Align Methionine synthase (cobalamin-dependent) (EC 2.1.1.13) (characterized)
to candidate GFF1321 PGA1_c13370 putative homocysteine S-methyltransferase
Query= reanno::DvH:207036 (804 letters) >FitnessBrowser__Phaeo:GFF1321 Length = 338 Score = 158 bits (399), Expect = 5e-43 Identities = 106/298 (35%), Positives = 150/298 (50%), Gaps = 16/298 (5%) Query: 4 FRQALRAGRRLLFDGGLGTMLQARGLPAGVSPEQFCLDRPDVLRGIHADYVRAGADILTT 63 F L LL DG GT L GL +G +PE + +D P + ++ V AG+D+ T Sbjct: 5 FTTLLETKDALLADGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDLFLT 64 Query: 64 NTFGGS--RFKLGDGFDVV-DFNRRMAAIAREAADASGRQAFVAGSIGPTGHFVKPLGEV 120 NTFGG+ R KL D V + N A + R AD S R+ VAGS+GPTG ++P+GE+ Sbjct: 65 NTFGGTAARLKLHDAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPVGEL 124 Query: 121 EPAALVAAFREQVRGLVAGGADLLMIETQFDLAEARAAVVAARAECSLPIAVSMTFEN-G 179 A V F EQ L GG D+L +ET E RAA A + +P +M+F+ G Sbjct: 125 SHALAVEMFHEQAEALKEGGVDVLWLETISAPEEYRAAAEAFKL-ADMPWCGTMSFDTAG 183 Query: 180 VSLTGSTPEVFVATMLNLGVDL------LGTNCSAGPDQMHDVVASLLASASV-PVLVEP 232 ++ G T A M L + G NC G + V A + P++ + Sbjct: 184 RTMMGVTS----ADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKG 239 Query: 233 NAGLPELIDGKTVFRLPPAPFAEKTAAFAAMGARVLGGCCGTTPDHIAALRQAVADIP 290 NAG+P+ +DG + P E A GA+++GGCCGT PDH+ A+R+A+ P Sbjct: 240 NAGIPKYVDGHIHYDGTPTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREALDTRP 297 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: 653 Number of extensions: 50 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: 804 Length of database: 338 Length adjustment: 35 Effective length of query: 769 Effective length of database: 303 Effective search space: 233007 Effective search space used: 233007 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 GFF1582 PGA1_c16040 pterin binding domain-containing protein
Query= reanno::DvH:207036 (804 letters) >FitnessBrowser__Phaeo:GFF1582 Length = 353 Score = 155 bits (391), Expect = 5e-42 Identities = 101/299 (33%), Positives = 153/299 (51%), Gaps = 16/299 (5%) Query: 302 VLTTRSHLVRVGGDAPVRIIGERINPTGKKQLIAELQAGDFSLALRFSDEQVEAGAPILD 361 V+ +++ +G D P +IGERINPTG+K+L AEL+AGDFS + + QV AGA ILD Sbjct: 5 VVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGANILD 64 Query: 362 VNVGA-------PMVDEEVLLPDLVQRLITRHGVPLSIDSSNAAAIERALPYCPGSTLVN 414 +N G P E L+ +V+ + PL IDSS A+E L G L+N Sbjct: 65 INAGVVYNSNPNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGRPLLN 124 Query: 415 SISGEPGRMERLGPLCRDHGAPFILLPLKGRKLPVAATERIAIIEELLVQAEGLGIPRRL 474 S++GE R+E + PL + + P + + + R A+ ++++ +A GIP Sbjct: 125 SVTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAADFGIPAHD 184 Query: 475 VMVDVLALAVSSKAEAARQCLETIRWCTAN-GFATTIGLSNISFGLPARELLNGTFLAMA 533 ++VD L + + + A A +Q +R G TT G SN+SFGLP R +N FL MA Sbjct: 185 IVVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNRHGINNAFLPMA 244 Query: 534 AGAGLSSCIAHP-----GNGRIRE---TVACADVLLARDANAERFIDAYAAWTPATQGG 584 GAG++S I +P +I E V A ++L E F+ + + + G Sbjct: 245 MGAGMTSAIMNPVALPITQKKIAEKKAEVEAAGIILPEGMEDEAFVQMFGLGSTKPRAG 303 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: 687 Number of extensions: 43 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: 353 Length adjustment: 35 Effective length of query: 769 Effective length of database: 318 Effective search space: 244542 Effective search space used: 244542 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