Align galactonate dehydratase (EC 4.2.1.6) (characterized)
to candidate 15702 b1581 predicted dehydratase (NCBI)
Query= BRENDA::G3Y8T6 (383 letters) >FitnessBrowser__Keio:15702 Length = 404 Score = 174 bits (441), Expect = 4e-48 Identities = 122/379 (32%), Positives = 187/379 (49%), Gaps = 44/379 (11%) Query: 19 VKVTDSEDKFGWGEATLEGHTQAVEGAL-DEIIGRIVGYEADDIEHVWQTIWRLGFYRGG 77 +K+T + G G+ATL G +V L D + +++G +A IE +WQ ++ ++R G Sbjct: 20 LKITTEDGITGLGDATLNGRELSVASYLQDHLCPQLIGRDAHRIEDIWQFFYKGAYWRRG 79 Query: 78 PVFMSALSGIDIALWDLKGRRLNVPVYQLLGGKVRNKVQVYAWIGG--------DRPSDV 129 PV MSA+S +D+ALWD+K + N+P+YQLLGG R V VY G D Sbjct: 80 PVTMSAISAVDMALWDIKAKAANMPLYQLLGGASREGVMVYCHTTGHSIDEALDDYARHQ 139 Query: 130 EVAAKA-RIAQGLKCVKMN-------------AT-----EDMNWLDSPSVLDSCIERIKQ 170 E+ KA R+ G+ +K AT E+ W + LD + Sbjct: 140 ELGFKAIRVQCGIPGMKTTYGMSKGKGLAYEPATKGQWPEEQLW-STEKYLDFMPKLFDA 198 Query: 171 VK-ALGLDAGL--DFHGRLHRPMAKQLAKALEPYRPLFIEEPLLVEHPEAIKQLSQHTTI 227 V+ G + L D H RL A + K++E YR ++E+P E+ E + + QHT Sbjct: 199 VRNKFGFNEHLLHDMHHRLTPIEAARFGKSIEDYRMFWMEDPTPAENQECFRLIRQHTVT 258 Query: 228 PIAFGERLYTRWDVKRFLEDASVDVLQPDIAHAGGISETKRIATMAETYDVAIAPHCP-- 285 PIA GE + WD K+ +E+ +D ++ + HAGGI+ +RIA A Y V H P Sbjct: 259 PIAVGEVFNSIWDCKQLIEEQLIDYIRTTLTHAGGITGMRRIADFASLYQVRTGSHGPSD 318 Query: 286 LGPIALAASMQVALSTPNFVIQEMSLGMHYNVEAGDIDLTSYLTNPTVFNIEEGYVPAPT 345 L P+ +AA++ L PNF +QE M Y+ + ++ P + + GY+ Sbjct: 319 LSPVCMAAALHFDLWVPNFGVQEY---MGYSEQMLEV-------FPHNWTFDNGYMHPGD 368 Query: 346 GAGLGVEIDEELVRRISRE 364 GLG+E DE+L + E Sbjct: 369 KPGLGIEFDEKLAAKYPYE 387 Lambda K H 0.320 0.138 0.425 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: 412 Number of extensions: 25 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: 383 Length of database: 404 Length adjustment: 31 Effective length of query: 352 Effective length of database: 373 Effective search space: 131296 Effective search space used: 131296 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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