Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF3260 PGA1_c33110 sarcosine dehydrogenase
Query= BRENDA::Q8U022 (378 letters) >FitnessBrowser__Phaeo:GFF3260 Length = 816 Score = 150 bits (380), Expect = 9e-41 Identities = 116/370 (31%), Positives = 176/370 (47%), Gaps = 29/370 (7%) Query: 4 IIGGGIIGVATAYELAKLG-EEVVVFEKRYFGSGSTFRCASGIRAQFTDEANI-KLMKYS 61 IIGGG+IG + AY L KLG ++VV+ E++ SG+T+ A+G+ AQ AN+ KL KYS Sbjct: 12 IIGGGVIGCSVAYHLTKLGWKDVVLLERKQLTSGTTWH-AAGLIAQLRATANMTKLAKYS 70 Query: 62 IERWKTLSEELGHNIMFQQTGYLFLATTEEEVEAFKKNIKLQNKFGVPTRLITPEEAKEI 121 E + L EE G F++ G + +A TEE E + + FGV I+PEE K Sbjct: 71 QELYGALEEETGVATGFKRCGSITVALTEERKEEIFRQAAMARAFGVEVEEISPEEVKTR 130 Query: 122 VPPLNADAFLAGAWNPEDGKASPFHTLYAYKKAGERLGVKFYEYTKVVGIEKDGSK---- 177 LN AG W P+DG+ P + A K + G E KV GI K+G + Sbjct: 131 YEHLNVGDVTAGVWLPKDGQGDPANIALALAKGARQRGALVKERIKVTGISKEGRRATGV 190 Query: 178 -WKI--KTTRGEFKVDIIINATNAWAREINKMIGKDIIPVTPYKHQLVKTEPIERGQIEP 234 W ++G + D+++N W E+ +M G + +P+ +H + TE I P Sbjct: 191 DWASDDSQSQGHIEADMVVNCAGMWGHEVGRMAGVN-VPLHACEHFYIVTEGITGLTQMP 249 Query: 235 LVCPPAWNDSYVIQDGEDGGVICGTALEYESSP---DDVTPTYEF---------VKEVLK 282 ++ P Y ED G I A E + P + + T+EF + +L+ Sbjct: 250 VLRVPDECAYY----KEDAGKILLGAFEPNAKPWAMNGIPDTFEFDQLPEDFDHFEPILE 305 Query: 283 WAVKIIPALKHVHVVRQWAGHYAKTPDKNPAIGMIEE--NFYVAVGFSGHGFMMAPAVAQ 340 A +P L + + G + TPD +G+ E N +VA GF+ G A Sbjct: 306 AACNRMPMLAEAGIHTFFNGPESFTPDDAYHLGLAPEMDNVWVAAGFNSIGIQSAGGAGM 365 Query: 341 ALAEKIVEGK 350 ALA+ + +G+ Sbjct: 366 ALAQWMEDGQ 375 Lambda K H 0.318 0.137 0.420 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: 751 Number of extensions: 42 Number of successful extensions: 4 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: 378 Length of database: 816 Length adjustment: 36 Effective length of query: 342 Effective length of database: 780 Effective search space: 266760 Effective search space used: 266760 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 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