Align 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase; EC 2.1.1.14 (characterized, see rationale)
to candidate PP_2698 PP_2698 5-methyltetrahydropteroyltriglutamate- homocysteine methyltransferase
Query= uniprot:Q6F6Z8 (344 letters) >FitnessBrowser__Putida:PP_2698 Length = 344 Score = 607 bits (1566), Expect = e-178 Identities = 295/341 (86%), Positives = 318/341 (93%) Query: 3 MKRVLPTSTAGSLPKPSWIAEPEKLWSPWKLEGADLAQGKRDALLVSLQEQLHAGIDIVS 62 M ++LPTSTAGSLPKP+W+A+PE LWSPWKL+ L +GK+DAL ++LQEQ HAGIDIVS Sbjct: 1 MNKLLPTSTAGSLPKPAWLAQPETLWSPWKLQDEQLVEGKQDALRLALQEQQHAGIDIVS 60 Query: 63 DGEQTRQHFVTTFIEHLDGVDFAKRETVRIRNRYDASVPTVVGAVSRQKPVFVEDAKFLR 122 DGEQTRQHFVTTFIEHL GVDF +R+TVRIR+RYDASVPTVVGAV+RQKPVFVEDAKFLR Sbjct: 61 DGEQTRQHFVTTFIEHLSGVDFEQRKTVRIRDRYDASVPTVVGAVARQKPVFVEDAKFLR 120 Query: 123 QQTTQPIKWALPGPMTMIDTLYDAHYKSREKLAWEFAKILNQEALELEAAGVDIIQFDEP 182 Q TTQPIKWALPGPMTMIDTLYD HYKSREKLAWEFAKILNQEA ELEAAGVDIIQFDEP Sbjct: 121 QHTTQPIKWALPGPMTMIDTLYDNHYKSREKLAWEFAKILNQEARELEAAGVDIIQFDEP 180 Query: 183 AFNVFFDEVNDWGVATLERALEGLKCETAVHICYGYGIKANTDWKKTLGSEWRQYEEAFP 242 AFNVFFDEVNDWGVATLERA+EGLKCETAVHICYGYGIKANTDWKKTLGSEWRQYE+AFP Sbjct: 181 AFNVFFDEVNDWGVATLERAIEGLKCETAVHICYGYGIKANTDWKKTLGSEWRQYEQAFP 240 Query: 243 KLQQSKIDIISLECHNSRVPMDLIELIRGKKVMVGAIDVATNTIETPEEVADTLRKALQF 302 KLQQS IDIISLECHNS VPMDL+ELIRGKKVMVGAIDVAT+ IETPE+VA TLRKALQF Sbjct: 241 KLQQSSIDIISLECHNSHVPMDLLELIRGKKVMVGAIDVATHVIETPEQVAATLRKALQF 300 Query: 303 VDADKLYPSTNCGMTPLSRDVARGKLQALSAGAEIIRRELS 343 VDADKLYP TNCGM PL R VA GKL+ALSAGA I+R+EL+ Sbjct: 301 VDADKLYPCTNCGMAPLPRQVASGKLKALSAGAAIVRQELA 341 Lambda K H 0.318 0.134 0.397 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: 524 Number of extensions: 7 Number of successful extensions: 1 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: 344 Length of database: 344 Length adjustment: 29 Effective length of query: 315 Effective length of database: 315 Effective search space: 99225 Effective search space used: 99225 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: 41 (21.7 bits) S2: 49 (23.5 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