Align Galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (characterized)
to candidate BPHYT_RS28730 BPHYT_RS28730 galactarate dehydratase
Query= SwissProt::P39829 (523 letters) >FitnessBrowser__BFirm:BPHYT_RS28730 Length = 503 Score = 322 bits (825), Expect = 2e-92 Identities = 198/500 (39%), Positives = 276/500 (55%), Gaps = 18/500 (3%) Query: 16 IKVHDTDNVAIIVNDNGLKAGTRFP-DGLELIEHIPQGHKVALLDIPANGEIIRYGEVIG 74 ++++ D+V I + L +GT + + + IP GHKVA DI + RYG+VIG Sbjct: 1 MRLNPADDVVIALEQ--LMSGTVIDKEAVTVSGLIPPGHKVATRDIRQGEAVHRYGQVIG 58 Query: 75 YAVRAIPRGSWIDESMVVLPEAPPLHTLPLATKVPEPLPPLEGYTFEGYRNADGSVGTKN 134 +A + I G + + + + + A + LP TF+G ADG V T+N Sbjct: 59 FASQPIRAGQHVHTHNLAMGDFARDYAFGQAAR--PTLPSNRPATFQGIVRADGRVATRN 116 Query: 135 LLGITTSVHCVAGVVDYVVKIIERDLLPK----YPNVDGVVGLNHLYGCGVAINAPAAVV 190 +GI TSV+C A V + RD+ P+ +PNVDGV+ L H GC + + Sbjct: 117 YIGILTSVNCSATVARAIADHFRRDIHPEELAEFPNVDGVIALTHGSGCAIDSEGDGLAI 176 Query: 191 PIRTIHNISLNPNFGGEVMVIGLGCEKLQPERLLTGTDDVQAIPV-ESASIVSLQDEKHV 249 RTI + +PNF V+V+GLGCE Q RLL + Q + + ++QD Sbjct: 177 LQRTIGGYACHPNFAS-VLVVGLGCETNQIPRLL----ETQGLREHDRLRTFTIQDSG-- 229 Query: 250 GFQSMVEDILQIAERHLQKLNQRQRETCPASELVVGMQCGGSDAFSGVTANPAVGYASDL 309 G S + +++ R L + N +RE AS L VG+QCGGSD +SG+TANP +G A DL Sbjct: 230 GTTSTIAKGIELVRRMLPEANDVRREAVSASHLTVGLQCGGSDGYSGITANPVLGAAVDL 289 Query: 310 LVRCGATVMFSEVTEVRDAIHLLTPRAVNEEVGKRLLEEMEWYDNYLNMGKTDRSANPSP 369 LVR G T + SE E+ A HLLT RA EVG++LL+ + W++ Y N + NPS Sbjct: 290 LVRHGGTAILSETPEIYGAEHLLTRRAATPEVGRKLLDRIRWWEAYANRHGAQMNNNPSA 349 Query: 370 GNKKGGLANVVEKALGSIAKSGKSAIVEVLSPGQRPTKRGLIYAATPASDFVCGTQQVAS 429 GNK GGL V+EK+LG IAK+G + + EV Q T RGL++ TP D V T QVA Sbjct: 350 GNKAGGLTTVLEKSLGGIAKAGSTNLTEVYEYAQPVTARGLVFMDTPGYDPVSATGQVAG 409 Query: 430 GITVQVFTTGRGTPYGLMAVPVIKMATRTELANRWFDLMDINAGTIATGEETIEEVGWKL 489 G + FTTGRG+ YG P +K+AT T L R D MD+N G + G TIE++G L Sbjct: 410 GANLICFTTGRGSAYGCAPTPSVKLATNTALWQRQSDDMDLNCGEVLEGRTTIEQLGGVL 469 Query: 490 FHFILDVASGKKKTFSDQWG 509 F +L+VASG +T S+Q G Sbjct: 470 FELLLEVASG-NRTRSEQHG 488 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: 694 Number of extensions: 37 Number of successful extensions: 5 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: 503 Length adjustment: 35 Effective length of query: 488 Effective length of database: 468 Effective search space: 228384 Effective search space used: 228384 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