Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) (EC 1.5.1.21) (characterized)
to candidate SM_b20261 SM_b20261 malate dehydrogenase
Query= BRENDA::Q9I492 (334 letters) >FitnessBrowser__Smeli:SM_b20261 Length = 345 Score = 356 bits (914), Expect = e-103 Identities = 183/331 (55%), Positives = 224/331 (67%), Gaps = 1/331 (0%) Query: 4 MTLDEVRELAVRILRRHAFSEAHVQAVADTLVAGERDECASHGIWRLLGCIATLKAGKVS 63 +T ++E I R+ + A+A +VAGERD C SHGI+R+ G + T+KAGKV Sbjct: 7 LTTTALQERVEAIFRKGGLNVVQAGALARVIVAGERDACKSHGIYRIEGALRTVKAGKVK 66 Query: 64 ADAEPEL-HDIAPGLLRVDAHGGFSQCAFRLGLPHLLEKARSQGIAAMAVNRCVHFSALW 122 DAEPE+ A +++V+A GGF+ AF LGLP L E+AR GIAA+A+N C HFSALW Sbjct: 67 PDAEPEIVAQEASAIVKVNAGGGFANPAFELGLPVLAERARKHGIAALAINDCTHFSALW 126 Query: 123 VEVEALTEAGLVALATTPSHAWVAPAGGRKPIFGTNPIAFGWPRPDGPPFVFDFATSAVA 182 E EALT GL L PS+A VAP GG KP+ GTNP AFGWPR PP+VFDFATS A Sbjct: 127 PEAEALTGEGLAGLVMCPSYATVAPTGGNKPLLGTNPFAFGWPRAGKPPYVFDFATSVAA 186 Query: 183 RGEIQLHERAGKPIPLGWGVDEQGEPTTDASAALRGAMLTFGGHKGSALAAMVELLAGPL 242 RGEI+LH RAGKP+P GW +D QG PTTD AAL GAML FGGHKGSA+ M+ELLAG + Sbjct: 187 RGEIELHRRAGKPLPEGWAIDAQGNPTTDPEAALAGAMLPFGGHKGSAIGTMIELLAGIM 246 Query: 243 IGDLTSAESLAYDEGSRSSPYGGELLIAIDPRRMLGASAEEHLARAETLFEGIVEQGARL 302 IGDLTS E L Y + +P+ GEL++A P+ + ARAE LFE IV QGARL Sbjct: 247 IGDLTSPEVLDYLGTTTLAPFHGELIVAFSPQAFAAGRPGDPFARAELLFEAIVGQGARL 306 Query: 303 PSQRRFEARERSARDGVTIPEALHRELLALL 333 PSQRRF AR +S +G+T+ A +L LL Sbjct: 307 PSQRRFAARAKSEAEGITLSAAEIEQLDRLL 337 Lambda K H 0.320 0.136 0.407 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: 386 Number of extensions: 19 Number of successful extensions: 2 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: 334 Length of database: 345 Length adjustment: 28 Effective length of query: 306 Effective length of database: 317 Effective search space: 97002 Effective search space used: 97002 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