Align Galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (characterized)
to candidate CA265_RS19875 CA265_RS19875 altronate hydrolase
Query= SwissProt::P39829 (523 letters) >FitnessBrowser__Pedo557:CA265_RS19875 Length = 548 Score = 232 bits (591), Expect = 3e-65 Identities = 171/532 (32%), Positives = 254/532 (47%), Gaps = 58/532 (10%) Query: 16 IKVHDTDNVAIIVNDNGLKAGTRFPDGLELI--EHIPQGHKVALLDIPANGEIIRYGEVI 73 +K+H DNV + + N K T DG E I + I HK + D+ A II YG ++ Sbjct: 6 LKIHPNDNVLVALQ-NLAKGETVIYDGHEYILQDDIQAKHKFFMQDMNAGDHIIMYGVLV 64 Query: 74 GYAVRAIPRGSWIDESMVVLPEAP----PLHTLPLATKVPEPLPPLEGYTFEGYRNADGS 129 G A I +G +D P P H A V + EG TF GY +DG Sbjct: 65 GKAQHFILKGGLMDTENTKHASDPYEFRPYHYEWHAPDVSK----FEGRTFNGYIRSDGR 120 Query: 130 VGTKNLLGITTSVHCVAGVVDYVVKIIERDL----LPKYP-------------------- 165 VGT N +V C +D + + + +L KY Sbjct: 121 VGTANYWLFIPTVFCENRNLDVIREALHNELGYAVTDKYKSYAHQLVEAYKNGEILAEAD 180 Query: 166 ----------------NVDGVVGLNHLYGCGVAINAPAAVVPIRTIHNISLNPNFGGEVM 209 NVDG+ LNH GCG AAV+ + + + +PN G V Sbjct: 181 PSSIGLANPSANRVFKNVDGIKFLNHQGGCG-GTRQDAAVLS-KLLAAYADHPNVAG-VT 237 Query: 210 VIGLGCEKLQPERLLTGTDDVQ-AIPVESASIVSLQDEKHVGFQSMVEDILQIAERHLQK 268 V+ LGC+ LQ + + DD++ P + + ++ + +V++ ++ L + Sbjct: 238 VLSLGCQNLQVKDFM---DDLKHRSPNFDKPLFVFEQQQSQSEEQLVKEAIRKTFIGLTE 294 Query: 269 LNQRQRETCPASELVVGMQCGGSDAFSGVTANPAVGYASDLLVRCGATVMFSEVTEVRDA 328 +N+ +R+ P S+LV+G++CGGSD FSG++ANPAVGY SDLLV G TV+ +E E+ A Sbjct: 295 INKIERQPAPLSKLVLGVKCGGSDGFSGISANPAVGYTSDLLVALGGTVLLAEFPELCGA 354 Query: 329 IHLLTPRAVNEEVGKRLLEEMEWYDNYLNMGKTDRSANPSPGNKKGGLANVVEKALGSIA 388 L R +E ++ ++ M Y+ + NPSPGN K GL K+ G+ Sbjct: 355 EQQLIDRTKDETAARKFIQLMTAYNQSAENVGSGFFMNPSPGNIKDGLITDAIKSTGAAK 414 Query: 389 KSGKSAIVEVLSPGQRPTKRGLIYAATPASDFVCGTQQVASGITVQVFTTGRGTPYGLMA 448 K G S + +VL + TK GL TP +D T + ASG T+ +FTTG GTP G Sbjct: 415 KGGTSPVEDVLDYTEPATKPGLNLVCTPGNDVEATTGKAASGATLILFTTGLGTPTGNPV 474 Query: 449 VPVIKMATRTELANRWFDLMDINAGTIATGEETIEEVGWKLFHFILDVASGK 500 P IK++T L R D++DIN G + GE+TIE++G + + + ASG+ Sbjct: 475 CPTIKVSTNNALTKRMGDIIDINCGPVIEGEKTIEQMGEDILEYCIKAASGE 526 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: 735 Number of extensions: 37 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 523 Length of database: 548 Length adjustment: 35 Effective length of query: 488 Effective length of database: 513 Effective search space: 250344 Effective search space used: 250344 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