Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate Ac3H11_4483 Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD
Query= BRENDA::O29853 (443 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4483 Length = 504 Score = 192 bits (487), Expect = 3e-53 Identities = 133/422 (31%), Positives = 212/422 (50%), Gaps = 20/422 (4%) Query: 38 VVVKPSNSEEVSAILKFANEKSIPVFMRGGGTGLSGGAVPTEEGIVLSTEKMTE-LEVDA 96 VV P +EV A+L+ + +PV RG GTGLSGGA+P G+ LS K L + Sbjct: 63 VVCLPETYDEVQAVLRACHRLQVPVVARGAGTGLSGGAMPHAMGVTLSLAKFNRILNLSP 122 Query: 97 DNRVAICGAGVTLKQLDDAAFRHGLSFPPHPGAETA-TVGGMIATNAGGVRALKYGTMRN 155 ++R A+ +GV + +AA H L + P P ++ A T+GG +A N+GGV LKYG + Sbjct: 123 ESRTAVVQSGVRNLAISEAAAPHNLYYAPDPSSQIACTIGGNVAENSGGVHCLKYGLTVH 182 Query: 156 YVLSLEAVLADGRIINVGGKTIKNSSGYSLLHLLVGSEGTLAVITKATIRLFPQMRDMTV 215 VL ++ +G + G + + +S GY LL ++GSEG LAVIT+ T+RL P+ + Sbjct: 183 NVLKVKGFTVEGEPVEFGSEAL-DSPGYDLLAAVIGSEGMLAVITEVTVRLIPKPQLARC 241 Query: 216 LAIPFPTMEDAMNCVVEV-ARKMLPMALEFMEKRAVEIGEKVSGERWVSREGEAHLLMVF 274 + F + A + V V A ++P LE M+K E + EA LL Sbjct: 242 IMASFDDVRKAGDAVAAVIAAGIIPAGLEMMDKPMTAAVEDFVHAGY-DLTAEAILLCES 300 Query: 275 ESFDE--AEEAAKIAQSLGAIDVYAATTKKDQDRLLKV-----RGMIYEGLRKEVIEVLD 327 + E EE ++++ L A A + +D+ L+ G +D Sbjct: 301 DGTPEEVEEEIGRMSEVLRAAGATAISVSRDEAERLRFWSGRKNAFPASGRISPDYMCMD 360 Query: 328 ACVPPAKIAEYWRRSNELAEEYGIELITYGHAGDGNVHQHPLV-YEGWEKSYFE----FR 382 + +P ++A+ E+ ++Y + HAGDGN+ HPL+ ++ + F Sbjct: 361 STIPRKRLADILLAIQEMEKKYQLRCANVFHAGDGNL--HPLILFDANDADQLHRCELFG 418 Query: 383 KSLLSLAVSLGGVISGEHGIGAVKLSEL-EELFPEQFELMRQIKLLFDPKNILNPGKVVR 441 +L +V++GG ++GEHG+G KL+ + + E+ M +K FDP +LNPGKV+ Sbjct: 419 ADILETSVAMGGTVTGEHGVGVEKLNSMCVQFTAEENAQMFGLKHAFDPAGLLNPGKVIP 478 Query: 442 KL 443 L Sbjct: 479 TL 480 Lambda K H 0.317 0.136 0.388 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: 478 Number of extensions: 18 Number of successful extensions: 6 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: 443 Length of database: 504 Length adjustment: 33 Effective length of query: 410 Effective length of database: 471 Effective search space: 193110 Effective search space used: 193110 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: 51 (24.3 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