Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_057687530.1 ABB28_RS16890 betaine-aldehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >NCBI__GCF_001431535.1:WP_057687530.1 Length = 490 Score = 303 bits (775), Expect = 1e-86 Identities = 173/472 (36%), Positives = 265/472 (56%), Gaps = 7/472 (1%) Query: 11 QQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAK 70 QQ Y+ G VDA +G+T + NPATG++I V A+ RA+ +A + W A+TA Sbjct: 7 QQLYIHGKLVDATSGKTFQSINPATGKVIAEVQIANQADVERAVASAAEGQKVWAAMTAM 66 Query: 71 ERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKG-EIAYAASFLEWFGEEAKRIYGD 129 ER+ LRR DL+ E D LA+L T++ GK L+E +I A LE++ A I G+ Sbjct: 67 ERSRILRRAVDLLRERNDALAQLETLDTGKALSETTTVDIVTGADVLEYYAGLATAIEGN 126 Query: 130 TIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSA 189 +P + ++P+GV A I WN+P + K+ PALAAG MV KP+ TP + Sbjct: 127 QVPLRE-SSFFYTRREPLGVVAGIGAWNYPVQIALWKSAPALAAGNAMVFKPSEVTPLTV 185 Query: 190 LALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECA-QD 248 + LA++ AG+P GVF+VV G EVG LT +P++ K++FTG E G+++MA A Sbjct: 186 IELAKIYTEAGVPDGVFNVVQGPGREVGQWLTEHPVIEKISFTGGVETGKKVMASAASSS 245 Query: 249 IKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDK 308 +K+V++ELGG +P ++ DDA L+ A + A+++ + ++GQ C R++V + AF Sbjct: 246 LKEVTMELGGKSPLVICDDAQLERAADIAVMANFFSSGQVCTNGTRVFVPRPMLAAFEAA 305 Query: 309 LKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALG---- 364 + V ++ IG+ +A GP+ + V I +GA++++GG G Sbjct: 306 VVERVKRIRIGDPQDAQTNFGPMTSFAHMDNVLRLIETGKREGARLLTGGGRATDGALAK 365 Query: 365 GTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLA 424 G + PT+ D + + ++E FGP+ + + DE EVIA +NDT FGLA+ + D+A Sbjct: 366 GAYVLPTVFSDCRDDMTIVREEIFGPVMSILAYDDEEEVIARANDTHFGLAAGVVSNDIA 425 Query: 425 RVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 476 R R+ +LE G+ INT S P GG K SG+GRE + Y IK Sbjct: 426 RAHRIIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGISTLAHYTRIK 477 Lambda K H 0.317 0.135 0.391 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: 28 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: 483 Length of database: 490 Length adjustment: 34 Effective length of query: 449 Effective length of database: 456 Effective search space: 204744 Effective search space used: 204744 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