Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF4005 HP15_3945 aldehyde dehydrogenase family protein
Query= BRENDA::Q97YT9 (492 letters) >FitnessBrowser__Marino:GFF4005 Length = 471 Score = 231 bits (588), Expect = 5e-65 Identities = 156/461 (33%), Positives = 236/461 (51%), Gaps = 24/461 (5%) Query: 18 YINGEFIDSKTDTIGKAYNPAKDEIIAEVPFSAKDEVEEAIQSAQEAFEKWREVPITTRI 77 YING+++ D I + ++IA VP + DE+E+AI +A AFE W E + RI Sbjct: 8 YINGQWVSWAGDMID-VHEAGTGDVIARVPAAGADEMEQAIAAADAAFESWSESTLEERI 66 Query: 78 QYLFALKNRLEEYSETIARIIVQNHGKTIQEARGDMRRTIENVEAAISAAYTLYKGEHLD 137 + L L L+E + IA + + G I+ A ++A + AA T + L Sbjct: 67 KVLEQLHAGLKERAPEIAETVCREVGMPIKLATP--------IQAGMPAAVTKSYLKLLP 118 Query: 138 Q---VSQEVDETVVREPLGVFGIITPFNFPTMVPFWFLPYAIVLGNTVVVKPSEITPVPM 194 Q + V P+GV G ITP+N+P + AI G TVV+KPSEI P Sbjct: 119 DFPFTEQSGNSEVQYAPVGVVGCITPWNYPLHQVILKIVPAIAAGCTVVLKPSEIAPQTA 178 Query: 195 DFIIRIFDEIKLPRGVVNVVHGAKDVV-DEFLTNKLVQGVTFVGSTRVGKYIYENAGKNG 253 + I D LP+GV N+V G V D + + V+ V+F GSTR G I A + Sbjct: 179 FILAEILDGTDLPKGVFNMVCGYGHTVGDTLIKHPDVRMVSFTGSTRTGNLIAHAAADDF 238 Query: 254 KKAIVQAGAKNFVVVMPDADLNKAIPSIVSAFFGNAGQRCLAAANLVAVGNIYDEVKRKF 313 K+ ++ G K+ V++PDADL A+ ++ N+GQ C A ++ + +DE Sbjct: 239 KRFALEMGGKSASVILPDADLAAAVKGTINNCLLNSGQTCTALTRMLVPADKHDEACELA 298 Query: 314 IEASKQLKIGYGLDESVDMGPVVTKDAKKRIIGYIEKGIEEGAKLLLDGRDVKVPEYP-- 371 A ++ G L+E+ +GP+ + + ++I YI+ G++EGAKL+ G PE P Sbjct: 299 AAAVAKMTPGNPLEETTRLGPLSSAQQRDKVIDYIKLGVQEGAKLIAGG-----PEAPEG 353 Query: 372 --NGYFLGPTVFDEVTPEMVIAKEEIFGPVASIIHVKNLDEAINIINRSNYGNASSIFTT 429 GYF+ TVF V P+ IA+EEIFGPV +I + EA+ I N + YG + ++++ Sbjct: 354 CEKGYFVKATVFGNVKPDSRIAQEEIFGPVLCVIPYNDEAEAVKIANGTQYGLSGAVWSG 413 Query: 430 SGYYARKFRREVNTGNIGINIGVAAPMAFFPFGGRKESFFG 470 A+K ++ TG + +N G PMA PFGG S G Sbjct: 414 DDAKAKKIASKLRTGQVFVNGGAFNPMA--PFGGFGHSGIG 452 Lambda K H 0.319 0.139 0.398 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: 540 Number of extensions: 23 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: 492 Length of database: 471 Length adjustment: 34 Effective length of query: 458 Effective length of database: 437 Effective search space: 200146 Effective search space used: 200146 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 (21.7 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