Align Lactaldehyde reductase (characterized, see rationale)
to candidate RR42_RS11005 RR42_RS11005 4-hydroxybutyrate dehydrogenase
Query= uniprot:Q8A199 (384 letters) >FitnessBrowser__Cup4G11:RR42_RS11005 Length = 382 Score = 201 bits (511), Expect = 3e-56 Identities = 128/371 (34%), Positives = 196/371 (52%), Gaps = 22/371 (5%) Query: 15 GCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYELYSDVKANPTIAN 74 G S + E R G ++ VTDK ++ GVA + I +P+E++ + +NPT A Sbjct: 15 GTISQLKAECERIGIRRPLVVTDKGVVAAGVAQQAIVALGG--LPHEIFDETPSNPTEAM 72 Query: 75 VQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNP-DFADVKSLE-GVADTKHKAVP 132 V+ A Y+ SG D ++A+GGGSSID AKGI I+ +P + ++E G A +A P Sbjct: 73 VKKAAAQYRDSGCDGLIAVGGGSSIDLAKGIAILATHPGELTTYATIEGGSARLTERAAP 132 Query: 133 TFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELMYSMPKGLTAATG 192 A+PTT+GT +EV +II ED R K+ + +P AI DP L +P GLTAATG Sbjct: 133 LIAVPTTSGTGSEVARGAIIILEDGR-KLGFHSWHLLPKSAICDPGLTLGLPAGLTAATG 191 Query: 193 MDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAREAMSQAQYIAGM 252 MDA+ H +E+++ P +D L +E ++++ A +G+D AR M A M Sbjct: 192 MDAIAHCVETFLAPAFNPPADGIALDGLERGWKHIERATRDGQDRDARLNMMSASMQGAM 251 Query: 253 GFSNVGLGIVHSMAHPLGAF-----YDTPHGVANALLLPYVMEYNAESPAA---PKYIHI 304 F GLG VHS++HPLG HG NA+++P V+ +NA++P+ +Y + Sbjct: 252 AFQK-GLGCVHSLSHPLGGLKVDGKTGLHHGTLNAVVMPAVLRFNADAPSVVRDNRYARL 310 Query: 305 AKAMGVNTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAFNDVCT 364 AMG+ D +AV ++ +G+P L ++ V E+ + A D C Sbjct: 311 RHAMGLPQDA--------DLAQAVHDMTARLGLPTGLRQMGVTEDMFDKVIAGALVDHCH 362 Query: 365 GGNPRPTSVAE 375 NP+ S A+ Sbjct: 363 KTNPKEASAAD 373 Lambda K H 0.317 0.133 0.379 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: 403 Number of extensions: 29 Number of successful extensions: 7 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: 384 Length of database: 382 Length adjustment: 30 Effective length of query: 354 Effective length of database: 352 Effective search space: 124608 Effective search space used: 124608 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: 50 (23.9 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