Align L-rhamnose isomerase (EC 5.3.1.14) (characterized)
to candidate CA265_RS02635 CA265_RS02635 sugar isomerase
Query= reanno::Cola:Echvi_1573 (427 letters) >FitnessBrowser__Pedo557:CA265_RS02635 Length = 426 Score = 557 bits (1436), Expect = e-163 Identities = 277/429 (64%), Positives = 341/429 (79%), Gaps = 5/429 (1%) Query: 1 MRIDKQKIKEVNDQALSEHRESFGHLSSVLGKKGIDVNVLVEKLKEFQVAVPSWALGTGG 60 M I++ +I++ ND L+ H+ L +D+ +++KL +FQ+A+PSWALGTGG Sbjct: 1 MNIEQNQIEKHNDSLLTSHQRKLSFLKEDWAH--VDLESVIQKLVDFQIAIPSWALGTGG 58 Query: 61 TRFGRFS-GGGEPGTLEDKISDVGLLHQLSQSAGAISLHIPWDIPNDVQAIKELAASHGL 119 TRFGRF+ GGEP T+E+KI DVGLLH L+ ++GAISLHIPWDIP + +A+K LAA +GL Sbjct: 59 TRFGRFAITGGEPRTIEEKIEDVGLLHALNGASGAISLHIPWDIPQNAEALKTLAAGYGL 118 Query: 120 IFDAVNSNTFQDQPDQELSYKFGSLCHADKKVRDQAVKHNLEVIKYGDALGSKSLTVWLA 179 FDA+NSNTFQDQ SYKFGSL + +K +R QA++HN+EVIK+G ALGS +LTVWLA Sbjct: 119 KFDAMNSNTFQDQKGAAHSYKFGSLQNVNKDIRKQAIEHNIEVIKHGIALGSDALTVWLA 178 Query: 180 DGSSFPGQLNFKKAFQRTLESLQEIYAGMPEDWKLFVEYKPYEPNFYSTVIQDWGTSHML 239 DGS FPGQLNF+KAF+ TLESLQEIY+ +PEDWK+FVEYK +EPNFYST + DWG S + Sbjct: 179 DGSCFPGQLNFRKAFENTLESLQEIYSALPEDWKMFVEYKAFEPNFYSTTVGDWGQSLLY 238 Query: 240 ADKLGDRAYSLVDLGHHLPNTNIEQIVATLMMVGKLGGFHFNDSKYGDDDVTVGSLKPYQ 299 A KLG +AY+LVDLGHHLPN NIEQIVA L+M GKLGGFHFNDSKYGDDD+T GS+KPYQ Sbjct: 239 ASKLGKKAYTLVDLGHHLPNANIEQIVALLLMEGKLGGFHFNDSKYGDDDLTAGSIKPYQ 298 Query: 300 LFLIFNELVDGMEDPSSNNPYP-AWMIDASHNLKDPLEDLLQSLEAIKLAYAQALLVDRD 358 LFLIFNELV+GM+ N+ WMIDASHN+KDPLEDLLQS+EAI +AYAQALLVDR Sbjct: 299 LFLIFNELVEGMDAKGMNHAKDLGWMIDASHNVKDPLEDLLQSVEAIMIAYAQALLVDRK 358 Query: 359 ALEEARENNDPALAQEILQAAYRTDVRSLLAEARLQADGALDPIAAYRKLNVRKELIAQR 418 AL EA+ NND A AQEILQ +R+D+R+L+AEARL+A AL PIA YR L VR +L+ R Sbjct: 359 ALNEAQNNNDVAKAQEILQHTFRSDLRALVAEARLRAGAALSPIALYRGLEVRNQLVNHR 418 Query: 419 GEKVISTGL 427 G ++TGL Sbjct: 419 G-NTVATGL 426 Lambda K H 0.316 0.135 0.391 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: 573 Number of extensions: 24 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: 427 Length of database: 426 Length adjustment: 32 Effective length of query: 395 Effective length of database: 394 Effective search space: 155630 Effective search space used: 155630 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: 51 (24.3 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