Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate N515DRAFT_4224 N515DRAFT_4224 coniferyl-aldehyde dehydrogenase
Query= reanno::psRCH2:GFF2388 (503 letters) >FitnessBrowser__Dyella79:N515DRAFT_4224 Length = 456 Score = 110 bits (276), Expect = 8e-29 Identities = 107/379 (28%), Positives = 158/379 (41%), Gaps = 15/379 (3%) Query: 71 RARIFLKYQQLIRENMKELAAILTAEQGKTLADAEG--DVFRGLEVVEHAAGIGNLQLGE 128 RAR LI E+ E+A + + G A +VF L + HA G + Sbjct: 16 RARRLRALNDLIGEHRGEIADAIHQDFGGRPAQETDLLEVFPSLSAIRHALAHGRRWMKP 75 Query: 129 LAN---NVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDP 185 + + QPLGV I P+N+P + A+A GN ++K SE P Sbjct: 76 RRSWPGLLFMPARNEIRPQPLGVVGIIVPWNYPLFLAAGPMVDALAAGNRVMVKMSEYTP 135 Query: 186 MVTMRLCELALEAGVPPGVLNVVHGGPDVVNAICDHPDIKAVSFVGSTKVGTHVYNRASQ 245 + +LA P V VV G DV A P + F GST VG HV AS Sbjct: 136 QFSALFAQLAARYFKPEEVC-VVTGDADVAQAFSALP-FDHLLFTGSTAVGRHVMRAASA 193 Query: 246 AGKRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEAQAWIPD 305 V +G K+ AIV P A + + AGQ C+A V+L +A + + Sbjct: 194 NLTPVTLELGGKSPAIVGPGARFANAVERILVGKLFNAGQTCIAPDYVLL---PRAQVDE 250 Query: 306 LVAKAQTLKVNAGVEA--GTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSVSGY 363 VA A+ + + ++S R++ L + R+GAKL L G Sbjct: 251 FVAAARDVAARLYPQPVRNEQYASIISERQYQRLAALRDDAARDGAKLTLLGDETDDIQR 310 Query: 364 ENGNFVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIFTRS 423 + P + +GV+ M+V QEEIFGP+L ++ +++AI + A+P+ +F Sbjct: 311 RR---MTPALLTGVSESMAVMQEEIFGPLLPLVPYDDIEQAIAYVAAHPHPLALYLFEED 367 Query: 424 GAAARHFQEEIDVGQVGIN 442 GA G V IN Sbjct: 368 GALVDRVLARTTAGGVTIN 386 Lambda K H 0.318 0.134 0.394 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: 506 Number of extensions: 20 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: 503 Length of database: 456 Length adjustment: 34 Effective length of query: 469 Effective length of database: 422 Effective search space: 197918 Effective search space used: 197918 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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