Align vitamin B12-dependent methionine synthase without a reactivation domain (EC 2.1.1.13) (characterized)
to candidate WP_106710138.1 CU102_RS06125 methyltetrahydrofolate cobalamin methyltransferase
Query= reanno::Miya:8499710 (818 letters) >NCBI__GCF_003010955.1:WP_106710138.1 Length = 319 Score = 180 bits (457), Expect = 9e-50 Identities = 116/315 (36%), Positives = 171/315 (54%), Gaps = 16/315 (5%) Query: 307 VLTTRAQAVHIGAGSPIRIIGERINPTGKKLLTAELQAGEFAQALRFADEQVEAGAPLLD 366 ++ + + + IG P +IGERINPTG+K L AE+ G F ++ A EQV AGA +LD Sbjct: 5 IVASATKEIIIGFDQPFCVIGERINPTGRKKLAAEMIEGNFDTVIKDALEQVAAGATMLD 64 Query: 367 VNVGAPMVDEAVLLPAL-------VERLVARHSLPLSLDSSNADAIAAALPFHPGSPLVN 419 VN G VD P L V+ LV +PLS+DSS AI AAL G PLVN Sbjct: 65 VNAGVTAVDPNATEPGLLVQTLEIVQNLV---DVPLSIDSSVTAAIEAALKVAKGRPLVN 121 Query: 420 SISGEPGRMEHLGPLCRDHGAPFILLPLKGRKLPVTAAERIAIIEELLQQADSLRIPRRL 479 S++GE ++E + PL + + P + + + + R A+ ++++++A IP Sbjct: 122 SVTGEEEKLEAILPLIKKYNVPVVAISNDETGISMDPDVRFAVAKKIVERAADFGIPSHD 181 Query: 480 VMVDVLALAVSSKAEAARHCLDTIRWCAAQ-GLPTTIGLSNISFGLPARELLNSTFLAMA 538 ++VD L + + + +A R +R + + TT GLSNISFGLP R +N+ F+ M Sbjct: 182 IVVDPLVMPIGALGDAGRQVFALLRRLREELKVNTTCGLSNISFGLPHRHGINAGFIPMV 241 Query: 539 AGAGLSSCIAHPGNARIREAVAASSVLLGLDANAESFIEGYSGWTPGGDATGATPAGVAG 598 GAG++S I +P + EAV A++VL G DAN +I+ Y P A GA P V Sbjct: 242 IGAGMTSAIMNPCRPQEMEAVHAANVLNGTDANCTYWIKKYRDHQPA--AAGAAPVSVPA 299 Query: 599 GTGGG---TGGVKAK 610 + GG GG +A+ Sbjct: 300 DSAGGGRRRGGREAR 314 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: 652 Number of extensions: 40 Number of successful extensions: 3 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: 319 Length adjustment: 34 Effective length of query: 784 Effective length of database: 285 Effective search space: 223440 Effective search space used: 223440 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: 52 (24.6 bits)
Align vitamin B12-dependent methionine synthase without a reactivation domain (EC 2.1.1.13) (characterized)
to candidate WP_106710129.1 CU102_RS06070 betaine--homocysteine S-methyltransferase
Query= reanno::Miya:8499710 (818 letters) >NCBI__GCF_003010955.1:WP_106710129.1 Length = 337 Score = 161 bits (407), Expect = 6e-44 Identities = 105/290 (36%), Positives = 153/290 (52%), Gaps = 7/290 (2%) Query: 14 LVFDGGMGTMLQSRGLPPGVSPELFCLARPDVLVGIHADYLRAGADVLTTNTFGGCIHKL 73 L+ DG GT L + GL G +PEL+ A+P+ + +H ++ AGAD++ TN+FGG H+L Sbjct: 17 LLADGATGTNLFATGLEAGEAPELWNEAQPEKITALHQGFVDAGADIILTNSFGGTRHRL 76 Query: 74 GTGPGAPDVVEFNRAMARAAREAVLASGREAFVAGSVGPSGHFMRPLGDLDPAELVAAFR 133 V E N+ A AR +GR+ VAGSVGP+G + PLG L + VAAF Sbjct: 77 KLHHAQDRVFELNKKAAELARGVADQAGRKVIVAGSVGPTGELLVPLGTLTEQDAVAAFT 136 Query: 134 AQIRGLVQGGVDLILAETQFDLAEARAIVLAARAECDLPVGVSMTFEN-GVSLTGTRPEV 192 Q+ GL GGVD+ ET E RA AA + LP + +F+ G ++ G P+ Sbjct: 137 EQLEGLKAGGVDVAWIETMSAPGEIRAAAEAA-VKVGLPYVYTGSFDTAGKTMMGLPPKD 195 Query: 193 F--VQSMLNMGVDLVGTNCSAGPEQ-MAEVADELLAISEVPVLVEPNAGLPELVDGKTVF 249 V L VG NC G +A + D A ++++ N G+PE G +F Sbjct: 196 IHGVVDGLAQRPVAVGANCGVGASDILASLLDMSEADPSATIVIKGNCGIPEF-RGAEIF 254 Query: 250 RLGPDDFARHTARFAAS-GVRMLGGCCGTTPDHIAALRGALDNLSGGLVP 298 G + A A + G +++GGCCGT+ +H+AA+R ALD+ + G P Sbjct: 255 YSGTPELMADYAHLAINGGAKIIGGCCGTSFEHLAAMRKALDSHTHGARP 304 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: 711 Number of extensions: 35 Number of successful extensions: 2 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: 337 Length adjustment: 35 Effective length of query: 783 Effective length of database: 302 Effective search space: 236466 Effective search space used: 236466 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: 52 (24.6 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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