Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_086510494.1 BZY95_RS13790 sarcosine oxidase subunit alpha family protein
Query= BRENDA::Q76M76 (483 letters) >NCBI__GCF_002151265.1:WP_086510494.1 Length = 1016 Score = 165 bits (417), Expect = 8e-45 Identities = 143/497 (28%), Positives = 227/497 (45%), Gaps = 96/497 (19%) Query: 15 RGRKVTIHFEGQPVEAYEGETIAMALHAAGIRVLSHSAEKHRPRGLFCAIGKCSSCLVKV 74 R RK+ F GQ + + G+T+A AL A G+ +++ S + RPRG+ A + + LV++ Sbjct: 19 RSRKLGFTFNGQHYQGHAGDTLASALLANGVDIVNRSFKYSRPRGIVAAGAEEPNALVQL 78 Query: 75 NG-----VPNVRSCITLVEEGMKVEMQRG------------------------------- 98 VPNVR+ + +G+ G Sbjct: 79 GSNEAAQVPNVRATQQALFDGLVARSTNGWPNVQRDVMSLVGKLGGRFMPPGFYYKTFMA 138 Query: 99 --------KETLPKGA---KPPAWKDAPRYK-----ADVVVIGGGPAGLMAAIHAADAGA 142 ++ + KGA + P D Y D++VIG GPAGL AA+ AA +GA Sbjct: 139 PASMWMTYEKYIRKGAGLGRSPMEADPDSYDHLNQHCDLLVIGAGPAGLAAALTAARSGA 198 Query: 143 SVILIDENPMLGGQLVKQTHKFFGKREQFAGVRGVKIAEILGEEVKKRGNIEVFLETSAV 202 VIL DE +GG L+ RE K AE + EE+ N+ + T+A Sbjct: 199 RVILADEQEEMGGSLLDS-------RELLDQQPAAKWAERVLEELAGLDNVMLLPRTTAN 251 Query: 203 GVFHEGEEKLVAAVRKNKELLEFLGKT---------------------LVVATGAMEKMI 241 G +H+ V ++ E LG+T +++ATGA E+ + Sbjct: 252 G-YHDHH-----FVTLHERRTEHLGETAPLVDGHRGVRSRMHRVRAGQVLLATGAHERPL 305 Query: 242 PFENNDLPGIYGAGAIQTLMNTYGVKPGDRVLIVGAGNVGLILAYQLIQAGVEVKAIVEA 301 + NND+PG AGA+ T + YGV PG+++++ + + A ++AG EV AIV+A Sbjct: 306 VYANNDVPGNLLAGAVSTYIRRYGVVPGNKLVLSTSNDHAYRAALDWVEAGREVVAIVDA 365 Query: 302 MPKVGGYFVHAAKVRRLGVPILTRHTILRAEGKDRVERAVIAQLDENWRPVPGTEKVFEV 361 G ++ AAK + G+ I+T ++ A+G+ RV A +A++D + V G + Sbjct: 366 RANPQGDWIDAAKAK--GIRIITGSAVIEAKGEKRVSAARVAKIDLDAFKVTGQAETLAC 423 Query: 362 DTIALAVGLRPSIELLHQAGCQVKFVRELSGHVAVRDGRMETTVQGIFVAGDSAGIEEAT 421 DTIA + G P I L G + + E+ G V + V+G+ AG + GI + Sbjct: 424 DTIASSGGYSPVIHLASHTGARPTWNEEILGFV-------PSLVKGVHAAGSARGIHDLA 476 Query: 422 TAMLEGKIAGIAAALKA 438 M +G +A A AL+A Sbjct: 477 AGMADG-VAMAAQALEA 492 Lambda K H 0.319 0.138 0.397 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: 1074 Number of extensions: 51 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 483 Length of database: 1016 Length adjustment: 39 Effective length of query: 444 Effective length of database: 977 Effective search space: 433788 Effective search space used: 433788 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: 54 (25.4 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