Align Proline dehydrogenase 1; PRODH 1; Proline oxidase 1; EC 1.5.5.2 (characterized)
to candidate WP_008629302.1 C943_RS14740 proline dehydrogenase family protein
Query= SwissProt::O32179 (302 letters) >NCBI__GCF_000330725.2:WP_008629302.1 Length = 311 Score = 163 bits (412), Expect = 5e-45 Identities = 91/273 (33%), Positives = 149/273 (54%), Gaps = 2/273 (0%) Query: 28 ARRFVAGDTIESAVKTVKRLNRSGLCATIDYLGEYAASEKEANQVAEECKKAIQAIAEHQ 87 A R++ G+T+E + ++R+NRSG T D++GE +EK+A + E AI H+ Sbjct: 40 ANRYIGGETLEETIHAIQRINRSGYRVTTDFMGESIRNEKDAREATTEFLAFAAAIQSHR 99 Query: 88 LNSELSLKLTSIGLDLSEELALTHLRAILSVAKQYDVAVTIDMEDYSHYEQTLSIYRQCK 147 LNS +SL L+ IG+ +S ELA+ +L + A + + V I ME + L IY++ Sbjct: 100 LNSSISLDLSHIGMLVSRELAMENLDLLCRAAAKSNQEVIISMEGTDRTDAILDIYKETL 159 Query: 148 QEFEKLGTVIQAYLYRAAEDIRKMRDLKPNLRLVKGAYKESAAVAFPDKRGTDLHFQSLI 207 + LG IQAYL+R ++D +++ L ++RLVKGAY + ++ P + D + + + Sbjct: 160 KTHPNLGITIQAYLHRTSDDFKEILQLPGSIRLVKGAYDTPSGLSIPRGKELDERYLNYV 219 Query: 208 KLQLLSGNYTAVATHDDDIIAFTKQLVAEHQIPASQFEFQMLYGIRPERQKELAKEGYRM 267 L + + A+A+HD+ I T +L+ +HQ + + L GI E + + G+ Sbjct: 220 DQLLANDHPCAIASHDEKIHQETVKLIHQHQ--PQNYVLERLLGICNEAFEAYKEAGHPC 277 Query: 268 RVYVPYGTDWFSYFMRRIAERPANAAFVLKGIL 300 R+YV YG +W+ Y R AE P N L IL Sbjct: 278 RIYVVYGKEWYLYLCNRWAEYPLNLFRGLADIL 310 Lambda K H 0.321 0.134 0.375 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: 206 Number of extensions: 5 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: 311 Length adjustment: 27 Effective length of query: 275 Effective length of database: 284 Effective search space: 78100 Effective search space used: 78100 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