Align Methylmalonate-semialdehyde dehydrogenase [acylating]; MMSDH; EC 1.2.1.27 (characterized)
to candidate GFF964 HP15_943 aldehyde dehydrogenase family protein
Query= SwissProt::P28810 (497 letters) >FitnessBrowser__Marino:GFF964 Length = 505 Score = 196 bits (499), Expect = 1e-54 Identities = 153/484 (31%), Positives = 232/484 (47%), Gaps = 27/484 (5%) Query: 6 RHLIAGAFVEGLGAQRIPVSNPLDNSTLAEIACASAEQVEQAVASARETFAS--WKETPV 63 R + G + + +P+D LA IA +QAV +AR F + W + Sbjct: 28 RAYLNGTYQWAANGEAFTSVSPIDGRELASIASCDQSDADQAVMAARAAFEAGIWSQLAP 87 Query: 64 SERARVMLRYQALLKEHHDELAKIVSSELGKTFEDAKG-DVWRGIEVVEHACNVPSLLMG 122 ++R V+LR+ L++ H DELA + + ++GK A DV + + G Sbjct: 88 AKRKAVLLRFAELIEAHGDELALLETLDMGKPINHASNVDVPATARAIRWTAEAIDKVYG 147 Query: 123 ETVENVARNIDTYSITQPLGVCVGITPFNFPAMIPLWMFPLAIACGNAFILKPSEQVPLT 182 E I S +P+GV I P+NFP ++ W A+A GN+ ILKPSE+ PL+ Sbjct: 148 ELAPTPHNQIGMIS-REPMGVVAAIVPWNFPMIMAAWKIAPALATGNSVILKPSEKSPLS 206 Query: 183 SVRLAELFLEAGAPKGVLQVVHGGKEQVDQLLK-HPQVKAVSFVGSVAVG-QYVYHTGTA 240 ++RLA L EAG P GV V+ G V + L H V + F GS V Q + + G + Sbjct: 207 AIRLAALAGEAGVPAGVFNVLPGYGHTVGKALALHMDVDCLVFTGSTNVAKQLMIYAGQS 266 Query: 241 HNKRVQSFAGAKNHMVIMPDA-DKAQVISNLVGASVGAAGQRCMAISVAVLVGAAR-EWI 298 + KRV AG K+ ++ DA D + + A G+ C A S ++ + R E++ Sbjct: 267 NMKRVWLEAGGKSPNIVFADAPDLKKAAAEAASAIAFNQGEVCTAGSRLLVENSIRAEFV 326 Query: 299 PEIRDALAKVRPGPWDDSGASYGPVINPQAKARIERLIGQGVEEGAQLLLDGRGYKVEGY 358 I +AL RPG D + G +++ RI IG G EGA+L+ G+ ++ Sbjct: 327 RLICEALKTWRPGHPLDPATTCGAIVDQAQLDRIIDYIGIGQSEGARLVEGGQ--RILEN 384 Query: 359 PDGNWVGPTLFAGVRPDMAIYREEVFGPVLCLAEVDSLEQAIRLINESPYGNGTSIFTSS 418 G +V PT+F GV M I EE+FGPVL + D+ ++A+ + N+S YG +++TS+ Sbjct: 385 TGGLFVQPTVFDGVNNQMRIASEEIFGPVLSVIGFDTADEAVAIANDSIYGLAAAVWTSN 444 Query: 419 GAAARTFQHHIEVGQVGINI----PIPVPLPFFSFTGWKGSFYG---DLHAYGKQGVRFY 471 A + G V IN + P F G+K S G +HA+ K Y Sbjct: 445 INTAHKVAKALRAGSVWINHYDGGDMTAP-----FGGFKQSGNGRDKSVHAFDK-----Y 494 Query: 472 TETK 475 TE K Sbjct: 495 TELK 498 Lambda K H 0.319 0.135 0.406 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: 592 Number of extensions: 29 Number of successful extensions: 6 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: 497 Length of database: 505 Length adjustment: 34 Effective length of query: 463 Effective length of database: 471 Effective search space: 218073 Effective search space used: 218073 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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