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 AZOBR_RS31690 AZOBR_RS31690 lactate dehydrogenase
Query= SwissProt::Q4U331 (343 letters) >FitnessBrowser__azobra:AZOBR_RS31690 Length = 327 Score = 422 bits (1084), Expect = e-123 Identities = 201/325 (61%), Positives = 248/325 (76%) Query: 18 LIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIFRIPGYLSSLASGWVDGKAVP 77 L+ LL RIF+ HGTS VA +LAENCAS +RDGS SHG+FRIPGY+ SL SGWVDG+A P Sbjct: 1 LVALLERIFLRHGTSERVAAILAENCASCERDGSTSHGVFRIPGYVGSLKSGWVDGRAEP 60 Query: 78 VVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVAILAIRGSHHFAALWPDVEPF 137 VE+ G AF+RVDA NGF QPA AAR ++ R GVA++AIR SHHF+ALWPDVEPF Sbjct: 61 TVEEAGPAFLRVDAANGFTQPAFLAARDRFLEMVRDNGVAVMAIRNSHHFSALWPDVEPF 120 Query: 138 AEQGLVALSMVNSMTCVVPHGARQPLFGTNPIAFGAPRAGGEPIVFDLATSAIAHGDVQI 197 A +GLVALS VNS CVVP G + ++GTNP+AF P AGG+P+VFD A S++A+GDV+I Sbjct: 121 AREGLVALSFVNSFACVVPSGGKAAVYGTNPMAFATPVAGGDPMVFDQAASSMANGDVRI 180 Query: 198 AAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHKGSALSMMVELLAAGLTGGNF 257 AAREG +PAG GVDRDG PT +P+A+LDGGALLPFGGHKG +++ M+E+LAA LTGG + Sbjct: 181 AAREGHAIPAGSGVDRDGKPTTDPKAVLDGGALLPFGGHKGGSIAFMIEVLAAALTGGKY 240 Query: 258 SFEFDWSKHPGAQTPWTGQLLIVIDPDKGAGQHFAQRSEELVRQLHGVGQERLPGDRRYL 317 S E DWS HPGA+TP TGQL IVIDP++G FA R L+ + GQ+R+PG+RRY Sbjct: 241 SREVDWSAHPGAETPCTGQLFIVIDPERGGTGAFADRVAGLIGDVKEAGQDRMPGERRYA 300 Query: 318 ERARSMAHGIVIAQADLERLQELAG 342 RAR++ GI + A L L+ LAG Sbjct: 301 RRARTLRDGIPLTPARLAELRALAG 325 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: 449 Number of extensions: 20 Number of successful extensions: 1 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: 327 Length adjustment: 28 Effective length of query: 315 Effective length of database: 299 Effective search space: 94185 Effective search space used: 94185 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