Align Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_008990629.1 I215_RS03780 proline dehydrogenase
Query= reanno::Pedo557:CA265_RS11605 (394 letters) >NCBI__GCF_000300875.1:WP_008990629.1 Length = 388 Score = 399 bits (1024), Expect = e-115 Identities = 188/384 (48%), Positives = 271/384 (70%) Query: 11 FDNTEVAFRQKTNGELKKAYWLFKMIGSNFLTKVGPAITNFFLNIGLPIQGAIKATIFQQ 70 FDNTE+AF+ K++ EL++AY+LFKMI L ++G A+TNF + LP++G I+AT+F Sbjct: 5 FDNTEIAFKLKSDSELERAYFLFKMIAHQPLVRIGTAVTNFAIKAHLPVEGLIRATVFDH 64 Query: 71 FCGGETIAECDKAIEQLHKGGVGTILDYSVEGEEEEQVFDETCAEIIRTIMRADGDVKIP 130 FCGG + +C K ++ +H GV ++LDYSVEG E ++ FD A ++ + IP Sbjct: 65 FCGGVSELDCMKTVDAIHTAGVSSVLDYSVEGNENDEEFDAVVARTLKILDLVKEKQAIP 124 Query: 131 ITVFKITGIGRFALLQKLDAKETLNASEKAEYEKVKQRCEKICQTAFDKGVPIMIDAEET 190 VFK T +GRF L K+ +TL+ E+ E+++V R E IC A++ V ++IDAEE+ Sbjct: 125 FAVFKPTAVGRFDLYVKIGEGKTLDKEEQQEWDRVCLRYETICNKAYELDVALLIDAEES 184 Query: 191 WIQDTIDELALDMMRKFNRERIIVYNTYQMYRHDKLADMKADHLIAKADGFILGVKMVRG 250 W+QD DE+ MM+K+NR + IV+NT Q+YR +++ +K H AK DGF++G+K+VRG Sbjct: 185 WMQDAADEIVEQMMKKYNRNKAIVFNTLQLYRWNRMDYLKGLHQRAKEDGFVVGMKLVRG 244 Query: 251 AYMEKERKRAAEMGYPSPIQPDKAASDRDYNESLRYCVDHIEEIAIVAGTHNEDSSRLLT 310 AYMEKE RA E GYP+PI K A+D +YN ++ Y +DHI E+ + G+HNE+S+ L Sbjct: 245 AYMEKENDRAEENGYPTPICESKKATDDNYNTAVGYMLDHIGELELFLGSHNEESTMLAL 304 Query: 311 YLLEEKNITHNHPHVYFAQLLGMSDNLSFNLADSNYNVAKYVPYGPIKAVMPYLFRRAQE 370 +++EKN+ N ++F QL GMSD++S+NLA+ NYNVAKY+P+GP++ VMPYL RRA+E Sbjct: 305 NIMKEKNLAVNDSRIWFGQLYGMSDHISYNLANRNYNVAKYLPFGPVRDVMPYLIRRAEE 364 Query: 371 NTSVAGQTGRELGLIERELKRRKL 394 NTSVAGQT REL L+ +E KRRKL Sbjct: 365 NTSVAGQTTRELSLLSQERKRRKL 388 Lambda K H 0.319 0.136 0.394 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: 428 Number of extensions: 11 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: 394 Length of database: 388 Length adjustment: 31 Effective length of query: 363 Effective length of database: 357 Effective search space: 129591 Effective search space used: 129591 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: 50 (23.9 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