Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_065398804.1 BBI00_RS10955 aldehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_001684965.1:WP_065398804.1 Length = 509 Score = 236 bits (601), Expect = 2e-66 Identities = 162/484 (33%), Positives = 255/484 (52%), Gaps = 17/484 (3%) Query: 9 NYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRR 68 NYI+G++ QY DVV+P + QV S+KED++ A AA+AF+TW + R Sbjct: 24 NYIDGKFTPPVKGQYFDVVSPVDGKNFTQVAHSSKEDLELAVDAAAKAFQTWKNTSSTER 83 Query: 69 ARILFNFQQLLSQHKEELAHLITIENGKNTKEAL-GEVGRGIENVEFAAGAPSLMMGDSL 127 + IL + Q+ E LA + TI+NGK +E L ++ I++ + A G S Sbjct: 84 SIILNKIADRIEQNLEYLATVETIDNGKAVRETLAADLPLAIDHFRYFASVIRADEG-SH 142 Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187 + D + P+GV+ I P+NFP+++ W A+A GN +LKP+E TP+ Sbjct: 143 NELDKDTVSLIVHEPLGVIAQIIPWNFPILMAVWKLAPALAAGNCVVLKPAESTPVSIMI 202 Query: 188 LVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKR 246 L+EL LP GV N+V G ++ ++ +P++ +F GS G V + +EN+ Sbjct: 203 LMELIGDL-LPAGVINIVNGFGAELGRALVTNPKVAKAAFTGSTATGRLVMQYATENIIP 261 Query: 247 VQSLTGAKNHTIVLN---DANLEDTVTNIVGAAFG--SAGERCMACAVVTVEEGIADEFM 301 V G K+ + N DA+ E I GA + GE C + + V+EGIAD F+ Sbjct: 262 VTLELGGKSPNVFFNSVMDADDEFLDKAIEGAVLFALNQGEICTCPSRLLVQEGIADAFI 321 Query: 302 AKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGREN----V 357 K+ E+V IK+GN LD V +G + K + LSYI+ G++EGA ++ G N Sbjct: 322 EKVIERVKAIKVGNPLDKTVMMGAQASKIQKDKILSYIQLGIDEGAEVLVGGDVNHLGED 381 Query: 358 SDDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTS 417 +DG+++ PTIF M I+++EIF PVL+ K+ +EA++IAN + + GA ++T Sbjct: 382 LEDGFYIQPTIFKG-NNRMRIFQEEIFGPVLAFTTFKDEEEAVKIANDTMYGLGAGVWTR 440 Query: 418 NSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVV 477 +++ + I+AG + +N P A PF G+K S G N K +D Y + K + Sbjct: 441 DAHQLYNIPRQIEAGRVWVNQYHSYP-AGAPFGGYKQSGIG--RENHKMMLDHYRQTKNM 497 Query: 478 TARY 481 Y Sbjct: 498 LISY 501 Lambda K H 0.318 0.136 0.396 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: 584 Number of extensions: 28 Number of successful extensions: 7 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: 487 Length of database: 509 Length adjustment: 34 Effective length of query: 453 Effective length of database: 475 Effective search space: 215175 Effective search space used: 215175 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