Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
Query= BRENDA::Q9S795 (501 letters) >MicrobesOnline__882:208845 Length = 1006 Score = 234 bits (596), Expect = 1e-65 Identities = 161/494 (32%), Positives = 244/494 (49%), Gaps = 24/494 (4%) Query: 7 TRQLFIDGEWREPILKKRIPIVNPATE-EVIGDIPAATTEDVDVAVNAARRALSRNKGKD 65 T L+I G R+ IP NPA EV+ I A ++D A+ AA++A Sbjct: 511 TVPLYIGG--RDVTTADLIPTTNPAKPAEVVASICQAGRPEIDDAIAAAKKA-----ALT 563 Query: 66 WAKAPGAVRAKYLRAIAAKVNERKTDLAKLEALDCGKPLDEAVWDMDDVAGCFEFYADLA 125 W A RA YLR A +R +L+ + ++ GK D+A D+ + E+YA Sbjct: 564 WRDTSPADRAAYLRRAADICRKRIWELSAWQVVEVGKQWDQAYHDVTEGIDFLEYYAREM 623 Query: 126 EGLDAKQKAPVSLPMESFKSYVLKQPLGVVGLITPWNYPLLMAVWKVAPSLAAGCTAILK 185 L A ++ + P E +++ QP G+ +I PWN+P +A+ + ++ G I K Sbjct: 624 LRLGAPRRMGRA-PGEH--NHLFYQPKGIAAVIAPWNFPFAIAIGMASAAIVTGNPVIFK 680 Query: 186 PSELASVTCLELADICREVGLPPGVLNVLTGFGSEAGAPLASHPGVDKIAFTGSFATGSK 245 PS ++S LA++ RE GLP GV N G S G L HP + I FTGS G + Sbjct: 681 PSSISSRIGYNLAEVFREAGLPEGVFNYCPGRSSIMGDYLVEHPDISLICFTGSMEVGLR 740 Query: 246 VMTAAAQL------VKPVSMELGGKSPLIVFDDVDLDKAAEWALFGCFWTNGQICSATSR 299 + AA++ K V E+GGK+ I+ DD DLD+A L+ F GQ CSA SR Sbjct: 741 IQEKAAKVQPGQRQCKRVIAEMGGKNATIIDDDADLDEAVLQVLYSAFGFQGQKCSACSR 800 Query: 300 LLVHESIASEFIEKLVKWSKNIKISDPMEEGCRLGPVVSKGQYEKILKFISTAKSEGATI 359 ++V ++I FIE+LVK + +I I + +GPV + + +I A+ EG + Sbjct: 801 VIVLDAIYDRFIERLVKAASSIHIGPSEDPSNYMGPVADATLQKNVSDYIRIAEEEGRVL 860 Query: 360 LHGGSRPEHLEKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFASEDEAIELANDSHY 419 L R + +G ++ TI+ D+ +I +EE+FGPVL V A+ DEA+ +AN + + Sbjct: 861 L---KRTDLPAEGCYVPLTIVGDIRPEHRIAQEEIFGPVLAVMRAATFDEALSIANGTRF 917 Query: 420 GLGAAVISNDTERCDRISEAFEAGIVWIN--CSQPCFTQAPWGGVKRSGFGRELGEWGLD 477 L AV S E D+ F G +++N + + P+GG SG G + G G D Sbjct: 918 ALTGAVFSRSPEHLDKARREFRVGNLYLNKGSTGALVERQPFGGFAMSGVGSKTG--GPD 975 Query: 478 NYLSVKQVTLYTSN 491 L + T N Sbjct: 976 YLLQFMDPRVVTEN 989 Lambda K H 0.318 0.135 0.416 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: 1136 Number of extensions: 43 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: 501 Length of database: 1006 Length adjustment: 39 Effective length of query: 462 Effective length of database: 967 Effective search space: 446754 Effective search space used: 446754 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: 55 (25.8 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