Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate WP_011766746.1 AZO_RS15175 aldehyde dehydrogenase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1229 (505 letters) >NCBI__GCF_000061505.1:WP_011766746.1 Length = 486 Score = 219 bits (559), Expect = 1e-61 Identities = 164/488 (33%), Positives = 249/488 (51%), Gaps = 35/488 (7%) Query: 16 IDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAFQ--TWKLTPIGAR 73 I GEW + + + P + VLA+V ++AA+VDAA++AA F W P R Sbjct: 13 IAGEWRAAISGATFAKLAPTSGAVLAEVANSSAADVDAAVAAARVQFDGGEWSRLPGAER 72 Query: 74 MRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHACSIGSLQ-MGEFA 132 R++ KL L+ ++R A +L+ EQG+ + + + +++ SI +L+ +A Sbjct: 73 GRLLNKLADLLARDAERFAHILAMEQGRPLME--------MRMLDLPMSIDTLRYFAGWA 124 Query: 133 ENVAG---------GVDT--YTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLK 181 + + G G T YT+R+ IGV A I P+N P MI +W A+A G T VLK Sbjct: 125 DKLEGRQIPTAGFMGRPTLNYTIREAIGVAALIVPWNAPLMIGIWKLAPALAAGCTVVLK 184 Query: 182 PSEQDPMSTMLLVELAIEAGIPPGVLNVVHG-GKDVVDALCTHKDIKAVSFVGSTAVGTH 240 PSE P++ L LA EAG P GV N+V+G G + L H + +SF GST VG Sbjct: 185 PSEDAPLALTALAGLAAEAGFPAGVFNLVNGMGPEAGATLVKHPGVDKISFTGSTEVGRI 244 Query: 241 VYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMA-TSVVVLVG 299 + A KR+ +G K ++ DAN + A+ + F GQ C A T ++V Sbjct: 245 IAREAAPLFKRLTLELGGKAPQIICADANLDAAIMGVAMGLFVNQGQTCAAGTRILVHRS 304 Query: 300 AAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRD 359 + L A+ + + + T +G +I+ R + R+ LI+SGI EGA L G Sbjct: 305 RYDDVVGALAGAAKSVTLGDPLDANTRMGALINARHRDRVAALIQSGIAEGAALVAGGEA 364 Query: 360 ISVPGYEKGNFVGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGT 419 + E G FV PT+F+G TP+M+I +EIFGPV VV+ D+ ++A+ L N PFG Sbjct: 365 LP----ENGFFVRPTVFAGGTPQMRIMREEIFGPVGVVVPFDSDEEAVQLANDTPFGLSA 420 Query: 420 GLFTQSGAAARKFQTEIDVGQVGIN--IPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF 477 L+TQ A A ++ VG V IN P+ +P+ + S + DL + + Sbjct: 421 SLWTQDIARAHTLAPKLRVGAVAINGWSPLDARLPWGGYKDSGVGR--DL---SRTALDA 475 Query: 478 YTQTKTVT 485 YT+ K V+ Sbjct: 476 YTEEKVVS 483 Lambda K H 0.319 0.135 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: 541 Number of extensions: 36 Number of successful extensions: 5 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: 505 Length of database: 486 Length adjustment: 34 Effective length of query: 471 Effective length of database: 452 Effective search space: 212892 Effective search space used: 212892 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 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