Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate WP_083441388.1 NITAL_RS09220 aldehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_5146 (508 letters) >NCBI__GCF_000969705.1:WP_083441388.1 Length = 526 Score = 229 bits (584), Expect = 2e-64 Identities = 150/488 (30%), Positives = 252/488 (51%), Gaps = 18/488 (3%) Query: 8 NDTTVQKVKLLIDGQWVESKTTEWHDIINPATQQVLAKVPFATAEEVDAAISAAHRAFQT 67 +D T Q L IDG+ E+ + ++ NPAT + V ATA++VD A+ AAHRAF Sbjct: 43 DDVTTQ---LWIDGEAAEATGAD-REVQNPATLATIETVKDATADDVDRAVQAAHRAFPG 98 Query: 68 WKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVVEHACSIG 127 W T + R I+ K L+ +H + + A L EQGK +A+G+ + + + Sbjct: 99 WAATDVTKRAGIVRKAADLLAQHREELVASLVQEQGKPTLEAKGEFGHFVNGLYFYSELA 158 Query: 128 SLQMGEFAENVAGGVDTY--TLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKP 185 S G + E + +Y T+R+P+GV I P+NFP + A+ GNT V KP Sbjct: 159 SKVRGGYQELPSQFGRSYGLTIRRPLGVVGAIVPWNFPLTLLANKLGPALVAGNTVVAKP 218 Query: 186 SEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDGLCTHKDIKAVSFVGSTAVGTHVY 245 +E P++T+ + EL EAG+PAGV+NVV G + + L TH ++ V+F G T+ G + Sbjct: 219 AETTPLTTLRVAELLGEAGVPAGVVNVVTGAAETGEALVTHPLVRRVAFTGQTSTGQRIA 278 Query: 246 DLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGAA- 304 +LAG+ KRV +G + ++VL DA+ + A+ + + GQ C+A +V Sbjct: 279 ELAGRDLKRVSLELGGSDPSIVLADADLDAAVKTIQIGRYWNCGQMCLAPKRAFVVDEVY 338 Query: 305 KQWLPDLKALAQKLKVNAGSEPGTD----VGPVISKKAKARILDLIESGIKEGAKLELDG 360 +++ + + ++ + G+EP +GP+ + + + D + + GAK+ + G Sbjct: 339 DRFVDTMVSRVERYEPGNGAEPAEKPKLRIGPLHTARQLQTLQDQLADAVDRGAKVLVGG 398 Query: 361 REISVP-GYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVNTLDEAIALVNANPFG 419 VP G G+F P + V D ++ T+E+FGPVL V V+ +D AI L N +G Sbjct: 399 ---GVPDGTSGGHFFQPAVVVDVPRDSRLATEEVFGPVLPVWRVDDVDHAIELANDTEYG 455 Query: 420 NGTGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQ 479 G+ ++T+ A K N ++ G +N + F G++ S +G +G + ++ Sbjct: 456 LGSSIWTRDAGAIDKAMNGLETGITWVN-QMHYGYDEMPFGGTKMSGVG--REHGAEALE 512 Query: 480 FYTQTKTV 487 Y + K+V Sbjct: 513 EYVEIKSV 520 Lambda K H 0.318 0.135 0.395 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: 621 Number of extensions: 24 Number of successful extensions: 3 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: 508 Length of database: 526 Length adjustment: 35 Effective length of query: 473 Effective length of database: 491 Effective search space: 232243 Effective search space used: 232243 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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