Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_068167924.1 HTA01S_RS06345 sarcosine oxidase subunit alpha family protein
Query= BRENDA::Q76M76 (483 letters) >NCBI__GCF_001592305.1:WP_068167924.1 Length = 997 Score = 139 bits (349), Expect = 6e-37 Identities = 136/485 (28%), Positives = 207/485 (42%), Gaps = 67/485 (13%) Query: 15 RGRKVTIHFEGQPVEAYEGETIAMALHAAGIRVLSHSAEKHRPRGLFCAIGKCSSCLVKV 74 R R + +F G+ + EG+T+A AL A G+ +++ S + HRPRG+ A + + LV++ Sbjct: 13 RRRTLNFNFNGRAYQGLEGDTLASALLANGVSMVARSWKYHRPRGILSAGVEEPNALVQL 72 Query: 75 ----NGVPNVRSCITLVEEGMKVEMQRGKETL---------------PKG-------AKP 108 VPN R + EG+ K ++ P G A Sbjct: 73 FDGARTVPNARMTEVALVEGLSARSIHAKPSIEFDTGAVNGWFSRLIPAGFYYKTFMASQ 132 Query: 109 PAWK-------------------DAPRYK-----ADVVVIGGGPAGLMAAIHAADAGASV 144 AW D RY DV+V+G G AGL AA+ AA AGA V Sbjct: 133 AAWHFFEKHIRAASGLGHSPTEHDPDRYDKRYAHCDVLVVGAGIAGLTAALTAARAGARV 192 Query: 145 ILIDENPMLGGQLVKQTHKFFGKRE-QFAGVRGVKIAEILGEEVKKRGNIEVFLETSAVG 203 +L DE GG L+ + G+ Q+ ++A + V R + + V Sbjct: 193 VLCDEQAEAGGWLLSSDEQVDGQSAAQWVAQALAELAALPDVTVLPRTTAFGYQDHDLVT 252 Query: 204 VFHEGEEKLVA--AVRKNKELLEFLGKTLVVATGAMEKMIPFENNDLPGIYGAGAIQTLM 261 + + L A A + L K +V+ATGA E+ + F NNDLPGI AGA+ T + Sbjct: 253 LVERRGDHLPAERAPVFRERLWRVRAKRVVIATGAHERPLVFGNNDLPGIMLAGAVSTYI 312 Query: 262 NTYGVKPGDRVLIVGAGNVGLILAYQLIQAGVEVKAIVEAMPKVGGYFVHAAKVRRLGVP 321 Y V PG ++ + G A L AG V+ +V+A + G AK + G+ Sbjct: 313 RRYAVLPGRNAVVFTNNDAGYDAALALKAAGASVQ-VVDARAQPSGSLSQRAKAQ--GIS 369 Query: 322 ILTRHTILRAEGKDRVERAVIAQLDENWRPVPGTEKVFEVDTIALAVGLRPSIELLHQAG 381 +L H I A G RV ++ +D R + G+ + D +AL+ G+ P + L QAG Sbjct: 370 VLAGHVITEARGGQRVSGVLVQAIDGQDR-LSGSVRDIACDLVALSGGVSPVVHLQCQAG 428 Query: 382 CQVKFVRELSGHVAVRDGRMETTVQGIFVAGDSAGIEEATTAMLEGKIAGI----AAALK 437 + + + + + E + AG AG + +G AG A L Sbjct: 429 SKAVWNDAQAAFLPGAPAQSEIS------AGACAGQLTLKASADDGAAAGAQALKALGLS 482 Query: 438 AGAAS 442 AGAA+ Sbjct: 483 AGAAA 487 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: 1002 Number of extensions: 46 Number of successful extensions: 5 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: 997 Length adjustment: 39 Effective length of query: 444 Effective length of database: 958 Effective search space: 425352 Effective search space used: 425352 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