Align Proline dehydrogenase 1; PRODH 1; Proline oxidase 1; EC 1.5.5.2 (characterized)
to candidate WP_075618754.1 GY23_RS08375 proline dehydrogenase
Query= SwissProt::Q8RMG1 (302 letters) >NCBI__GCF_001939075.1:WP_075618754.1 Length = 330 Score = 285 bits (728), Expect = 1e-81 Identities = 135/302 (44%), Positives = 203/302 (67%), Gaps = 2/302 (0%) Query: 1 MLRHVFLFLSQNKTLTKFAKAYGTRLGARRFVAGDTIESAVKTVKRLNRSGLCATIDYLG 60 +L+ VF+ LSQN+ L AK YG ++GA+ VAG +E +K++K LN G+ AT+D LG Sbjct: 3 ILKDVFMSLSQNQLLNSAAKKYGLKMGAQTVVAGTNVEETIKSIKELNAQGISATVDNLG 62 Query: 61 EYAASEKEANQVAEECKKAIQAIAEHQLDSELSLKLTSIGLDLSEELALTHLRAILSVAK 120 E+ ++EA + + I+AI EH +D+ +SLK T +GLD+ + +L+ I++ A Sbjct: 63 EFVFEKEEAIKAKNNILEVIEAINEHGVDAHISLKATQLGLDIDFDFCYENLKGIVAAAS 122 Query: 121 QYDVAVTIDMEDYSHYEQTLSIYRQCKQEFEKLGTVIQAYLYRAAEDIKKMRDLKPNLRL 180 +YD+ + IDMEDY H + + + + QE+ +GTVIQAY YRA +DI++ ++L+ LR+ Sbjct: 123 KYDMHINIDMEDYGHLQPSFDLMDKLLQEYSNVGTVIQAYFYRAQDDIEQYKNLR--LRI 180 Query: 181 VKGAYKESAAVAFPDKRGTDLHFQSLIKLQLLSGNYTAVATHDDDIIKFTKQLVAEHRIP 240 VKGAYKESA A+ K D ++ LI+ LL+G ++++ATHD ++I K+ V EH+IP Sbjct: 181 VKGAYKESAEHAYQTKEEIDANYIKLIEYHLLNGKFSSIATHDHNVINHVKKFVEEHQIP 240 Query: 241 ASQFEFQMLYGIRPERQKELAKEGYRMRVYVPYGTDWFSYFMRRIAERPANAAFVLKGIL 300 ++EFQMLYG R + Q +LAK+GY YVP+G DW+ YFMRR+AERPAN V+K + Sbjct: 241 KDKYEFQMLYGFRKDMQVDLAKQGYNFCTYVPFGDDWYGYFMRRLAERPANLNLVVKQVF 300 Query: 301 KK 302 K Sbjct: 301 NK 302 Lambda K H 0.321 0.134 0.376 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: 270 Number of extensions: 9 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: 302 Length of database: 330 Length adjustment: 27 Effective length of query: 275 Effective length of database: 303 Effective search space: 83325 Effective search space used: 83325 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 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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