Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_012590504.1 MSIL_RS07550 2-hydroxymuconic semialdehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000021745.1:WP_012590504.1 Length = 504 Score = 308 bits (789), Expect = 3e-88 Identities = 192/485 (39%), Positives = 265/485 (54%), Gaps = 19/485 (3%) Query: 24 FINNEFVQS-KSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQV 82 FIN EF Q SK + SP I +V E ++D AV AA AA +W Sbjct: 24 FINGEFTQGLTSKGWWENRSPLDNSVIGRVPEGGQAEVDAAVHAARAALDGTWGKMTVAQ 83 Query: 83 RMKVLYKLADLIDEHADTLAHIEALDNGKSL-MCSKGDVALTAAYFRSCAGWTDKIKGSV 141 R +L +A+ ID D E LD GK + S D+ AA F+ A D +K Sbjct: 84 RTDLLAAVANEIDARFDEFLAAECLDTGKPYSLASHIDIPRGAANFKMFA---DTVKNVS 140 Query: 142 IET-------GDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAES 194 ET G + NY R P G+ I PWN PLL+ +WK+GP L G T V+K +E Sbjct: 141 TETFILDTPDGKSAVNYGLRRPKGLIAVISPWNLPLLLMTWKVGPALACGNTVVVKPSEE 200 Query: 195 TPLSALYLASLIKEAGAPPGVVNVVSGFGP-TAGAPISSHPKIKKVAFTGSTATGRHIMK 253 TPL+A L ++ + G P GV NVV G GP +AG ++ HP + + FTG T TG IM+ Sbjct: 201 TPLTATLLGEVMNKVGVPKGVYNVVHGLGPNSAGEFLTQHPLVNGITFTGETRTGEAIMR 260 Query: 254 AAAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIY 313 AA +++V+ ELGGK+P IVF D D+ I+ + F N G+VC R+YV+ I+ Sbjct: 261 QAA-LGVRQVSFELGGKNPAIVFADCDLDKAIEGTMRSAFANCGQVCLGTERVYVERPIF 319 Query: 314 DKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG---E 370 D V+ K AE+L++G P T +G SQ K+L Y + +EGAT++TGG + Sbjct: 320 DSFVARMKGDAEALRLGRPEDGATNLGPLISQEHRSKVLSYYKLALEEGATLVTGGGVPD 379 Query: 371 RFGN--KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAG 428 G G +++PTI+ +K+D + V +EIFGP I F T EE + LAN + YGLAA Sbjct: 380 MPGELALGAWVQPTIWTGLKDDARAVNEEIFGPCCHIRPFDTEEEAVRLANSTPYGLAAA 439 Query: 429 VHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKA 488 V T N+S A V++K++ G WVN++ FGG QSGIGRE G +L+ YT++ Sbjct: 440 VWTENVSRAHRVASKMDVGICWVNSWFLRDLRTAFGGAKQSGIGREGGLHSLEFYTELSN 499 Query: 489 VRIGL 493 V I L Sbjct: 500 VCIKL 504 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: 579 Number of extensions: 31 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: 495 Length of database: 504 Length adjustment: 34 Effective length of query: 461 Effective length of database: 470 Effective search space: 216670 Effective search space used: 216670 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 Apr 09 2024. 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