Align Altronate dehydratase (EC 4.2.1.7) (characterized)
to candidate CA265_RS04670 CA265_RS04670 altronate hydrolase
Query= reanno::Pedo557:CA265_RS19875 (548 letters) >FitnessBrowser__Pedo557:CA265_RS04670 Length = 545 Score = 784 bits (2025), Expect = 0.0 Identities = 383/544 (70%), Positives = 450/544 (82%), Gaps = 3/544 (0%) Query: 5 ILKIHPNDNVLVALQNLAKGETVIYDGHEYILQDDIQAKHKFFMQDMNAGDHIIMYGVLV 64 ++KI+ DNVLVALQ+L K ++++G+ Y+ D+I AKHKFFMQDM AGD ++MYGVLV Sbjct: 5 VIKINHADNVLVALQDLPKNTEIVHEGNTYVTVDEIPAKHKFFMQDMKAGDEVMMYGVLV 64 Query: 65 GKAQHFILKGGLMDTENTKHASDPYEFRPYHYEWHAPDVSKFEGRTFNGYIRSDGRVGTA 124 GK Q + G M+ ENTKHA++P+ +R +Y+W APDVSK+ R+FNGY R +G VGTA Sbjct: 65 GKVQFDVKAGMRMNVENTKHAAEPFAYRNVNYKWEAPDVSKYANRSFNGYHRKNGEVGTA 124 Query: 125 NYWLFIPTVFCENRNLDVIREALHNELGYAVTDKYKSYAHQLVEAYKNGEILAEADPSSI 184 NYWLFIPTVFCENRNLD+I+E+L++ELGYAV DKYKSY H+LV+AY+NGE + S Sbjct: 125 NYWLFIPTVFCENRNLDIIKESLYSELGYAVDDKYKSYTHKLVQAYENGEDIHNI---SF 181 Query: 185 GLANPSANRVFKNVDGIKFLNHQGGCGGTRQDAAVLSKLLAAYADHPNVAGVTVLSLGCQ 244 A+R FKNVDGIKFL H GGCGGTRQD+ LSKLLAAYA HPNVAG+TVLSLGCQ Sbjct: 182 EPKVDKASRTFKNVDGIKFLTHNGGCGGTRQDSDTLSKLLAAYAHHPNVAGITVLSLGCQ 241 Query: 245 NLQVKDFMDDLKHRSPNFDKPLFVFEQQQSQSEEQLVKEAIRKTFIGLTEINKIERQPAP 304 +LQV+DF DL P+FDKPL +FEQQ++QSEE+L++ +IR TF GL INK R AP Sbjct: 242 HLQVEDFKRDLFALDPDFDKPLLIFEQQKAQSEEELIQNSIRSTFEGLMFINKQARAAAP 301 Query: 305 LSKLVLGVKCGGSDGFSGISANPAVGYTSDLLVALGGTVLLAEFPELCGAEQQLIDRTKD 364 LSK+ +GVKCGGSDGFSGISANP+VGY +DLLVALG VLLAEFPELCG EQ++IDR+ D Sbjct: 302 LSKMCVGVKCGGSDGFSGISANPSVGYCADLLVALGAKVLLAEFPELCGVEQEMIDRSVD 361 Query: 365 ETAARKFIQLMTAYNQSAENVGSGFFMNPSPGNIKDGLITDAIKSTGAAKKGGTSPVEDV 424 + A KFI+LMT Y+ A VGSGF+MNPSPGNIKDGLITDAIKS GAA+K G++P+ DV Sbjct: 362 QPTAEKFIRLMTEYDDLAHKVGSGFYMNPSPGNIKDGLITDAIKSAGAARKAGSAPIVDV 421 Query: 425 LDYTEPATKPGLNLVCTPGNDVEATTGKAASGATLILFTTGLGTPTGNPVCPTIKVSTNN 484 LDYTEPATKPGL+LVCTPGNDVEATTGKAA+GATLILFTTGLGTPTGNPVCPTIKV+TN+ Sbjct: 422 LDYTEPATKPGLSLVCTPGNDVEATTGKAAAGATLILFTTGLGTPTGNPVCPTIKVATNS 481 Query: 485 ALTKRMGDIIDINCGPVIEGEKTIEQMGEDILEYCIKAASGEVIPKAVLLNQDDFIPWKR 544 L KRM DIIDI+ G VI GEKTI +MGEDILEYCIK ASGE IPKAV LNQDDFIPWKR Sbjct: 482 ILAKRMSDIIDIDTGAVINGEKTINEMGEDILEYCIKVASGEEIPKAVQLNQDDFIPWKR 541 Query: 545 GVSL 548 GVSL Sbjct: 542 GVSL 545 Lambda K H 0.317 0.136 0.400 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: 914 Number of extensions: 32 Number of successful extensions: 2 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: 548 Length of database: 545 Length adjustment: 36 Effective length of query: 512 Effective length of database: 509 Effective search space: 260608 Effective search space used: 260608 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: 52 (24.6 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