Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Miya:8501416 Length = 1013 Score = 239 bits (610), Expect = 3e-67 Identities = 162/465 (34%), Positives = 240/465 (51%), Gaps = 15/465 (3%) Query: 8 PMYIDGQFVTWRGDAWIDVVNPATEA-VISRIPDGQAEDARKAIDAAERAQPEWEALPAI 66 P++I G+ VT D I NPA A VI+R+ G + AI+AA++A P W Sbjct: 520 PLFIGGKDVTT--DDTIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPA 577 Query: 67 ERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEI 126 +RA +L + + R R E+SA V E GK A +V D++DY A R Sbjct: 578 DRAMFLHRAADIARRRMFELSAWQVLEVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGTPR 637 Query: 127 IQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAI 186 PGE LF + G+ I PWNFPF + A A++TGN ++ KPS Sbjct: 638 RMGRAPGELNHLFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGY 697 Query: 187 AFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAK--- 243 +I E GLP GVFN V GR +G L +P+V+M+ TGS+ G +I AAK Sbjct: 698 NLTEIFREAGLPEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQP 757 Query: 244 ---NITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQ 300 +V E+GGK I+ DDADL+ AV ++ S GQ C+ RV V IYD+ Sbjct: 758 GQMQCKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDR 817 Query: 301 FVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEG 360 FV RL +A QA++ G P+E MGP+ +A+ + + + V A +EG +V + Sbjct: 818 FVERLVKAAQAIKIG-PSEDPANYMGPVADASLQKNILEYVKVAEQEG-KVLVKRTDIPA 875 Query: 361 KGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNL 420 +G Y P T++ ++ I EE FGPVL V+ ++A+++AN + + LT +++++ Sbjct: 876 EGCYVPLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRSP 935 Query: 421 NVAMKAIKGLKFGETYINRENFEAM---QGFHAGWRKSGIGGADG 462 KA + + G Y+NR + AM Q F G++ SG+G G Sbjct: 936 ENLTKARREFRVGNLYLNRGSTGAMVERQPF-GGFKMSGVGSKTG 979 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: 1113 Number of extensions: 56 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: 479 Length of database: 1013 Length adjustment: 39 Effective length of query: 440 Effective length of database: 974 Effective search space: 428560 Effective search space used: 428560 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 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