Align Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_008623424.1 C943_RS00910 proline dehydrogenase family protein
Query= reanno::Cola:Echvi_0119 (398 letters) >NCBI__GCF_000330725.2:WP_008623424.1 Length = 396 Score = 550 bits (1417), Expect = e-161 Identities = 271/395 (68%), Positives = 326/395 (82%) Query: 1 MNTKPNISFENTEIAFASRTDAELRKMYLFFAVMDKNWAVKIGTNLSAVAFKLKLPVKGI 60 M KPNISFEN E+AFAS++DAEL+KMYL FA ++ N AV +GT L+ +F L LP+KG+ Sbjct: 1 MQVKPNISFENLEVAFASKSDAELKKMYLIFATINNNLAVSVGTKLANWSFALGLPIKGL 60 Query: 61 MKKTIFGHFCGGESVEDCSKSIQELQEFGIGTILDYSVEGTGTEKSYDFTRDEILRTIER 120 MKKT+FGHFCGGE++EDC KS+ L ++ I TILDYSVEG G E+S+D T++EIL+TIER Sbjct: 61 MKKTMFGHFCGGENIEDCQKSVDVLAKYHIHTILDYSVEGKGDEESFDATKNEILKTIER 120 Query: 121 SAGASEIPFSVFKVTGLGSYKIMTKVQAGQKLSAKEQEAFERLKDRVDTLCKAAYENDVR 180 SAG +PF+VFKVTGLG + IMTK+QAGQ+LS E+E+FE+LK RVD LC AA+ + + Sbjct: 121 SAGDENMPFAVFKVTGLGDFGIMTKIQAGQQLSNGEKESFEKLKARVDELCAAAHAANTK 180 Query: 181 IMIDGEESWFQDVIDDMAYEAMEKYNKEKAIVYNTFQMYRKDMLGLLKKAHEEAELKGYH 240 I+ID EESWFQ+VID MAYEAMEKYN+E IVYNTFQMYR DMLG LKKAH+ A KGY Sbjct: 181 ILIDAEESWFQEVIDKMAYEAMEKYNRESCIVYNTFQMYRHDMLGRLKKAHQIALEKGYW 240 Query: 241 VGAKLVRGAYMEKERDRAEDRGYPSPIQDTKEDTDNAYNDALKFSMEHKDRIYLVSGSHN 300 GAKLVRGAYMEKERDRA + GYPSPIQ TKE +D YN AL++ MEH + LVSGSHN Sbjct: 241 FGAKLVRGAYMEKERDRAAEMGYPSPIQPTKEASDRDYNAALEYCMEHIATMGLVSGSHN 300 Query: 301 ELSNIILTELMNLHGVAANDKRVYFSQLYGMSDNISYNLAFAGYNVAKYVPYGPVESVMP 360 E SNI+LT+L++ +G++A+D RVYF+QLYGMSDNISYNLA AGYNV KYVPYGPVE VMP Sbjct: 301 EQSNILLTQLLSKYGISASDDRVYFAQLYGMSDNISYNLAKAGYNVVKYVPYGPVEKVMP 360 Query: 361 YLYRRASENTSVAGQSSREFELIKNEMARRASLKK 395 YL RRA ENTSVAGQSSREF+L+K E+ARR LK+ Sbjct: 361 YLSRRAEENTSVAGQSSREFDLVKREIARRKKLKR 395 Lambda K H 0.316 0.132 0.371 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: 559 Number of extensions: 17 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: 398 Length of database: 396 Length adjustment: 31 Effective length of query: 367 Effective length of database: 365 Effective search space: 133955 Effective search space used: 133955 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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