Align Lmo2663 protein (characterized, see rationale)
to candidate 3610773 Dshi_4159 Alcohol dehydrogenase GroES domain protein (RefSeq)
Query= uniprot:Q8Y414 (343 letters) >FitnessBrowser__Dino:3610773 Length = 350 Score = 173 bits (439), Expect = 5e-48 Identities = 114/348 (32%), Positives = 185/348 (53%), Gaps = 20/348 (5%) Query: 10 GYDQMELKDVEEPQVYGDKVKIKVAFTGICGSDIHTF--------KGE---YKNPTTPVT 58 G + ++DV+EP +VKIKVA+TGICGSD+H F GE + P+T Sbjct: 8 GAKDIRVEDVDEPTPGAGEVKIKVAWTGICGSDLHEFLAGPIFVPVGEDHPLSHDKAPIT 67 Query: 59 LGHEFSGVVVEVGPDVTSIKVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGIG-TQAN 117 +GHE+ G + E+G VT + VGDRV E F CG C C++ YNLC +G + + Sbjct: 68 MGHEYCGEITELGDGVTDLSVGDRVAIEPIF-ACGTCAACRDGRYNLCEKLGFVGLSGGH 126 Query: 118 GSFAEFVLSREESCHVLDERISLEAAALTEPLACCVHSALEKTTIRPDDTVLVFGPGPIG 177 G FA + + H + E +S+E AL EP A +H A+ + + D VFG GPIG Sbjct: 127 GGFAAYSVVPARMLHRMPEGLSMEQGALVEPAAVALH-AVRVSAFKAGDRAAVFGAGPIG 185 Query: 178 LLLAQVVKAQGATVIMAGITKDSDRLRLAKELGMDRIVDTLKEDLAEVVLGMTGGYGAER 237 LL+ + ++ GA+ I+ + R A ELG VD ED V G G E Sbjct: 186 LLVVESLRIAGASKIVV-VEPSETRRAKAMELGATTAVDPGAEDAVAAVQAACPG-GVEV 243 Query: 238 VFDCSGAVPAVNQGLPLTKKKGDFVQVGLFAEKKNAIDEESIIQREIAYIGSRSQKPSSW 297 F+ +G + Q + T+ +G+ + V ++ E + + +++ +E G+ + + + + Sbjct: 244 AFEVTGVPAVLAQAIDATRYEGETLVVSIW-ETEASFQPNTVVLKERNIKGTIAYR-NVY 301 Query: 298 ILALDLLANGKIDTDKMITKVYGLDD-WREAFEAVMA-GNEIKVLVKS 343 +DL+ G ++++T+ GLDD R+ FEA++A ++IK+LV++ Sbjct: 302 PAVMDLMQQGYFQAERLVTRRIGLDDIVRDGFEALVAEKSQIKILVEA 349 Lambda K H 0.317 0.135 0.392 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: 321 Number of extensions: 26 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: 343 Length of database: 350 Length adjustment: 29 Effective length of query: 314 Effective length of database: 321 Effective search space: 100794 Effective search space used: 100794 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 (21.6 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