Align Lmo2664 protein (characterized, see rationale)
to candidate BWI76_RS24895 BWI76_RS24895 galactitol-1-phosphate 5-dehydrogenase
Query= uniprot:Q8Y413 (350 letters) >FitnessBrowser__Koxy:BWI76_RS24895 Length = 347 Score = 213 bits (543), Expect = 5e-60 Identities = 117/319 (36%), Positives = 178/319 (55%), Gaps = 2/319 (0%) Query: 1 MRAAVLYENNVIKAEQIDEATCG-KDQVRVEVKAVGICGSDIHKMQTRWKYPLPAVMGHE 59 M++ V++ ++ E+ T ++ V V+V + G+CGSDI ++ + + P +GHE Sbjct: 1 MQSVVIHAEGTVRVEERPIPTLQTENDVLVKVVSSGLCGSDIPRIFAKGAHYYPITLGHE 60 Query: 60 FAGVITEIGSEVTNVAMGDRVAGIPLEPCMECNYCKAGDFALCDNYRMVGSHFHGGFAEN 119 F+G + GS VT++ GD VA +PL PC C C+ F+LC Y+ VGS GG AE Sbjct: 61 FSGYVESYGSAVTDLQPGDAVACVPLLPCFNCPQCQREYFSLCKQYQFVGSRSEGGNAEY 120 Query: 120 VVMKADNVISIGD-LDFEEGAMIEPLAVSMHGVLGIQPRLGDTVIVFGIGTIGILVVQCL 178 VV+K N+ + D + ++GA IEP+ V +H Q G VI+ G GTIG+L +QC Sbjct: 121 VVVKRANLFRLPDRMPIDDGAFIEPMTVGLHAFHLAQGCEGKNVIIIGAGTIGLLALQCA 180 Query: 179 LLAGVKDIIAVDISDKKLADAREFGCKYTINPKNEDLKERVFAYTNGLGADIALECAGSK 238 G K I A+DI+ ++LA A+ G Y N K KE A + LE AG+ Sbjct: 181 RELGAKSITAIDINPQRLALAKTLGATYVFNSKEMSSKEIQTALEEIQFDQLVLETAGTP 240 Query: 239 ITQEQCLLVTKKKGKVGFLGIAYADVLLHEEAFENIFRRELTLKGFWNSYSAPFPGEEWR 298 T + V + ++ +G + D+ L F I R+ELT+ G W +YS P+PGEEW+ Sbjct: 241 QTVALGIEVAGPRAQLALVGTLHHDLTLLSATFGQILRKELTIVGSWMNYSGPWPGEEWQ 300 Query: 299 TSIEFVKQGRIKLKPLISH 317 T++ + + RI+L PLI+H Sbjct: 301 TAVRLLTEKRIQLVPLIAH 319 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: 270 Number of extensions: 12 Number of successful extensions: 3 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