Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate Synpcc7942_1372 Synpcc7942_1372 methionine synthase (B12-dependent)
Query= reanno::Phaeo:GFF1582 (353 letters) >FitnessBrowser__SynE:Synpcc7942_1372 Length = 1190 Score = 132 bits (332), Expect = 5e-35 Identities = 92/265 (34%), Positives = 140/265 (52%), Gaps = 17/265 (6%) Query: 18 DEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGANILDINAGVVYNSNPNP 77 D F +IGER+N +G KK+ L D+ + A +QV GA++LD+N V Sbjct: 349 DNSFLIIGERLNASGSKKVRELLNEEDWDGLVAIARSQVKEGAHVLDVNVDYVGRDGERD 408 Query: 78 NETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGRPLLNSVTGEE--ERLEH 135 M ++V + + PL +DS+ +EAGL+ A G+ +LNS E+ ER Sbjct: 409 -------MGELVSRLVTNVNLPLMLDSTEWQKMEAGLKKAGGKCILNSTNYEDGDERFFK 461 Query: 136 VLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAADFGIPAHDIVVDPLVMPIG 195 VL L K+Y +V + D+ G++ + +FA+A++ A +FGIPAH+I DPL +PI Sbjct: 462 VLELAKQYGAGIVVGTIDEEGMARTAEKKFAIAQRAYRDALEFGIPAHEIFYDPLALPIS 521 Query: 196 AMATA----GQQVFALVRRLREEL-GVNTTCGASNVSFGL--PNRHGINNAFLPMAMGAG 248 G++ +R +RE L GV+ G SN+SFGL R +N+ FL A AG Sbjct: 522 TGIEEDRGNGRETIESIRLIRENLPGVHILLGVSNISFGLNPAARIVLNSVFLHDACEAG 581 Query: 249 MTSAIMNPVALPITQKKIAEKKAEV 273 M AI++ + + KI EK +V Sbjct: 582 MDGAIVSAAKI-LPLSKIDEKPLQV 605 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: 709 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: 1190 Length adjustment: 38 Effective length of query: 315 Effective length of database: 1152 Effective search space: 362880 Effective search space used: 362880 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 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