Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate H281DRAFT_02409 H281DRAFT_02409 glycine dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5558 (953 letters) >FitnessBrowser__Burk376:H281DRAFT_02409 Length = 978 Score = 1280 bits (3313), Expect = 0.0 Identities = 640/955 (67%), Positives = 765/955 (80%), Gaps = 16/955 (1%) Query: 11 FIARHIGPRASDEQAMLERLGYDSLEALSASVIPESIKGTSVLDMG---DGQSEADALAS 67 F RHIGP A+D++AMLE LG+ S AL +VIP++I+ T L +G +SEA+ALA+ Sbjct: 26 FAERHIGPDAADQEAMLEALGFTSRAALIDAVIPKTIRRTEPLPLGPFAQPKSEAEALAA 85 Query: 68 IKAIAAKNQLFKTYIGQGYYNCHTPAPILRNLLENPAWYTAYTPYQPEISQGRLEALLNF 127 ++ +A KNQ+F++YIGQGYYN HTP ILRN+LENPAWYTAYTPYQPEISQGRLEALLNF Sbjct: 86 LRELADKNQVFRSYIGQGYYNAHTPTVILRNVLENPAWYTAYTPYQPEISQGRLEALLNF 145 Query: 128 QTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASVHSHPQTLDVLRTR 187 Q +I DLTGL I+NASLLDEATAAAEAMT +R+ K K SN FF + PQT++V++TR Sbjct: 146 QQMIVDLTGLAISNASLLDEATAAAEAMTLLQRVGKPK-SNVFFVADDVLPQTIEVVKTR 204 Query: 188 AEPLGIDVVVGDERELSDVSGFFGALLQYPASNGDLFDYRELTERFHTANALVAVAADLL 247 A P+GI+V VG E ++ + F G LLQYP NGD+ DYR LTE H A V VAADLL Sbjct: 205 ATPVGIEVKVGPAAEAANANAF-GVLLQYPGVNGDVRDYRALTEAIHAAGGHVVVAADLL 263 Query: 248 ALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFG 307 ALT+LTPPGE+GADVA+G+ QRFGVP+GFGGPHAAY + +D FKR MPGRLVGV+VD G Sbjct: 264 ALTVLTPPGEWGADVAVGNTQRFGVPVGFGGPHAAYLAVRDEFKRQMPGRLVGVTVDAQG 323 Query: 308 KPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLVQIANRIHHLTAI 367 PALRLA+QTREQHIRREKATSN+CTAQ LLA +ASMYAVYHGP+GL IA R++ + A+ Sbjct: 324 NPALRLALQTREQHIRREKATSNVCTAQALLAIMASMYAVYHGPRGLKTIALRVNRIAAL 383 Query: 368 LAKGLGALGLSVEQESFFDTLTLRTGAQTAALHDKARAQRINLRVVDAERLGLSLDETTS 427 LA+G LG ++ E+FFDTLT TGA+T ALHD A+A+RINLR V ++G+S+DETTS Sbjct: 384 LAEGAKQLGYTLVNETFFDTLTFDTGARTQALHDAAKAKRINLRRVSDTQVGVSIDETTS 443 Query: 428 QADVEALLRLIGNLMADGKAVPDF----AALAASVQSHIPAELVRQSAILSHPVFNRYHS 483 + D+ LL + A K P AA+ AS + +PA L R SA L+H VFNR+HS Sbjct: 444 RRDLGDLLAVFAQA-AGAKDAPQVDTLDAAITASSTASVPAALERTSAYLTHHVFNRHHS 502 Query: 484 ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAG 543 ETE++RYLR L+DKDLALDR+MIPLGSCTMKLNA SEM+PVTW EFG +HPFAPAEQ+ G Sbjct: 503 ETEMLRYLRSLSDKDLALDRSMIPLGSCTMKLNATSEMLPVTWPEFGQIHPFAPAEQTVG 562 Query: 544 YQQLTDELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSA 603 Y+++ D+LE ML AATGY AVSLQPNAGSQGEYAGLL I AYH SRGE R++CLIP+SA Sbjct: 563 YREMIDQLEEMLVAATGYAAVSLQPNAGSQGEYAGLLIIHAYHASRGEAHRNVCLIPASA 622 Query: 604 HGTNPATAHMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI 663 HGTNPA+A MAGM+VVV ACDA+GNVD+EDL+ KA +H + LAA+MITYPSTHGVFE+ + Sbjct: 623 HGTNPASAQMAGMQVVVVACDAQGNVDVEDLKKKADQHADKLAAIMITYPSTHGVFEQNV 682 Query: 664 REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI 723 REIC I+H GGQVY+DGANMNAMVGL APG+FGGDVSHLNLHKTFCIPHGGGGPGVGP+ Sbjct: 683 REICEIVHARGGQVYVDGANMNAMVGLTAPGQFGGDVSHLNLHKTFCIPHGGGGPGVGPV 742 Query: 724 GVKSHLAPFLPGHASMERKQ-----GAVCAAPFGSASILPITWMYIRMMGGAGLKRASQL 778 V +HLAPFLP S ++ GAV AP+GSASILPI+WMYI MMG L A++ Sbjct: 743 AVGAHLAPFLPNQISSGYERAPNGIGAVSGAPYGSASILPISWMYIAMMGAKNLTAATET 802 Query: 779 AILNANYIARRLEEHYPVLYSGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHA 838 AILNANY+A++L HYPVLYSG GLVAHECILDLRP+K++SGI+VDDVAKRL D+GFHA Sbjct: 803 AILNANYVAKKLAPHYPVLYSGPGGLVAHECILDLRPIKETSGITVDDVAKRLADYGFHA 862 Query: 839 PTMSFPVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGSLDKDDNPLKNAPHTA 898 PTMSFPV GTLM+EPTESESKEELDRF +AMI IR EIRAVE G D++DNPLK+APHTA Sbjct: 863 PTMSFPVPGTLMVEPTESESKEELDRFIEAMIAIRNEIRAVEEGRSDREDNPLKHAPHTA 922 Query: 899 AEIVG-EWTHPYSREQAVYPVASLIDGKYWPPVGRVDNVFGDRNLVCACPSIESY 952 A ++ EW H Y+RE A YP+ +LI KYWPPVGR DNV+GDRNL C+C + Y Sbjct: 923 AVVIADEWKHAYARETAAYPLPTLIAKKYWPPVGRADNVYGDRNLFCSCVPVADY 977 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: 2260 Number of extensions: 90 Number of successful extensions: 10 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: 953 Length of database: 978 Length adjustment: 44 Effective length of query: 909 Effective length of database: 934 Effective search space: 849006 Effective search space used: 849006 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 H281DRAFT_02409 H281DRAFT_02409 (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.13902.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 1475.4 0.1 0 1475.3 0.1 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_02409 H281DRAFT_02409 glycine dehydrog Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_02409 H281DRAFT_02409 glycine dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1475.3 0.1 0 0 1 939 [] 29 971 .. 29 971 .. 0.97 Alignments for each domain: == domain 1 score: 1475.3 bits; conditional E-value: 0 TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkle...apakeyealaelkkiasknk 63 rh+Gpd+a+q+ ml++lGf + ali+ ++pk ir + pl l+ p++e eala l+++a+kn+ lcl|FitnessBrowser__Burk376:H281DRAFT_02409 29 RHIGPDAADQEAMLEALGFTSRAALIDAVIPKTIRRTEPLPLGpfaQPKSEAEALAALRELADKNQ 94 9***************************************9973324677**************** PP TIGR00461 64 kvksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevana 129 +++syiG+Gyy++ +p vi+rn+lenp wytaytpyqpeisqGrleallnfq++++dltGl ++na lcl|FitnessBrowser__Burk376:H281DRAFT_02409 95 VFRSYIGQGYYNAHTPTVILRNVLENPAWYTAYTPYQPEISQGRLEALLNFQQMIVDLTGLAISNA 160 ****************************************************************** PP TIGR00461 130 slldegtaaaeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdv 195 sllde+taaaeam l +rv k k+n f+va+dv pqt+evvktra p+giev v+ a + + + lcl|FitnessBrowser__Burk376:H281DRAFT_02409 161 SLLDEATAAAEAMTLLQRVGKPKSNVFFVADDVLPQTIEVVKTRATPVGIEVKVGPAAEAAN-ANA 225 *******************************************************9999776.578 PP TIGR00461 196 lGvllqypatdGeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplG 261 +Gvllqyp+ +G++ dy+al+++++ v vaadllalt+ltppg+ Gad+++G +qrfGvp+G lcl|FitnessBrowser__Burk376:H281DRAFT_02409 226 FGVLLQYPGVNGDVRDYRALTEAIHAAGGHVVVAADLLALTVLTPPGEWGADVAVGNTQRFGVPVG 291 ****************************************************************** PP TIGR00461 262 yGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanv 327 +GGphaa++av+de+kr++pGr+vGv+ da+Gn+alrlalqtreqhirr+katsn+ctaq+lla + lcl|FitnessBrowser__Burk376:H281DRAFT_02409 292 FGGPHAAYLAVRDEFKRQMPGRLVGVTVDAQGNPALRLALQTREQHIRREKATSNVCTAQALLAIM 357 ****************************************************************** PP TIGR00461 328 aslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeea 393 as+yavyhGp+Glk ia r+ r++++la g k+ +y l n+t+fdtlt + g ++ ++ aa+++ lcl|FitnessBrowser__Burk376:H281DRAFT_02409 358 ASMYAVYHGPRGLKTIALRVNRIAALLAEGAKQLGYTLVNETFFDTLTFDTGARTQ-ALHDAAKAK 422 ****************************************************9987.9******** PP TIGR00461 394 einlravvltevgialdetttkedvldllkvlagkd..nlglsseelsedvan....sfpaellrd 453 inlr v t+vg+++dett+++d+ dll v+a + + ++++l+ ++ s+pa+l+r+ lcl|FitnessBrowser__Burk376:H281DRAFT_02409 423 RINLRRVSDTQVGVSIDETTSRRDLGDLLAVFAQAAgaKDAPQVDTLDAAITAsstaSVPAALERT 488 ********************************87541133456778887766555679******** PP TIGR00461 454 deilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpf 519 + +l+++vfnr+hsete+lryl +l kdlal++smiplGsctmklnat emlp+twpef++ihpf lcl|FitnessBrowser__Burk376:H281DRAFT_02409 489 SAYLTHHVFNRHHSETEMLRYLRSLSDKDLALDRSMIPLGSCTMKLNATSEMLPVTWPEFGQIHPF 554 ****************************************************************** PP TIGR00461 520 apaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipa 585 apaeq+ Gy+e+i qle+ lv tG+ a+slqpn+G+qGeyaGl +i yh srge hrn+clipa lcl|FitnessBrowser__Burk376:H281DRAFT_02409 555 APAEQTVGYREMIDQLEEMLVAATGYAAVSLQPNAGSQGEYAGLLIIHAYHASRGEAHRNVCLIPA 620 ****************************************************************** PP TIGR00461 586 sahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetirevi 651 sahGtnpasa+maG++vv+v+cd +Gn+d++dlk+ka++++d+laa+m+typst+Gvfe+ +re++ lcl|FitnessBrowser__Burk376:H281DRAFT_02409 621 SAHGTNPASAQMAGMQVVVVACDAQGNVDVEDLKKKADQHADKLAAIMITYPSTHGVFEQNVREIC 686 ****************************************************************** PP TIGR00461 652 divhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshlapfl 717 +ivh GGqvy+dGanmna vGlt+pg++G dv+hlnlhktf+iphGGGGpg+gp++v +hlapfl lcl|FitnessBrowser__Burk376:H281DRAFT_02409 687 EIVHARGGQVYVDGANMNAMVGLTAPGQFGGDVSHLNLHKTFCIPHGGGGPGVGPVAVGAHLAPFL 752 ****************************************************************** PP TIGR00461 718 pktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasevailnanylakrlk 783 p+ ++ s e + igavs apyGsasilpis+myi+mmGa+ l+ a+e ailnany+ak+l lcl|FitnessBrowser__Burk376:H281DRAFT_02409 753 PN-QISSG--YERAPNGIGAVSGAPYGSASILPISWMYIAMMGAKNLTAATETAILNANYVAKKLA 815 *9.56654..4556789************************************************* PP TIGR00461 784 daykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmveptese 849 +y++l+ g + vahecildlr++ke +gi + dvakrl dyGfhapt+sfpv+Gtlmveptese lcl|FitnessBrowser__Burk376:H281DRAFT_02409 816 PHYPVLYSGPGGLVAHECILDLRPIKETSGITVDDVAKRLADYGFHAPTMSFPVPGTLMVEPTESE 881 ****************************************************************** PP TIGR00461 850 sleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaaypapvlk 915 s+eeldrfi+amiai++ei av +G+ + edn+lk aph++ +i+ ew+++y+re aayp+p l lcl|FitnessBrowser__Burk376:H281DRAFT_02409 882 SKEELDRFIEAMIAIRNEIRAVEEGRSDREDNPLKHAPHTAAVVIADEWKHAYARETAAYPLPTLI 947 ****************************************************************** PP TIGR00461 916 yfkfwptvarlddtyGdrnlvcsc 939 k+wp v+r d++yGdrnl+csc lcl|FitnessBrowser__Burk376:H281DRAFT_02409 948 AKKYWPPVGRADNVYGDRNLFCSC 971 ************************ PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (939 nodes) Target sequences: 1 (978 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: 9.21 // [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