Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate WP_012406895.1 NPUN_RS00340 methionine synthase
Query= reanno::Phaeo:GFF1582 (353 letters) >NCBI__GCF_000020025.1:WP_012406895.1 Length = 1177 Score = 128 bits (321), Expect = 9e-34 Identities = 89/247 (36%), Positives = 129/247 (52%), Gaps = 16/247 (6%) Query: 18 DEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGANILDINAGVVYNSNPNP 77 D F ++GER+N +G KK L A D+ + A AQV GA+ILDIN V Sbjct: 339 DNSFLIVGERLNASGSKKCRDLLNAEDWDGLVSMARAQVKEGAHILDINVDYVGRDGVRD 398 Query: 78 NETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGRPLLNSVTGE--EERLEH 135 M ++V + PL +DS+ +EAGL+ A G+ LLNS E E R Sbjct: 399 -------MHELVSRIVNNVTLPLMLDSTEWEKMEAGLKVAGGKCLLNSTNYEDGEPRFLK 451 Query: 136 VLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAADFGIPAHDIVVDPLVMPIG 195 VL L KKY V+ + D+ G++ D +FA+A + +A ++GIP +I D L +PI Sbjct: 452 VLELAKKYGAGVIIGTIDEDGMARTADKKFAIAGRAYRQAVEYGIPPTEIFFDTLALPIS 511 Query: 196 AMATA----GQQVFALVRRLREEL-GVNTTCGASNVSFGL--PNRHGINNAFLPMAMGAG 248 G+ +RR+R+EL G + G SN+SFGL +R +N+ FL A AG Sbjct: 512 TGIEEDRENGKATIESIRRIRQELPGSHVILGVSNISFGLTPASRMVLNSVFLHEATTAG 571 Query: 249 MTSAIMN 255 M +AI++ Sbjct: 572 MDAAIVS 578 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: 668 Number of extensions: 37 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: 353 Length of database: 1177 Length adjustment: 38 Effective length of query: 315 Effective length of database: 1139 Effective search space: 358785 Effective search space used: 358785 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: 54 (25.4 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