Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase (TIGR)
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__DvH:208845 Length = 1006 Score = 234 bits (597), Expect = 1e-65 Identities = 157/465 (33%), Positives = 238/465 (51%), Gaps = 15/465 (3%) Query: 8 PMYIDGQFVTWRGDAWIDVVNPATEA-VISRIPDGQAEDARKAIDAAERAQPEWEALPAI 66 P+YI G+ VT I NPA A V++ I + AI AA++A W Sbjct: 513 PLYIGGRDVTTAD--LIPTTNPAKPAEVVASICQAGRPEIDDAIAAAKKAALTWRDTSPA 570 Query: 67 ERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEI 126 +RA++LR+ + R+R E+SA V E GK A +V D+++Y A R Sbjct: 571 DRAAYLRRAADICRKRIWELSAWQVVEVGKQWDQAYHDVTEGIDFLEYYAREMLRLGAPR 630 Query: 127 IQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAI 186 PGE+ LF + G+ I PWNFPF + + A++TGN ++ KPS + Sbjct: 631 RMGRAPGEHNHLFYQPKGIAAVIAPWNFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGY 690 Query: 187 AFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAK--- 243 A++ E GLP GVFN GR +G L +P ++++ TGS+ G +I AAK Sbjct: 691 NLAEVFREAGLPEGVFNYCPGRSSIMGDYLVEHPDISLICFTGSMEVGLRIQEKAAKVQP 750 Query: 244 ---NITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQ 300 +V E+GGK I+ DDADL+ AV ++ S GQ C+ RV V IYD+ Sbjct: 751 GQRQCKRVIAEMGGKNATIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDAIYDR 810 Query: 301 FVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEG 360 F+ RL +A ++ G P+E MGP+ +A + V + A EEG RV + Sbjct: 811 FIERLVKAASSIHIG-PSEDPSNYMGPVADATLQKNVSDYIRIAEEEG-RVLLKRTDLPA 868 Query: 361 KGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNL 420 +G Y P T++ D+R E I EE FGPVL V+ T ++A+S+AN + + LT ++++++ Sbjct: 869 EGCYVPLTIVGDIRPEHRIAQEEIFGPVLAVMRAATFDEALSIANGTRFALTGAVFSRSP 928 Query: 421 NVAMKAIKGLKFGETYINRENFEAM---QGFHAGWRKSGIGGADG 462 KA + + G Y+N+ + A+ Q F G+ SG+G G Sbjct: 929 EHLDKARREFRVGNLYLNKGSTGALVERQPF-GGFAMSGVGSKTG 972 Score = 29.3 bits (64), Expect = 7e-04 Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 6/86 (6%) Query: 19 RGDAWIDVVNPATEAVISRIP-DGQAEDARKAIDAAERAQPEWEALPA---IERASW--L 72 R D + V+ EA +S + A+ + +DA R Q +W+ALP +E W Sbjct: 137 RKDGFTFTVDLLGEATVSEEESEAYAQGYHEVVDAIAREQEKWKALPGNGPVEGFDWGAT 196 Query: 73 RKISAGIRERASEISALIVEEGGKIQ 98 K++ I+ A A V+ G ++ Sbjct: 197 PKVNVSIKPSALYSQAKPVDVEGSVR 222 Lambda K H 0.318 0.135 0.392 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: 1042 Number of extensions: 49 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 479 Length of database: 1006 Length adjustment: 39 Effective length of query: 440 Effective length of database: 967 Effective search space: 425480 Effective search space used: 425480 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: 54 (25.4 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