Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate GFF2135 PGA1_c21670 betaine aldehyde dehydrogenase BetB
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Phaeo:GFF2135 Length = 485 Score = 346 bits (888), Expect = e-100 Identities = 187/469 (39%), Positives = 282/469 (60%), Gaps = 5/469 (1%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FIN E+V+ + + +T E+I V+ A ++ A+ A AA +W+ R Sbjct: 12 FINGEYVEDTAGTPIPVIYAATGEQIATVHAATPAIVEQALSTAKAA-QKAWARMTGTER 70 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSK-GDVALTAAYFRSCAGWTDKIKGSVI 142 ++L + AD++ E L+ +E D GK L + D A G + G I Sbjct: 71 GRILRRAADIMRERNHDLSVLETYDTGKPLQETLVADATSGADALEYFGGLAASLTGEHI 130 Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 G+ + YT+RE +G+C I WN+P +A WK P L G + V K +E+TPL AL + Sbjct: 131 PLGED-WVYTKREALGLCVGIGAWNYPTQIACWKGAPALACGNSMVFKPSETTPLCALKV 189 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 A ++ EAGAP GV NVV G G GA ++ P++ KV+ TGS TG+ + AAAE +K Sbjct: 190 AEILIEAGAPAGVFNVVQGMGEVGGALVTD-PRVDKVSLTGSVPTGKKVYAAAAEG-MKH 247 Query: 263 VTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKN 322 VT+ELGGKSP I+FDDAD+ + + + G FY++G+VC G+R++VQ+GI +K ++ Sbjct: 248 VTMELGGKSPLIIFDDADIDNAVGGAINGNFYSSGQVCSNGTRVFVQKGIKEKFLARLAE 307 Query: 323 AAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKPT 382 + +GDP E T G ++ Q++ +L YI+ GK+EGA +I GG R GYFI+PT Sbjct: 308 RTGNAILGDPMDEATSFGPMVTENQMNIVLGYIEKGKEEGARLICGGRRADMDGYFIEPT 367 Query: 383 IFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSN 442 +F DV +D I R+EIFGPV+++ F T EEV+A AND+E+GL+AGV T + + A V Sbjct: 368 VFADVTDDMTIAREEIFGPVMSVLDFDTEEEVVARANDTEFGLSAGVFTKDFTRAHRVIG 427 Query: 443 KINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRI 491 + +G+ ++N+YND PFGG SG+GRE +EA+ +++QVK+V + Sbjct: 428 NLEAGSCFINSYNDAPVEAPFGGVKASGVGRENSKEAIKHFSQVKSVYV 476 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: 684 Number of extensions: 33 Number of successful extensions: 5 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: 485 Length adjustment: 34 Effective length of query: 461 Effective length of database: 451 Effective search space: 207911 Effective search space used: 207911 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 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