAMLCAATGYDSVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSAH 601
QLT ELE MLCA TGYD+VSLQPNAGSQGEYAGLLAIRAYH SRGE RD+CLIPSSAH
Sbjct: 549 AQLTAELEQMLCACTGYDAVSLQPNAGSQGEYAGLLAIRAYHASRGEGHRDVCLIPSSAH 608
Query: 602 GTNPATAQMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGIR 661
GTNPATA MAGMRVVV ACDA GNVD+ DLRAKA +H + LAA+MITYPS HGVFE +R
Sbjct: 609 GTNPATANMAGMRVVVVACDANGNVDVADLRAKAAQHADQLAAIMITYPSIHGVFETAVR 668
Query: 662 EICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIG 721
EI I+H +GGQVYIDGAN+NAMVGLC PG+FGGDVSHLNLHKTFCIPHGGGGPGVGPIG
Sbjct: 669 EITDIVHAHGGQVYIDGANLNAMVGLCGPGQFGGDVSHLNLHKTFCIPHGGGGPGVGPIG 728
Query: 722 VKSHLAPFLPGHAQMERKE-GAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNA 780
VK+HLAPFLPGH + + GAV AAP+GSASILPITW YI +MG GL+ A+ AILNA
Sbjct: 729 VKAHLAPFLPGHGSVGLEGIGAVAAAPWGSASILPITWTYITLMGREGLRHATVTAILNA 788
Query: 781 NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF 840
NYI++RLE HYPVLY G NGLVAHECILDLRPLKDS+GISVDDVAKRL+DFGFHAPTMSF
Sbjct: 789 NYIAQRLEPHYPVLYRGENGLVAHECILDLRPLKDSTGISVDDVAKRLMDFGFHAPTMSF 848
Query: 841 PVAGTLMIEPTESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTAKELVG 900
PV GTLMIEPTESESK ELDRFCDAMI IREEI V +G D DNPL NAPHTA+ + G
Sbjct: 849 PVPGTLMIEPTESESKAELDRFCDAMIAIREEIAKVASGEYDPRDNPLVNAPHTAEAIAG 908
Query: 901 EWSHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESY 949
EWSHPYSRE A YPVASL KYW PVGRVDNV+GDRNLVCACP + Y
Sbjct: 909 EWSHPYSREVAAYPVASLRGNKYWSPVGRVDNVYGDRNLVCACPPLSDY 957
Lambda K H
0.319 0.135 0.398
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: 2396
Number of extensions: 93
Number of successful extensions: 6
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: 950
Length of database: 960
Length adjustment: 44
Effective length of query: 906
Effective length of database: 916
Effective search space: 829896
Effective search space used: 829896
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_004304844.1 C665_RS07885 (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.6488.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 1513.8 0.0 0 1513.6 0.0 1.0 1 lcl|NCBI__GCF_000310185.1:WP_004304844.1 C665_RS07885 glycine dehydrogena
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000310185.1:WP_004304844.1 C665_RS07885 glycine dehydrogenase (aminomethyl-transferring)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1513.6 0.0 0 0 1 939 [] 24 951 .. 24 951 .. 0.99
Alignments for each domain:
== domain 1 score: 1513.6 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyi 69
rh+Gpd+ae + ml+ lG d+l++li++++p +i+ a pl l+ +e e+la l++ia n++++s+i
lcl|NCBI__GCF_000310185.1:WP_004304844.1 24 RHVGPDAAETRAMLDVLGLDSLDQLIDKVIPASILSAAPLALPEGRSEPETLALLRAIAGTNRVLRSFI 92
9******************************************************************** PP
TIGR00461 70 GkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaa 138
G Gy +t +p vi+rn+lenp wytaytpyqpeisqGrleallnfqt+v+dltGle+anasllde+taa
lcl|NCBI__GCF_000310185.1:WP_004304844.1 93 GTGYHDTFTPTVILRNVLENPAWYTAYTPYQPEISQGRLEALLNFQTMVTDLTGLEIANASLLDEATAA 161
********************************************************************* PP
TIGR00461 139 aeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdG 207
aeama+++r+sk+k+++f+v++d+hpqt+evv+traeplg+eviv+da + a +v+Gvllqypa++G
lcl|NCBI__GCF_000310185.1:WP_004304844.1 162 AEAMAFCQRLSKSKSKAFFVSRDCHPQTIEVVRTRAEPLGFEVIVGDAATELAAHEVFGVLLQYPASTG 230
********************************************************************* PP
TIGR00461 208 eildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdey 276
e+ d a++ ++++rkalv vaadllaltll+ppg++Gad+++Gs+qrfG+p+G+GGphaa+fa++de+
lcl|NCBI__GCF_000310185.1:WP_004304844.1 231 EVVDHAAIVAAAHDRKALVVVAADLLALTLLKPPGEFGADVAIGSTQRFGIPMGFGGPHAAYFATRDEH 299
********************************************************************* PP
TIGR00461 277 krklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniar 345
kr +pGr+vGvs d++Gn a rla+qtreqhirr+katsnictaq+lla +as+ya yhGp Gl iar
lcl|NCBI__GCF_000310185.1:WP_004304844.1 300 KRVMPGRVVGVSIDSHGNKAYRLAMQTREQHIRREKATSNICTAQALLAIMASMYACYHGPAGLTTIAR 368
********************************************************************* PP
TIGR00461 346 rifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeeaeinlravvltevgialdettt 414
r++rlt+ laagl+r + ++ +fdt+tv+v++ aa v aa++a++nlr +++++vgialdett
lcl|NCBI__GCF_000310185.1:WP_004304844.1 369 RVHRLTATLAAGLRRLGIDVPTTAFFDTITVRVADAAA--VHAAARAAGMNLREIDAGTVGIALDETTR 435
***********************************999..***************************** PP
TIGR00461 415 kedvldllkvlagkdnlglsseelsedvansfpaellrddeilrdevfnryhsetellrylhrleskdl 483
++dv+ l+ v+ + + + +++ v++++pa+ lr++ +l+++vf y set +lryl +l kdl
lcl|NCBI__GCF_000310185.1:WP_004304844.1 436 RADVEALWAVFGS-GVAAPDFDAVESLVQEALPAAQLRSSAFLTHPVFSAYQSETRMLRYLRSLADKDL 503
***********88.5577899************************************************ PP
TIGR00461 484 alnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdaislqp 552
al+++miplGsctmklnat+em+p+twpef+ +hpfapa+q++Gy +l a+le+ l+ tG+da+slqp
lcl|NCBI__GCF_000310185.1:WP_004304844.1 504 ALDRTMIPLGSCTMKLNATTEMIPVTWPEFGGLHPFAPADQTQGYAQLTAELEQMLCACTGYDAVSLQP 572
********************************************************************* PP
TIGR00461 553 nsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlkak 621
n+G+qGeyaGl +ir yh srge+hr++clip sahGtnpa+a+maG++vv+v+cd +Gn+d+ dl+ak
lcl|NCBI__GCF_000310185.1:WP_004304844.1 573 NAGSQGEYAGLLAIRAYHASRGEGHRDVCLIPSSAHGTNPATANMAGMRVVVVACDANGNVDVADLRAK 641
********************************************************************* PP
TIGR00461 622 aekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlh 690
a +++d+laa+m+typs +Gvfe+++re+ divh GGqvy+dGan+na vGl+ pg++G dv+hlnlh
lcl|NCBI__GCF_000310185.1:WP_004304844.1 642 AAQHADQLAAIMITYPSIHGVFETAVREITDIVHAHGGQVYIDGANLNAMVGLCGPGQFGGDVSHLNLH 710
********************************************************************* PP
TIGR00461 691 ktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmm 759
ktf+iphGGGGpg+gpigvk+hlapflp+ + + + igav+aap+Gsasilpi++ yi +m
lcl|NCBI__GCF_000310185.1:WP_004304844.1 711 KTFCIPHGGGGPGVGPIGVKAHLAPFLPG---HG----SVGLEGIGAVAAAPWGSASILPITWTYITLM 772
*****************************...33....4456679************************ PP
TIGR00461 760 GaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGf 828
G eGl++a++ ailnany+a+rl+ +y++l++g+++ vahecildlr+lk+ +gi++ dvakrl+d+Gf
lcl|NCBI__GCF_000310185.1:WP_004304844.1 773 GREGLRHATVTAILNANYIAQRLEPHYPVLYRGENGLVAHECILDLRPLKDSTGISVDDVAKRLMDFGF 841
********************************************************************* PP
TIGR00461 829 haptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivae 897
hapt+sfpv+Gtlm+epteses+ eldrf+damiai+eei +v +Ge++++dn+l+naph++ + i++e
lcl|NCBI__GCF_000310185.1:WP_004304844.1 842 HAPTMSFPVPGTLMIEPTESESKAELDRFCDAMIAIREEIAKVASGEYDPRDNPLVNAPHTA-EAIAGE 909
************************************************************66.579*** PP
TIGR00461 898 wadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
w +pysre+aayp++ l+ +k+w v+r+d++yGdrnlvc+c
lcl|NCBI__GCF_000310185.1:WP_004304844.1 910 WSHPYSREVAAYPVASLRGNKYWSPVGRVDNVYGDRNLVCAC 951
*****************************************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (960 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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 9.62
//
[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