Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 6939342 Sama_3435 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::Q97YT9 (492 letters) >FitnessBrowser__SB2B:6939342 Length = 506 Score = 197 bits (501), Expect = 7e-55 Identities = 142/468 (30%), Positives = 241/468 (51%), Gaps = 25/468 (5%) Query: 13 GKLKLYINGEFIDSKTDTIGKAYNPAKDEIIAEVPFSAKDEVEEAIQSAQEAFEKWREVP 72 GK + GE+ D+ + GK + + S ++E A+ +A A + W + Sbjct: 25 GKWVPPVGGEYFDNVSPVDGKVF--------CQAARSDYRDIELALDAAHAAKDSWGKTS 76 Query: 73 ITTRIQYLFALKNRLEEYSETIARIIVQNHGKTIQEA-RGDMRRTIENVEAAISAAYTLY 131 +T R L + +R+E++ E +A + +GK ++E D+ +++ + Sbjct: 77 VTERSNLLLKIADRVEQHLERLAVVETWENGKAVRETLNADLPLFVDHFRY-FAGCIRAQ 135 Query: 132 KGEHLDQVSQEVDETVVREPLGVFGIITPFNFPTMVPFWFLPYAIVLGNTVVVKPSEITP 191 +G D + V + EPLGV G I P+NFP ++ W + A+ GN VV+KP+E TP Sbjct: 136 EGSAADLDANTVSYHLP-EPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTP 194 Query: 192 VPMDFIIRIFDEIKLPRGVVNVVHG-AKDVVDEFLTNKLVQGVTFVGSTRVGKYIYENAG 250 + ++ +++ LP GV+NVV+G + T+K + + F GST VG +I + A Sbjct: 195 ASIMVLLETIEDL-LPPGVLNVVNGFGAEAGAALATSKRIAKLAFTGSTEVGNHILKCAA 253 Query: 251 KNGKKAIVQAGAKN----FVVVMPDAD--LNKAIPSIVSAFFGNAGQRCLAAANLVAVGN 304 +N + V+ G K+ F VM D L+KAI ++ AFF N G+ C + ++ + Sbjct: 254 ENLIPSTVELGGKSPNIYFADVMNHEDNYLDKAIEGMLLAFF-NQGEVCTCPSRVLVQES 312 Query: 305 IYDEVKRKFIEASKQLKIGYGLDESVDMGPVVTKDAKKRIIGYIEKGIEEGAKLLLDGRD 364 IYD K I +K ++ G LD +G +++ +I+GY++ G EGAK+L+ G + Sbjct: 313 IYDAFIEKVIARAKTIRQGSPLDTDTQVGAQASREQYDKILGYLDIGRAEGAKVLMGG-E 371 Query: 365 VKVPEYP--NGYFLGPTVFDEVTPEMVIAKEEIFGPVASIIHVKNLDEAINIINRSNYGN 422 K+ + P GY++ PT+ + +M + +EEIFGPV S+ K+ EA+ I N + YG Sbjct: 372 FKLQDGPEKGGYYIQPTIL-KGHNKMRVFQEEIFGPVVSVTTFKDEAEALAIANDTQYGL 430 Query: 423 ASSIFTTSGYYARKFRREVNTGNIGINIGVAAPMAFFPFGGRKESFFG 470 + ++T A++ R + G + IN A P A FGG K+S G Sbjct: 431 GAGVWTRDMNLAQRMGRGIQAGRVWINCYHAYP-AHAAFGGYKKSGIG 477 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: 526 Number of extensions: 27 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: 492 Length of database: 506 Length adjustment: 34 Effective length of query: 458 Effective length of database: 472 Effective search space: 216176 Effective search space used: 216176 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