Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate WP_027178998.1 G496_RS0109010 methionine synthase
Query= reanno::Phaeo:GFF1582 (353 letters) >NCBI__GCF_000429985.1:WP_027178998.1 Length = 804 Score = 164 bits (414), Expect = 1e-44 Identities = 102/313 (32%), Positives = 159/313 (50%), Gaps = 24/313 (7%) Query: 5 VVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGANILD 64 V+ S+ ++ +GF+ +IGERINPTG+K L+AEL+ G F+ K A Q+ AGA ILD Sbjct: 302 VITSRAESVCIGFNHTGVIIGERINPTGKKVLSAELQEGRFTEALKFAGQQIEAGAPILD 361 Query: 65 INAGVVYNSNPNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGRPLLN 124 +N G P E ++ + + + PL IDS+ P A+EA L G PL+N Sbjct: 362 VNVGA-------PMVDETMILPALCKEIIAQHQVPLSIDSTNPDAVEAALWNYPGTPLVN 414 Query: 125 SVTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAADFGIPAHD 184 S++GE R+E + PL KK+ P + + + + + + V +K++ A GIP Sbjct: 415 SISGEPGRMERLGPLCKKFGAPFILLPIIGSKLPFECKDKIEVTEKLLREAEALGIPRRL 474 Query: 185 IVVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNRHGINNAFLPMA 244 I+VD L + + + A + +R +EE + T G SNVSFGLP R +N+ FL + Sbjct: 475 IMVDALALTVSSRPMAARHCMDFIRHCKEEWNLPTVLGLSNVSFGLPARELLNSTFLTLC 534 Query: 245 MGAGMTSAIMNPVALPITQKKIAEKKAEVEAAGIILPEGMEDEAFVQMF---------GL 295 G G+ + I NP A + + +A ++L + E F+ M+ Sbjct: 535 QGQGLCAFISNP--------NSARLRESLYSAEVLLARDKQAENFIDMYSEWSPAAPSST 586 Query: 296 GSTKPRAGKEMEA 308 G TK GK+ A Sbjct: 587 GGTKGGEGKKSGA 599 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: 571 Number of extensions: 24 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: 804 Length adjustment: 35 Effective length of query: 318 Effective length of database: 769 Effective search space: 244542 Effective search space used: 244542 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 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