Align Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase; Pyr2C/Pip2C reductase; N-methyl-L-amino acid dehydrogenase; EC 1.5.1.21; EC 1.4.1.17 (characterized)
to candidate 3608646 Dshi_2039 Malate/L-lactate dehydrogenase (RefSeq)
Query= SwissProt::Q4U331 (343 letters) >FitnessBrowser__Dino:3608646 Length = 339 Score = 206 bits (523), Expect = 9e-58 Identities = 127/332 (38%), Positives = 176/332 (53%), Gaps = 2/332 (0%) Query: 10 TQTVSYPQLIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIFRIPGYLSSLASG 69 T+T+S P DLL R F +G A A+ +A+ +G HG R+ Y++ SG Sbjct: 6 TETLSLPDARDLLFRAFTANGVPEGAARSTADALVAAEAEGQVGHGFSRLEDYVAQARSG 65 Query: 70 WVDGKAVPVVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVAILAIRGSHHFAA 129 + A + + VDA +GFA PAL A I AR G A +A+ SHH A Sbjct: 66 KIVAGAEVTITRPAPTTLLVDAGHGFAYPALERAIDEGIAVARELGTAAIAVTRSHHCGA 125 Query: 130 LWPDVEPFAEQGLVALSMVNSMTCVVPHGARQPLFGTNPIAFGAPRAGGEPIVFDLATSA 189 L VE A+ GLVA+ +VN+ + P G + PLFGTNPIAF PRAG P+V DL+ S Sbjct: 126 LSIHVERAAKAGLVAMMVVNAPAAIAPWGGKTPLFGTNPIAFATPRAGSAPLVIDLSLSK 185 Query: 190 IAHGDVQIAAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHKGSALSMMVELLA 249 +A G V A + G+ +P G +D G PT + A L GG ++P G KG+AL++MVE+L+ Sbjct: 186 VARGKVMNAKKAGKPIPEGWALDAAGNPTTDAEAAL-GGTMVPIGEAKGTALALMVEILS 244 Query: 250 AGLTGGNFSFEFDWSKHPGAQTPWTGQLLIVIDPDKGAGQHFAQRSEELVRQLHGVGQER 309 A +TG S E P GQ L + P +GA + F R L+ Q+ + R Sbjct: 245 AVMTGAALSTEAGSFFSADGPPPGVGQFLTLWRPPEGA-EAFTARLAPLLAQIETMEGAR 303 Query: 310 LPGDRRYLERARSMAHGIVIAQADLERLQELA 341 LPG RR + AHGI + +A L+ + LA Sbjct: 304 LPGTRRLAALNAAQAHGIAVPRAYLDGARRLA 335 Lambda K H 0.320 0.137 0.412 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: 351 Number of extensions: 24 Number of successful extensions: 3 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: 343 Length of database: 339 Length adjustment: 29 Effective length of query: 314 Effective length of database: 310 Effective search space: 97340 Effective search space used: 97340 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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