Align Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_062057831.1 N456_RS13080 proline dehydrogenase
Query= reanno::Pedo557:CA265_RS11605 (394 letters) >NCBI__GCF_001401755.1:WP_062057831.1 Length = 390 Score = 377 bits (969), Expect = e-109 Identities = 183/384 (47%), Positives = 268/384 (69%) Query: 11 FDNTEVAFRQKTNGELKKAYWLFKMIGSNFLTKVGPAITNFFLNIGLPIQGAIKATIFQQ 70 FDNTE AF K++ EL++AY+LFKMI + L ++G A+TNF + LP+QG I+AT+F Sbjct: 7 FDNTETAFVLKSDSELERAYFLFKMISNEPLVRIGTAVTNFAIKAHLPVQGLIRATVFDH 66 Query: 71 FCGGETIAECDKAIEQLHKGGVGTILDYSVEGEEEEQVFDETCAEIIRTIMRADGDVKIP 130 FCGG + +C +++++ V ++LDYSVEG+EEE FD + I + AD +P Sbjct: 67 FCGGVSEQDCMPVVDKMYTKKVCSVLDYSVEGKEEEAQFDAVLKKTIDLLEFADEKDAMP 126 Query: 131 ITVFKITGIGRFALLQKLDAKETLNASEKAEYEKVKQRCEKICQTAFDKGVPIMIDAEET 190 VFK TG+GRF + QK +L E+ E+ ++++R + +C+ A+D V ++ID EE+ Sbjct: 127 FGVFKPTGLGRFLIWQKKTEGTSLTEEEEKEWNRIEERFDIVCKKAYDCDVALLIDGEES 186 Query: 191 WIQDTIDELALDMMRKFNRERIIVYNTYQMYRHDKLADMKADHLIAKADGFILGVKMVRG 250 W+QD DEL MMRK+N+++ I+YNT Q+YRHD+LA ++ H A+ F +GVK+VRG Sbjct: 187 WMQDAADELVAKMMRKYNKDKAIIYNTLQLYRHDRLAYLQQLHEEARVYDFKIGVKIVRG 246 Query: 251 AYMEKERKRAAEMGYPSPIQPDKAASDRDYNESLRYCVDHIEEIAIVAGTHNEDSSRLLT 310 AYMEKE +RA E GYP+PI DK +D++++ ++ Y +I++I++ GTHNE+SS Sbjct: 247 AYMEKENERAKEKGYPTPICKDKQHTDQNFDMTMEYIFQNIKDISVFIGTHNEESSYKAM 306 Query: 311 YLLEEKNITHNHPHVYFAQLLGMSDNLSFNLADSNYNVAKYVPYGPIKAVMPYLFRRAQE 370 L+++ +I + V+F QL GMSD++SFN A YNVAKY+P+GP++ VMPYL RRA+E Sbjct: 307 QLMKQFHIPKDDFRVWFGQLYGMSDHISFNQATKGYNVAKYLPFGPVRDVMPYLIRRAEE 366 Query: 371 NTSVAGQTGRELGLIERELKRRKL 394 NTSVAGQT REL L+ +E KRRKL Sbjct: 367 NTSVAGQTSRELNLLSQEKKRRKL 390 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: 433 Number of extensions: 12 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: 390 Length adjustment: 31 Effective length of query: 363 Effective length of database: 359 Effective search space: 130317 Effective search space used: 130317 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