Align Altronate dehydratase (EC 4.2.1.7) (characterized)
to candidate WP_053935921.1 WG78_RS01020 altronate dehydratase
Query= reanno::Pedo557:CA265_RS19875 (548 letters) >NCBI__GCF_001294205.1:WP_053935921.1 Length = 532 Score = 553 bits (1425), Expect = e-162 Identities = 280/545 (51%), Positives = 373/545 (68%), Gaps = 17/545 (3%) Query: 5 ILKIHPNDNVLVALQNLAKGETVIYDGHEYILQDDIQAKHKFFMQDMNAGDHIIMYGVLV 64 IL IHP+D++LVAL +LA G+ V ++G ++ + AKHKF +++ G+ + +YGV V Sbjct: 4 ILCIHPDDDMLVALVDLAAGQLVSWEGDSILINTPVAAKHKFARRNLAQGELLKLYGVPV 63 Query: 65 GKAQHFILKGGLMDTENTKH-ASDPYEFRPYHYEWHAPDVSKFEGRTFNGYIRSDGRVGT 123 G+A I +G + TEN +H A+D Y+W APD+++++ TF G +R+DGRVGT Sbjct: 64 GRAMAPIRRGEAVTTENLEHYAADVEIAATQPYQWTAPDMARWQDATFEGVVRADGRVGT 123 Query: 124 ANYWLFIPTVFCENRNLDVIREALHNELGYAVTDKYKSYAHQLVEAYKNGEILAEADPSS 183 ANYWL P VFCENRN++ +R AL LGYA D +Y L+ GE +A Sbjct: 124 ANYWLIFPLVFCENRNVEHLRNALEGPLGYATQD-LAAYTLALL-----GEEMA------ 171 Query: 184 IGLANPSANRVFKNVDGIKFLNHQGGCGGTRQDAAVLSKLLAAYADHPNVAGVTVLSLGC 243 A + R F NVDG++ + H GGCGGTR DA L K+LAAYADHPNVAG+TV SLGC Sbjct: 172 ---APRAVTRPFANVDGVRIITHAGGCGGTRADARSLCKVLAAYADHPNVAGITVFSLGC 228 Query: 244 QNLQVKDFMDDLKHRSPNFDKPLFVFEQQQSQSEEQLVKEAIRKTFIGLTEINKIERQPA 303 QN Q+ F D LK R+P FDKP ++EQQ+ SE+ ++K ++ T GL N + RQP Sbjct: 229 QNAQISMFQDALKARNPAFDKPCLIYEQQKWDSEDAMMKAVLQDTLNGLKAANAVTRQPV 288 Query: 304 PLSKLVLGVKCGGSDGFSGISANPAVGYTSDLLVALGGTVLLAEFPELCGAEQQLIDRTK 363 PLS L +GVKCGGSDGFSG+SANPA+G SD++VA+GG +LAEFPELCG E LI+R + Sbjct: 289 PLSALKIGVKCGGSDGFSGLSANPAMGLVSDMVVAVGGGSILAEFPELCGVEASLIERCQ 348 Query: 364 DETAARKFIQLMTAYNQSAENVGSGFFMNPSPGNIKDGLITDAIKSTGAAKKGGTSPVED 423 ++ R+F+ +M + A+ VG+ F NPSPGNI+DGLITDAIKS GAAKKGGTSP+ Sbjct: 349 NDDDKRRFLGMMRDFEARAQAVGTSFAANPSPGNIRDGLITDAIKSAGAAKKGGTSPIVS 408 Query: 424 VLDYTEPATKPGLNLVCTPGNDVEATTGKAASGATLILFTTGLGTPTGNPVCPTIKVSTN 483 VLDY EPA +PGL+L+CTPG DVE+ TG ASGA ++LF+TGLGTPTGNP+ P +K++TN Sbjct: 409 VLDYGEPAARPGLSLLCTPGGDVESVTGIVASGANVVLFSTGLGTPTGNPIVPVLKIATN 468 Query: 484 NALTKRMGDIIDINCGPVIEGEKTIEQMGEDILEYCIKAASGEVIPKAVLLNQDDFIPWK 543 + R+ D+ID +CGPVI G + ++ E + E ++ A G KA L Q DFI WK Sbjct: 469 TRMATRLKDMIDFDCGPVISG-TPLPEVAEGLFEMVLQTAGGRYRAKADRLQQYDFIFWK 527 Query: 544 RGVSL 548 R +SL Sbjct: 528 RDISL 532 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: 770 Number of extensions: 41 Number of successful extensions: 4 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: 532 Length adjustment: 35 Effective length of query: 513 Effective length of database: 497 Effective search space: 254961 Effective search space used: 254961 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 24 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