Align Galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (characterized)
to candidate BPHYT_RS27220 BPHYT_RS27220 galactarate dehydratase
Query= SwissProt::P39829 (523 letters) >FitnessBrowser__BFirm:BPHYT_RS27220 Length = 508 Score = 314 bits (805), Expect = 4e-90 Identities = 188/497 (37%), Positives = 275/497 (55%), Gaps = 15/497 (3%) Query: 18 VHDTDNVAIIVNDNGLKAGTRFPDGLELIE---HIPQGHKVALLDIPANGEIIRYGEVIG 74 +H+ DNVA+ + L+AGT G + + I GHK+A+ I + +Y + IG Sbjct: 9 LHNEDNVAVALR--ALEAGTPVEAGGQRVVVRGSIAAGHKLAIRRIARGSAVTKYRQTIG 66 Query: 75 YAVRAIPRGSWIDESMVVLPEAPPLHTLPLATKVPEPLPPLEGY-TFEGYRNADGSVGTK 133 A+ + G + V +PE P P + L P++ F+G+ ADG VGT+ Sbjct: 67 IALADVEPGEHVHVHNVGMPEHHPHR--PTHSDAVRSLAPVDRPGAFQGFVRADGQVGTR 124 Query: 134 NLLGITTSVHCVAGVVDYVVKIIERDLLPKYPNVDGVVGLNHLYGCGVAINAPAAVVPIR 193 N +G+ SV+C A V + + D + + VDGVV + H GCG++ + R Sbjct: 125 NYIGVIASVNCSASVCHAIADAFKGDAMDPFSTVDGVVAITHQSGCGMSATGDGMALLRR 184 Query: 194 TIHNISLNPNFGGEVMVIGLGCEKLQPERLLTGTDDVQAIPVESASIVSLQDEKHVGFQS 253 T+ + NPNF G V+++GLGCE Q L + VE+ I QDE G + Sbjct: 185 TLTGYACNPNFAG-VLLVGLGCEVNQVSGLTRSLEAGSPALVETLVI---QDEG--GVRE 238 Query: 254 MVEDILQIAERHLQKLNQRQRETCPASELVVGMQCGGSDAFSGVTANPAVGYASDLLVRC 313 V + I L ++ +R PA+ L VG+QCGGSD +SG+TANPA+G A DLLVR Sbjct: 239 TVARGIAIVREMLSAASRIRRIEVPAARLKVGLQCGGSDGYSGITANPALGAAVDLLVRH 298 Query: 314 GATVMFSEVTEVRDAIHLLTPRAVNEEVGKRLLEEMEWYDNYLNMGKTDRSANPSPGNKK 373 G T + SE E+ A HLLT RAV+ +V RLL+++ W++ Y D + NPSPGNK Sbjct: 299 GGTAILSETPEIYGAEHLLTARAVSSDVAGRLLDKLRWWERYAAEAGGDMNNNPSPGNKA 358 Query: 374 GGLANVVEKALGSIAKSGKSAIVEVLSPGQRPTKRGLIYAATPASDFVCGTQQVASGITV 433 GG+ ++EK+LG+++K G +A+ V +R ++ GL++ TP D V T Q+A G + Sbjct: 359 GGITTILEKSLGAVSKGGSTALNAVYEYAERASESGLVFMDTPGYDPVSATGQIAGGANL 418 Query: 434 QVFTTGRGTPYGLMAVPVIKMATRTELANRWFDLMDINAGTIATGEETIEEVGWKLFHFI 493 FTTGRG+ +G VP IK+AT T L R MD N G I G T+E+ G ++F + Sbjct: 419 VCFTTGRGSVFGSKPVPTIKLATTTGLFERMRADMDFNCGQIVDGSLTVEQAGAQVFQLM 478 Query: 494 LDVASGKKKTFSDQWGL 510 LD+ASG KT S+Q G+ Sbjct: 479 LDIASG-TKTHSEQNGM 494 Lambda K H 0.317 0.136 0.403 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: 38 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: 523 Length of database: 508 Length adjustment: 35 Effective length of query: 488 Effective length of database: 473 Effective search space: 230824 Effective search space used: 230824 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 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