Align Lmo2664 protein (characterized, see rationale)
to candidate 16198 b2091 galactitol-1-phosphate dehydrogenase, Zn-dependent and NAD(P)-binding (NCBI)
Query= uniprot:Q8Y413 (350 letters) >FitnessBrowser__Keio:16198 Length = 346 Score = 214 bits (546), Expect = 2e-60 Identities = 119/347 (34%), Positives = 188/347 (54%), Gaps = 3/347 (0%) Query: 1 MRAAVLYENNVIK-AEQIDEATCGKDQVRVEVKAVGICGSDIHKMQTRWKYPLPAVMGHE 59 M++ V + +++ AE + +D+VRV++ + G+CGSD+ ++ + P +GHE Sbjct: 1 MKSVVNDTDGIVRVAESVIPEIKHQDEVRVKIASSGLCGSDLPRIFKNGAHYYPITLGHE 60 Query: 60 FAGVITEIGSEVTNVAMGDRVAGIPLEPCMECNYCKAGDFALCDNYRMVGSHFHGGFAEN 119 F+G I +GS V ++ GD VA +PL PC C C G ++ C Y +GS GGFAE Sbjct: 61 FSGYIDAVGSGVDDLHPGDAVACVPLLPCFTCPECLKGFYSQCAKYDFIGSRRDGGFAEY 120 Query: 120 VVMKADNVISI-GDLDFEEGAMIEPLAVSMHGVLGIQPRLGDTVIVFGIGTIGILVVQCL 178 +V+K NV ++ D+ E+GA IEP+ V +H Q VI+ G GTIG+L +QC Sbjct: 121 IVVKRKNVFALPTDMPIEDGAFIEPITVGLHAFHLAQGCENKNVIIIGAGTIGLLAIQCA 180 Query: 179 LLAGVKDIIAVDISDKKLADAREFGCKYTINPKNEDLKERVFAYTNGLGADIALECAGSK 238 + G K + A+DIS +KLA A+ FG T N + + LE AG Sbjct: 181 VALGAKSVTAIDISSEKLALAKSFGAMQTFNSSEMSAPQMQSVLRELRFNQLILETAGVP 240 Query: 239 ITQEQCLLVTKKKGKVGFLGIAYADVLLHEEAFENIFRRELTLKGFWNSYSAPFPGEEWR 298 T E + + ++ +G + D+ L F I R+ELT+ G W +YS+P+PG+EW Sbjct: 241 QTVELAVEIAGPHAQLALVGTLHQDLHLTSATFGKILRKELTVIGSWMNYSSPWPGQEWE 300 Query: 299 TSIEFVKQGRIKLKPLISHRYKLEETKEAFDMILSREHDYNKVMILP 345 T+ + + ++ L+PLI+HR E +A I +R KV+++P Sbjct: 301 TASRLLTERKLSLEPLIAHRGSFESFAQAVRDI-ARNAMPGKVLLIP 346 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: 293 Number of extensions: 14 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: 346 Length adjustment: 29 Effective length of query: 321 Effective length of database: 317 Effective search space: 101757 Effective search space used: 101757 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