Align Methionine synthase (cobalamin-dependent) (EC 2.1.1.13) (characterized)
to candidate 3608273 Dshi_1677 Methionine synthase (RefSeq)
Query= reanno::DvH:207036 (804 letters) >FitnessBrowser__Dino:3608273 Length = 329 Score = 167 bits (422), Expect = 1e-45 Identities = 111/316 (35%), Positives = 162/316 (51%), Gaps = 28/316 (8%) Query: 302 VLTTRSHLVRVGGDAPVRIIGERINPTGKKQLIAELQAGDFSLALRFSDEQVEAGAPILD 361 V+ +++ V +G D P +IGERINPTG+K+L AEL+AGDFS + + EQV GA +LD Sbjct: 5 VIESKTKTVTIGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALEQVACGAMVLD 64 Query: 362 VNVGAPMVD--------------EEVLLPDLVQRLITRHGVPLSIDSSNAAAIERALPYC 407 VN GA + E +L+ +LV R+ +PL IDSS A+E L Sbjct: 65 VNSGAVFTNKMAEDPRYADNNFVEPMLMKELVARVQALVDIPLCIDSSVPGALENGLEMA 124 Query: 408 PGSTLVNSISGEPGRMERLGPLCRDHGAPFILLPLKGRKLPVAATERIAIIEELLVQAEG 467 G L+NS++GE R+E + PL + + P + + + R A+ ++++ +A Sbjct: 125 EGRPLLNSVTGEEDRLETILPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAAD 184 Query: 468 LGIPRRLVMVDVLALAVSSKAEAARQCLETI-RWCTANGFATTIGLSNISFGLPARELLN 526 GIP ++VD L + V + A A RQ + R G TT G SN+SFGLP R L Sbjct: 185 FGIPAHDIVVDPLVMPVGAMATAGRQVFTLVARLREELGVNTTCGASNVSFGLPNRHGLG 244 Query: 527 GTFLAMAAGAGLSSCIAHPGNGRIRETVACADVLLARDANA------ERFIDAYAAWTP- 579 FL MA +G++S I +P + E V A+ L+ D N R ++A+ A P Sbjct: 245 AAFLPMAIASGMTSAIMNPIRPQEMEAVHAANFLMNHDPNGATWINFARVMEAHKAGMPF 304 Query: 580 ------ATQGGPVASG 589 T GG SG Sbjct: 305 PEAAKAGTSGGGGRSG 320 Lambda K H 0.320 0.137 0.392 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: 625 Number of extensions: 27 Number of successful extensions: 4 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: 804 Length of database: 329 Length adjustment: 35 Effective length of query: 769 Effective length of database: 294 Effective search space: 226086 Effective search space used: 226086 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 Methionine synthase (cobalamin-dependent) (EC 2.1.1.13) (characterized)
to candidate 3607665 Dshi_1074 homocysteine S-methyltransferase (RefSeq)
Query= reanno::DvH:207036 (804 letters) >FitnessBrowser__Dino:3607665 Length = 341 Score = 162 bits (411), Expect = 2e-44 Identities = 107/288 (37%), Positives = 148/288 (51%), Gaps = 12/288 (4%) Query: 14 LLFDGGLGTMLQARGLPAGVSPEQFCLDRPDVLRGIHADYVRAGADILTTNTFGG--SRF 71 LL DG GT L GL +G +PE + D PD + ++ V AG+D+ TN+FGG SR Sbjct: 16 LLTDGATGTTLFNMGLSSGDAPELWNTDHPDRIAALYQGAVDAGSDLFLTNSFGGNASRL 75 Query: 72 KLGDGFDVV-DFNRRMAAIAREAADASGRQAFVAGSIGPTGHFVKPLGEVEPAALVAAFR 130 KL D V + NR A I R AD + R+ VAGS+GPTG + P+G + V F Sbjct: 76 KLHAAQDRVRELNRLAAEIGRGVADKADRKVLVAGSMGPTGEIMAPMGPLTHDIAVEMFH 135 Query: 131 EQVRGLVAGGADLLMIETQFDLAEARAAVVAARAECSLPIAVSMTFEN-GVSLTGSTPEV 189 EQ GL GGAD+L +ET E AA A A +P +M+F+ G ++ G+T Sbjct: 136 EQAEGLKEGGADILWVET-ISAPEEYAAAAEAAARADMPWCGTMSFDTAGRTMMGTTSAT 194 Query: 190 FVATMLNLGVD--LLGTNCSAG-PDQMHDVVASLLASASVPVLVEPNAGLPELIDGKTVF 246 + L G NC G D + V+ A P++ + NAG+P+ +DG + Sbjct: 195 MARMVEKLAHPPVAFGANCGVGASDLLRTVLGFAAAGTERPIIAKGNAGIPKYVDGHIHY 254 Query: 247 RLPPAPFAEKTAAFAAMGARVLGGCCGTTPDHI----AALRQAVADIP 290 P A+ A GA V+GGCCGTT +H+ AAL + AD+P Sbjct: 255 DGTPDLMAQYAILARASGASVIGGCCGTTFEHLRHMRAALDASAADMP 302 Lambda K H 0.320 0.137 0.392 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: 660 Number of extensions: 37 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 804 Length of database: 341 Length adjustment: 35 Effective length of query: 769 Effective length of database: 306 Effective search space: 235314 Effective search space used: 235314 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 Apr 09 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