Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate 8499710 DvMF_0476 homocysteine S-methyltransferase (RefSeq)
Query= reanno::Phaeo:GFF1582 (353 letters) >FitnessBrowser__Miya:8499710 Length = 818 Score = 155 bits (393), Expect = 3e-42 Identities = 96/287 (33%), Positives = 153/287 (53%), Gaps = 16/287 (5%) Query: 5 VVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGANILD 64 V+ ++ + +G P +IGERINPTG+K L AEL+AG+F+ + A QV AGA +LD Sbjct: 307 VLTTRAQAVHIGAGSPIRIIGERINPTGKKLLTAELQAGEFAQALRFADEQVEAGAPLLD 366 Query: 65 INAGVVYNSNPNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGRPLLN 124 +N G P E L+ +VE + PL +DSS A+ A L G PL+N Sbjct: 367 VNVGA-------PMVDEAVLLPALVERLVARHSLPLSLDSSNADAIAAALPFHPGSPLVN 419 Query: 125 SVTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAADFGIPAHD 184 S++GE R+EH+ PL + + P + + + R A+ ++++++A IP Sbjct: 420 SISGEPGRMEHLGPLCRDHGAPFILLPLKGRKLPVTAAERIAIIEELLQQADSLRIPRRL 479 Query: 185 IVVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNRHGINNAFLPMA 244 ++VD L + + + A A + +R + G+ TT G SN+SFGLP R +N+ FL MA Sbjct: 480 VMVDVLALAVSSKAEAARHCLDTIRWCAAQ-GLPTTIGLSNISFGLPARELLNSTFLAMA 538 Query: 245 MGAGMTSAIMNPVALPITQKKIAEKKAEVEAAGIILPEGMEDEAFVQ 291 GAG++S I +P A + V A+ ++L E+F++ Sbjct: 539 AGAGLSSCIAHP--------GNARIREAVAASSVLLGLDANAESFIE 577 Lambda K H 0.315 0.134 0.379 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: 614 Number of extensions: 36 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: 353 Length of database: 818 Length adjustment: 35 Effective length of query: 318 Effective length of database: 783 Effective search space: 248994 Effective search space used: 248994 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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