Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_057687530.1 ABB28_RS16890 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_001431535.1:WP_057687530.1 Length = 490 Score = 352 bits (902), Expect = e-101 Identities = 185/476 (38%), Positives = 286/476 (60%), Gaps = 6/476 (1%) Query: 23 LFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQV 82 L+I+ + V + S KTF +++P+T + I +V A D++ AV A+ A W+ Sbjct: 9 LYIHGKLVDATSGKTFQSINPATGKVIAEVQIANQADVERAV-ASAAEGQKVWAAMTAME 67 Query: 83 RMKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKGDVALTAAYFRSCAGWTDKIKGSV 141 R ++L + DL+ E D LA +E LD GK+L + D+ A AG I+G+ Sbjct: 68 RSRILRRAVDLLRERNDALAQLETLDTGKALSETTTVDIVTGADVLEYYAGLATAIEGNQ 127 Query: 142 IETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALY 201 + ++ F YTRREP+GV I WN+P+ +A WK P L G V K +E TPL+ + Sbjct: 128 VPLRESSFFYTRREPLGVVAGIGAWNYPVQIALWKSAPALAAGNAMVFKPSEVTPLTVIE 187 Query: 202 LASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLK 261 LA + EAG P GV NVV G G G ++ HP I+K++FTG TG+ +M +AA S+LK Sbjct: 188 LAKIYTEAGVPDGVFNVVQGPGREVGQWLTEHPVIEKISFTGGVETGKKVMASAASSSLK 247 Query: 262 KVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFK 321 +VT+ELGGKSP ++ DDA ++ V F+++G+VC G+R++V + + Sbjct: 248 EVTMELGGKSPLVICDDAQLERAADIAVMANFFSSGQVCTNGTRVFVPRPMLAAFEAAVV 307 Query: 322 NAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN----KGY 377 + ++IGDP T G TS +D +L+ I+ GK+EGA ++TGG R + KG Sbjct: 308 ERVKRIRIGDPQDAQTNFGPMTSFAHMDNVLRLIETGKREGARLLTGGGRATDGALAKGA 367 Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437 ++ PT+F D ++D IVR+EIFGPV++I + EEVIA AND+ +GLAAGV + +++ A Sbjct: 368 YVLPTVFSDCRDDMTIVREEIFGPVMSILAYDDEEEVIARANDTHFGLAAGVVSNDIARA 427 Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493 + +++ +G W+NT+ + +P GGY QSG+GRE G L +YT++K+V++ L Sbjct: 428 HRIIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGISTLAHYTRIKSVQVEL 483 Lambda K H 0.316 0.133 0.389 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: 573 Number of extensions: 38 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: 495 Length of database: 490 Length adjustment: 34 Effective length of query: 461 Effective length of database: 456 Effective search space: 210216 Effective search space used: 210216 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 (21.6 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