Align Lmo2664 protein (characterized, see rationale)
to candidate 3607129 Dshi_0551 Alcohol dehydrogenase GroES domain protein (RefSeq)
Query= uniprot:Q8Y413 (350 letters) >FitnessBrowser__Dino:3607129 Length = 347 Score = 134 bits (337), Expect = 4e-36 Identities = 106/356 (29%), Positives = 161/356 (45%), Gaps = 30/356 (8%) Query: 2 RAAVLYENNVIKAEQID-EATCGKDQVRVEVKAVGICGSDIHKMQTRWKYPL----PAVM 56 RA VL + ID G + VR+ + VG+CGSD+H P P V+ Sbjct: 3 RALVLEAARKLALRDIDLPDELGPEDVRIAIDTVGVCGSDVHYYTHGKIGPFVVKQPMVL 62 Query: 57 GHEFAGVITEIGSEVTNVAMGDRVAGIPLEPCMECNYCKAGDFALCDNYRMVGSH-FHGG 115 GHE AG++TEIG+ VT++A+GDRV P P K G + + + + HG Sbjct: 63 GHEAAGIVTEIGAAVTHLALGDRVCMEPGIPNGSSKASKLGVYNVDPAVQFWATPPVHGC 122 Query: 116 FAENVVMKADNVISIGD-LDFEEGAMIEPLAVSMHGVLGIQPRLGDTVIVFGIGTIGILV 174 +VV A + D + F EGAM+EP A+ M + + GD +V G G IG++V Sbjct: 123 LTPSVVHPAAFTFKLPDHVSFAEGAMVEPFAIGMQAAAKARIKPGDVALVTGAGPIGVMV 182 Query: 175 VQCLLLAGVKDIIAVDISDKKLADAREFGCKYTINPKNEDLKERVFAYTNGLGADIALEC 234 L G + D+ + KLA A + + I ++ E + T G GAD+ EC Sbjct: 183 ALAALAGGCAKVFVSDLVEDKLAIAAGYDNIHPILIPRDNPAEVLQEATEGWGADVVFEC 242 Query: 235 AGSKITQEQCLLVTKKKGKVGFLGIAY----ADVLL---HEEAFENIFRRELTLKGFWNS 287 AG+ + + L G V ++G+ D++L E E +FR + N Sbjct: 243 AGAAASIQAALEAAAPAGCVVWVGMPVDPVPVDIVLAQSRELRMETVFR-------YANM 295 Query: 288 YSAPFPGEEWRTSIEFVKQGRIKLKPLISHRYKLEETKEAFDMILSREHDYNKVMI 343 Y +I + G++ LKPLIS + E++ AFD + K+ I Sbjct: 296 YD---------RAIALLASGKVDLKPLISATFPFEDSIAAFDRAVEARPTDVKIQI 342 Lambda K H 0.321 0.139 0.417 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: 280 Number of extensions: 12 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: 350 Length of database: 347 Length adjustment: 29 Effective length of query: 321 Effective length of database: 318 Effective search space: 102078 Effective search space used: 102078 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: 49 (23.5 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