Align vitamin B12-dependent methionine synthase without a reactivation domain (EC 2.1.1.13) (characterized)
to candidate WP_013537367.1 THEAM_RS03095 homocysteine S-methyltransferase
Query= reanno::Miya:8499710 (818 letters) >NCBI__GCF_000185805.1:WP_013537367.1 Length = 841 Score = 616 bits (1588), Expect = e-180 Identities = 364/838 (43%), Positives = 503/838 (60%), Gaps = 45/838 (5%) Query: 15 VFDGGMGTMLQSRGLPPGVSPELFCLARPDVLVGIHADYLRAGADVLTTNTFGGCIHKLG 74 V DGGMGTML ++G+ +PEL + +P+VL IH++Y+ AGAD++ TNTFG KL Sbjct: 14 VLDGGMGTMLMAKGVDVNFAPELLNVEKPEVLKEIHSEYVEAGADIIETNTFGSNRIKLS 73 Query: 75 TGPGAPDVVEFNRAMARAAREAVLASGREAFVAGSVGPSGHFMRPLGDLDPAELVAAFRA 134 V E A + A+EA A GR A VA SVGP+G F P+GD ELV F+ Sbjct: 74 HYGLENRVKELTAAGVKLAKEA--ARGR-ALVALSVGPTGVFAEPVGDYTFDELVDVFKE 130 Query: 135 QIRGLVQGGVDLILAETQFDLAEARAIVLAARAECDLPVGVSMTF-ENGVSLTGTRPEVF 193 QI + G DL+L ET D+ EA+A V AAR CDLPV VSMT+ E+G +L GT PEV Sbjct: 131 QIEAGAEAGADLVLIETMSDIKEAKAAVFAAREVCDLPVLVSMTYQEDGRTLLGTPPEVA 190 Query: 194 VQSMLNMGVDLVGTNCSAGPEQMAEVADELLAISEVPVLVEPNAGLPELVDGKTVFRLGP 253 V VG NCS GPE E+ +++ P++V NAGLP L +GKTV+ P Sbjct: 191 AAVFEGFNVAAVGANCSLGPESFVEIIKRTASVTTTPIIVYANAGLPVLENGKTVYPEPP 250 Query: 254 DDFARHTARFAASGVRMLGGCCGTTPDHIAALRGALDNLSGGLVPDPARRD---GIVLTT 310 + F ++ F +G ++GGCCGTTPDHI A++ A++ L P R+ G+ + + Sbjct: 251 ETFEKYAVEFVKAGANIIGGCCGTTPDHIRAIKRAVEGLK------PVERNPVKGVKVAS 304 Query: 311 RAQAVHIGAGSPIRIIGERINPTGKKLLTAELQAGEFAQALRFADEQVEAGAPLLDVNVG 370 R + V IG G P RIIGERINPTGKK L L+A +F+ + A +QVE GA LLDVNVG Sbjct: 305 RTKLVLIGTGHPTRIIGERINPTGKKKLQEALKAKDFSLVKQEAKKQVEEGADLLDVNVG 364 Query: 371 APMVDEAVLLPALVERLVARHSLPLSLDSSNADAIAAALPFHPGSPLVNSISGEPGRMEH 430 P DE L+ V+ ++ +PL +D+ + A+ AL G P+VNS+SGE +E Sbjct: 365 VPGADEPSLMREAVKTVMEAVDVPLVIDTKDPKAVEEALKMCDGRPVVNSVSGEKKDVEQ 424 Query: 431 LGPLCRDHGAPFILLPLKGRKLPVTAAERIAIIEELLQQADSLRIPRRLVMVDVLALAVS 490 + P+ +GA +LL + L A ER+ IIE LL++ + + + R + DVL LAVS Sbjct: 425 ILPVAAKYGANVLLLAIDDEGLKEKAQERVEIIERLLKECEKVGVDRSSTVADVLNLAVS 484 Query: 491 SKAEAARHCLDTIRWCAAQ-GLPTTIGLSNISFGLPARELLNSTFLAMAAGAGLSSCIAH 549 + ++ L IR + G+ TT+G+SN+SFGLP+R L+NS F+AMA AGL S I + Sbjct: 485 AMPDSTVETLKAIRLVKERFGIATTLGVSNVSFGLPSRSLINSAFMAMAIYAGLDSGIVN 544 Query: 550 PGNARIREAVAASSVLLGLDANAESFIEGYSGWTPGGDATGATPA-----GVAGGTGGGT 604 PG++R+ E + AS VL+G D AE F+ + ++P G+ A +AG G Sbjct: 545 PGDSRMVETIFASDVLVGKDRGAERFVSRFQNYSPKGEDAECRKALERICQIAGAVLGTV 604 Query: 605 -------GGVKAKAATLEEA----------------VIRGDREGALALVERALSEGADPF 641 KAK T EEA V+ GDREG + E AL E DP Sbjct: 605 PQAFSHEAEEKAKGETTEEASDSEAPAGILGTIFKKVLEGDREGIVGPTEEALKE-FDPV 663 Query: 642 SLVQEKLIPGITEVGRRYERREYFLPQLIRSAETMQHAFRKLQPLLEAQRGH-EARPVII 700 + LIP + VG+R+E+ E FLPQ++RSA+ +Q AF L+ ++ + G+ + I+ Sbjct: 664 EVSDRALIPALDVVGKRFEKGEIFLPQMLRSAQAVQAAFEVLKREMKKKGGNLKLGGKIV 723 Query: 701 MATVEGDIHDIGKNIVTLMLGNHGFDVVDLGKDVKAADIVEAAERHGARVIGLSALMTTT 760 MATV GD+H+IGKNIV ML N GFDV+DLG +V A++V AA+ H A ++GLSALMTTT Sbjct: 724 MATVHGDVHEIGKNIVITMLENSGFDVIDLGTNVPPAEVVRAAKEHNADIVGLSALMTTT 783 Query: 761 MVRMEDTVRLVRERGLPVKVMVGGAVVTPAYAEAIGADGYSADAVEAVRVAKELLTVQ 818 + ME+T++ +R+ G+ V V+VGGAVVTP YAE+IG Y DA EAV++ K+LL V+ Sbjct: 784 LPAMEETIKALRDAGVEVPVIVGGAVVTPEYAESIGGI-YGGDAQEAVKIVKKLLKVE 840 Lambda K H 0.320 0.137 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: 1643 Number of extensions: 71 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: 818 Length of database: 841 Length adjustment: 42 Effective length of query: 776 Effective length of database: 799 Effective search space: 620024 Effective search space used: 620024 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: 56 (26.2 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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