Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate WP_057509138.1 ABB28_RS13625 glycine dehydrogenase (aminomethyl-transferring)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1868
(950 letters)
>NCBI__GCF_001431535.1:WP_057509138.1
Length = 955
Score = 1225 bits (3169), Expect = 0.0
Identities = 613/941 (65%), Positives = 736/941 (78%), Gaps = 8/941 (0%)
Query: 10 NEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGLSEADALALI 69
N F+ RHIGP + ML +G SL+AL+ +++P IK + L L + ++E ALA I
Sbjct: 15 NAFVERHIGPNDAEIAQMLGVVGHASLDALTDAIVPARIKSPAPLALPESITEVQALAKI 74
Query: 70 KSIATKNQLFKTFIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQ 129
++IA +N + ++FIGQGYYGTHTP+ ILRN+LENPAWYTAYTPYQ EISQGR+EAL+NFQ
Sbjct: 75 RAIADQNTVLRSFIGQGYYGTHTPNVILRNILENPAWYTAYTPYQAEISQGRMEALINFQ 134
Query: 130 TLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQTLDVLRTRA 189
TL +DLTG+ IANASLLDEATAAAEAMT KR +K+K S FF HPQTL++LRTRA
Sbjct: 135 TLCADLTGMEIANASLLDEATAAAEAMTLAKRSAKSK-SDTFFVHDAVHPQTLELLRTRA 193
Query: 190 EPLGIDVVVGDERELTDVTPFFGALLQYPASNGDVFDYRELTERFHAANALVAVAADLLA 249
EPLGI + VG E + F G LLQYP + G V D++ L + HA LVAVA DLLA
Sbjct: 194 EPLGIVLRVGTPAEALEAEAF-GLLLQYPDTFGQVADHKALVDAVHARGGLVAVATDLLA 252
Query: 250 LTVLTAPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFGN 309
LT+L APGE+GAD+ +G++QRFGVP GFGGPHAA+ + +DA+KR MPGRL+GVS+D GN
Sbjct: 253 LTLLAAPGEWGADIVVGNSQRFGVPFGFGGPHAAFMACRDAYKRSMPGRLIGVSIDAQGN 312
Query: 310 PALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIANRVHHLTAIL 369
PA RL +QTREQHIRREKATSNICTAQVLLA +ASMYAVYHGP GLT+IA R H L AIL
Sbjct: 313 PAYRLTLQTREQHIRREKATSNICTAQVLLAVMASMYAVYHGPDGLTRIARRTHRLAAIL 372
Query: 370 AKGLSALGLSVEQASFFDTLTVKAGAQTAALHDKAHAQRINLRVVDGERLGLSLDETTTQ 429
A L + G++V + FFDTL V G AA+H A A NLR +D + +SLDET T+
Sbjct: 373 AAALRSNGVAVG-SEFFDTLHV-TGIDAAAIHQAARAAGYNLRAIDSSSVSISLDETATR 430
Query: 430 ADVETLWSLLSDGKALPDFAALAASVQSAIPATLVRQSPILSHPVFNRYHSETELMRYLR 489
DV L ++ A D AL S AIPA LVR+S L+HPVFN +HSE EL+RYLR
Sbjct: 431 EDVVALAAVFG---AQADVDALDGSTADAIPAELVRRSDFLTHPVFNTHHSEHELLRYLR 487
Query: 490 KLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYQQLTDELE 549
LADKDLA+DRTMIPLGSCTMKLNA +EMIPVTW EFG +HP PA+Q+ GY+ L + LE
Sbjct: 488 SLADKDLAMDRTMIPLGSCTMKLNATAEMIPVTWPEFGNIHPLVPADQAVGYKALIEGLE 547
Query: 550 AMLCAATGYDSVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSAHGTNPATAQ 609
AML TGYD+VSLQPN+G+QGEYAGLLAIRAYH+SRG+D RDICLIP SAHGTNPA+AQ
Sbjct: 548 AMLVECTGYDAVSLQPNSGAQGEYAGLLAIRAYHRSRGDDHRDICLIPDSAHGTNPASAQ 607
Query: 610 MAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGIREICGIIHD 669
M GM+VVVT DA GNVD+ED+R A ++ + LAALM+TYPSTHGVFEE I EIC IIH
Sbjct: 608 MCGMKVVVTKTDANGNVDVEDIRRNAEKYSDRLAALMVTYPSTHGVFEEEIVEICEIIHQ 667
Query: 670 NGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSHLAPF 729
+GGQVY DGANMNA+VG+ PGK+G DVSHLNLHKTFCIPHGGGGPGVGP VKSHLAPF
Sbjct: 668 HGGQVYTDGANMNALVGVAKPGKWGSDVSHLNLHKTFCIPHGGGGPGVGPCAVKSHLAPF 727
Query: 730 LPGHAQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNANYISRRLEE 789
LP E G V AA FGSASILPI+WMYI +MG GL++A+Q+A+LNANYI+ RL
Sbjct: 728 LPRVLGGEGDVGMVSAASFGSASILPISWMYITLMGSEGLRKATQVALLNANYIATRLAP 787
Query: 790 HYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAGTLMIE 849
H+ LYTG NGLVAHECILD+RPL+ +SGI +D+AKRLIDFGFHAPT+SFPVAGTLM+E
Sbjct: 788 HFKTLYTGRNGLVAHECILDVRPLEKTSGIGAEDIAKRLIDFGFHAPTLSFPVAGTLMVE 847
Query: 850 PTESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTAKEL-VGEWSHPYSR 908
PTESES+ ELDRF DAMI+IREEI A+E+G L+++DNPLKNAPHTA + EW+H Y R
Sbjct: 848 PTESESQHELDRFIDAMIQIREEIAAIEDGRLEREDNPLKNAPHTATAVTASEWTHAYPR 907
Query: 909 EQAVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESY 949
E A +P+ASL + KYWPPV RVDNV+GD+N++CAC +++Y
Sbjct: 908 ELAAFPLASLKQSKYWPPVARVDNVYGDKNVMCACIPVDAY 948
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: 2242
Number of extensions: 96
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: 950
Length of database: 955
Length adjustment: 44
Effective length of query: 906
Effective length of database: 911
Effective search space: 825366
Effective search space used: 825366
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_057509138.1 ABB28_RS13625 (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.23788.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 1448.3 0.0 0 1448.1 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057509138.1 ABB28_RS13625 glycine dehydrogen
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057509138.1 ABB28_RS13625 glycine dehydrogenase (aminomethyl-transferring)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1448.1 0.0 0 0 1 939 [] 20 942 .. 20 942 .. 0.99
Alignments for each domain:
== domain 1 score: 1448.1 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyi 69
rh+Gp++ae +ml +G+ +l+al++ +vp i+ + pl l+ + +e +ala++++ia++n +++s+i
lcl|NCBI__GCF_001431535.1:WP_057509138.1 20 RHIGPNDAEIAQMLGVVGHASLDALTDAIVPARIKSPAPLALPESITEVQALAKIRAIADQNTVLRSFI 88
9******************************************************************** PP
TIGR00461 70 GkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaa 138
G+Gyy+t +p vi+rn+lenp wytaytpyq+eisqGr+eal+nfqt+ dltG+e+anasllde+taa
lcl|NCBI__GCF_001431535.1:WP_057509138.1 89 GQGYYGTHTPNVILRNILENPAWYTAYTPYQAEISQGRMEALINFQTLCADLTGMEIANASLLDEATAA 157
********************************************************************* PP
TIGR00461 139 aeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdG 207
aeam l++r +k+k+ f+v + vhpqtle+++traeplgi + v+ + + + +G llqyp t G
lcl|NCBI__GCF_001431535.1:WP_057509138.1 158 AEAMTLAKRSAKSKSDTFFVHDAVHPQTLELLRTRAEPLGIVLRVGTPAEALE-AEAFGLLLQYPDTFG 225
*****************************************888887777665.578************ PP
TIGR00461 208 eildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdey 276
++ d kal+d+++ r lv+va+dllaltll +pg+ Gadiv+G +qrfGvp+G+GGphaaf+a++d y
lcl|NCBI__GCF_001431535.1:WP_057509138.1 226 QVADHKALVDAVHARGGLVAVATDLLALTLLAAPGEWGADIVVGNSQRFGVPFGFGGPHAAFMACRDAY 294
********************************************************************* PP
TIGR00461 277 krklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniar 345
kr++pGr++Gvs da+Gn+a rl+lqtreqhirr+katsnictaqvlla++as+yavyhGp Gl +iar
lcl|NCBI__GCF_001431535.1:WP_057509138.1 295 KRSMPGRLIGVSIDAQGNPAYRLTLQTREQHIRREKATSNICTAQVLLAVMASMYAVYHGPDGLTRIAR 363
********************************************************************* PP
TIGR00461 346 rifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeeaeinlravvltevgialdettt 414
r +rl++ilaa+l+ ++ + + +fdtl v + aa + +aa++a+ nlra++ ++v+i+ldet+t
lcl|NCBI__GCF_001431535.1:WP_057509138.1 364 RTHRLAAILAAALRSNGVAVG-SEFFDTLHVTGIDAAA--IHQAARAAGYNLRAIDSSSVSISLDETAT 429
**************9999875.679*****99888777..***************************** PP
TIGR00461 415 kedvldllkvlagkdnlglsseelsedvansfpaellrddeilrdevfnryhsetellrylhrleskdl 483
+edv+ l v+ ++ +++ l+ a+++pael r +++l+++vfn++hse ellryl +l kdl
lcl|NCBI__GCF_001431535.1:WP_057509138.1 430 REDVVALAAVFGAQA----DVDALDGSTADAIPAELVRRSDFLTHPVFNTHHSEHELLRYLRSLADKDL 494
***********9966....99************************************************ PP
TIGR00461 484 alnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdaislqp 552
a++++miplGsctmklnataem+p+twpef++ihp+ pa+q+ Gyk li le+ lve tG+da+slqp
lcl|NCBI__GCF_001431535.1:WP_057509138.1 495 AMDRTMIPLGSCTMKLNATAEMIPVTWPEFGNIHPLVPADQAVGYKALIEGLEAMLVECTGYDAVSLQP 563
********************************************************************* PP
TIGR00461 553 nsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlkak 621
nsGaqGeyaGl +ir yh srg++hr+iclip sahGtnpasa+m+G+kvv+ k d +Gn+d++d++
lcl|NCBI__GCF_001431535.1:WP_057509138.1 564 NSGAQGEYAGLLAIRAYHRSRGDDHRDICLIPDSAHGTNPASAQMCGMKVVVTKTDANGNVDVEDIRRN 632
********************************************************************* PP
TIGR00461 622 aekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlh 690
aek++d+laa+mvtypst+Gvfee i e+++i+h+ GGqvy dGanmna vG+++pg+ G+dv+hlnlh
lcl|NCBI__GCF_001431535.1:WP_057509138.1 633 AEKYSDRLAALMVTYPSTHGVFEEEIVEICEIIHQHGGQVYTDGANMNALVGVAKPGKWGSDVSHLNLH 701
********************************************************************* PP
TIGR00461 691 ktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmm 759
ktf+iphGGGGpg+gp +vkshlapflp+ + g++ +g+vsaa +Gsasilpis+myi +m
lcl|NCBI__GCF_001431535.1:WP_057509138.1 702 KTFCIPHGGGGPGVGPCAVKSHLAPFLPR--------VLGGEGDVGMVSAASFGSASILPISWMYITLM 762
*****************************........66788899************************ PP
TIGR00461 760 GaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGf 828
G+eGl+ka++va+lnany+a+rl ++k l++gr++ vahecild+r+l + +gi a+d+akrl+d+Gf
lcl|NCBI__GCF_001431535.1:WP_057509138.1 763 GSEGLRKATQVALLNANYIATRLAPHFKTLYTGRNGLVAHECILDVRPLEKTSGIGAEDIAKRLIDFGF 831
********************************************************************* PP
TIGR00461 829 haptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivae 897
haptlsfpvaGtlmvepteses++eldrfidami i+eei a+ G+++ edn+lknaph++ + ++e
lcl|NCBI__GCF_001431535.1:WP_057509138.1 832 HAPTLSFPVAGTLMVEPTESESQHELDRFIDAMIQIREEIAAIEDGRLEREDNPLKNAPHTATAVTASE 900
********************************************************************* PP
TIGR00461 898 wadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
w+++y re aa+p++ lk+ k+wp var+d++yGd+n++c+c
lcl|NCBI__GCF_001431535.1:WP_057509138.1 901 WTHAYPRELAAFPLASLKQSKYWPPVARVDNVYGDKNVMCAC 942
*****************************************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (955 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: 13.32
//
[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