Align Probable galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (uncharacterized)
to candidate WP_053935921.1 WG78_RS01020 altronate dehydratase
Query= curated2:P42240 (510 letters) >NCBI__GCF_001294205.1:WP_053935921.1 Length = 532 Score = 189 bits (480), Expect = 2e-52 Identities = 151/493 (30%), Positives = 233/493 (47%), Gaps = 47/493 (9%) Query: 41 LVLEEDVPQGHKVALTDLNQGDEIVRYGEVIGFADETIKRGSWIREALVRMPAPPALDDL 100 +++ V HK A +L QG+ + YG +G A I+RG EA+ D+ Sbjct: 33 ILINTPVAAKHKFARRNLAQGELLKLYGVPVGRAMAPIRRG----EAVTTENLEHYAADV 88 Query: 101 PLANRVPQP--RPPLEGY---TFEGYRNADGSAGTKNILGITTSVQC-----------VV 144 +A P P + + TFEG ADG GT N I V C + Sbjct: 89 EIAATQPYQWTAPDMARWQDATFEGVVRADGRVGTANYWLIFPLVFCENRNVEHLRNALE 148 Query: 145 GVLDYAVKRI---------KEELLPK-----YPNVDDVVPLHHQYGCGVAINAPDAVIPI 190 G L YA + + +E P+ + NVD V + H GCG DA Sbjct: 149 GPLGYATQDLAAYTLALLGEEMAAPRAVTRPFANVDGVRIITHAGGCGGT--RADARSLC 206 Query: 191 RTIQNLAKHPNFGGEVMVIGLGCEK----LLPERIASEN---DDDILSLQDHRGFA--AM 241 + + A HPN G + V LGC+ + + + + N D L + + + AM Sbjct: 207 KVLAAYADHPNVAG-ITVFSLGCQNAQISMFQDALKARNPAFDKPCLIYEQQKWDSEDAM 265 Query: 242 IQSILEMAEERLIRLNSRTRVSCPVSDLVIGLQCGGSDAFSGVTANPAVGYAADLLVRAG 301 ++++L+ L N+ TR P+S L IG++CGGSD FSG++ANPA+G +D++V G Sbjct: 266 MKAVLQDTLNGLKAANAVTRQPVPLSALKIGVKCGGSDGFSGLSANPAMGLVSDMVVAVG 325 Query: 302 ATVLFSEVTEVRDAIHLLTPRAVSEEVGQSLIKEMKWYDSYLRRGDADRSANPSPGNKKG 361 + +E E+ L R +++ + + M+ +++ + +ANPSPGN + Sbjct: 326 GGSILAEFPELCGVEASLIERCQNDDDKRRFLGMMRDFEARAQAVGTSFAANPSPGNIRD 385 Query: 362 GLSNVVEKALGSVAKSGTSPISGVLGPGERAKQKGLLFAATPASDFVCGTLQLAAGMNLQ 421 GL K+ G+ K GTSPI VL GE A + GL TP D T +A+G N+ Sbjct: 386 GLITDAIKSAGAAKKGGTSPIVSVLDYGEPAARPGLSLLCTPGGDVESVTGIVASGANVV 445 Query: 422 VFTTGRGTPYGLAAAPVLKVSTRHSLSEHWADLIDINAGRIATGEASIEDVGWEIFRTIL 481 +F+TG GTP G PVLK++T ++ D+ID + G + +G + +V +F +L Sbjct: 446 LFSTGLGTPTGNPIVPVLKIATNTRMATRLKDMIDFDCGPVISG-TPLPEVAEGLFEMVL 504 Query: 482 DVASGRKQTWADR 494 A GR + ADR Sbjct: 505 QTAGGRYRAKADR 517 Lambda K H 0.318 0.136 0.406 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: 667 Number of extensions: 35 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: 510 Length of database: 532 Length adjustment: 35 Effective length of query: 475 Effective length of database: 497 Effective search space: 236075 Effective search space used: 236075 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 (21.7 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