Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__Miya:8501416 Length = 1013 Score = 212 bits (539), Expect = 6e-59 Identities = 150/450 (33%), Positives = 222/450 (49%), Gaps = 13/450 (2%) Query: 20 TDQYEDVVNPATK-EVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRARILFNFQQL 78 TD NPA EV+ +V K ++D A + A +AF W + RA L + Sbjct: 530 TDDTIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADRAMFLHRAADI 589 Query: 79 LSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLASIATDVEAAN 138 + EL+ +E GK +A +VG GI+ +++ A L +G E + Sbjct: 590 ARRRMFELSAWQVLEVGKQWDQAFHDVGEGIDFLDYYAHE-MLRLGTPRRMGRAPGELNH 648 Query: 139 YRY-PIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLVELFEKAGL 197 Y P G+ IAP+NFP + M AI GN I KPS + L E+F +AGL Sbjct: 649 LFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLTEIFREAGL 708 Query: 198 PKGVFNVVYGAHDVVNGIL-EHPEIKAISFVGSKPVGEYVYKK------GSENLKRVQSL 250 P+GVFN V G V+ L EHP++ I F GS VG + +K G KRV + Sbjct: 709 PEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQMQCKRVIAE 768 Query: 251 TGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEKVAD 310 G KN I+ +DA+L++ V ++ +AFG G++C AC+ V V + I D F+ +L + Sbjct: 769 MGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFVERLVKAAQA 828 Query: 311 IKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGPTIFD 370 IKIG D ++GPV +K L Y++ +EG LV R ++ +G +V TI + Sbjct: 829 IKIGPSEDPANYMGPVADASLQKNILEYVKVAEQEGKVLV--KRTDIPAEGCYVPLTIVE 886 Query: 371 NVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFRENID 430 + I ++EIF PVL+V+R N EA+ IAN + FA +F+ + + R Sbjct: 887 GIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRSPENLTKARREFR 946 Query: 431 AGMLGINLGVPAPMA-FFPFSGWKSSFFGT 459 G L +N G M PF G+K S G+ Sbjct: 947 VGNLYLNRGSTGAMVERQPFGGFKMSGVGS 976 Lambda K H 0.318 0.136 0.396 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: 1040 Number of extensions: 52 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: 487 Length of database: 1013 Length adjustment: 39 Effective length of query: 448 Effective length of database: 974 Effective search space: 436352 Effective search space used: 436352 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