Align Altronate dehydratase; D-altronate hydro-lyase; EC 4.2.1.7 (characterized)
to candidate PP_2834 PP_2834 Putative D-galactarate dehydratase/Altronate dehydratase
Query= SwissProt::P42604 (495 letters) >FitnessBrowser__Putida:PP_2834 Length = 513 Score = 283 bits (725), Expect = 8e-81 Identities = 176/492 (35%), Positives = 264/492 (53%), Gaps = 17/492 (3%) Query: 4 IKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIG 63 I+++ LDNV +A L G V +D + +T+RQ + GHK A +A+G + +YG IG Sbjct: 13 IRLNPLDNVVIARQALLPG--VRLDAEAITVRQPIPSGHKLATEPVAQGQPLRRYGQIIG 70 Query: 64 YALADIAAGVHVHAHNTRTNLSDLDQYRYQPDFQDLPAQAADREVQIYRRANGDVGVRNE 123 +A I AG HVH HN + D Y + D + LP AA + Q RA+G V RN Sbjct: 71 FASQAIDAGDHVHVHNVQMGDFARD-YAFGVDTRSLPGSAA--QFQGIVRADGRVATRNY 127 Query: 124 LWILPTVGCVNGIARQIQNRFLKETN-----NAEGTDGVFLFSHTYGCS--QLGDDHINT 176 + IL +V C +AR + + F ++ + + DGV SH+ GC+ G+ Sbjct: 128 IGILTSVNCSATVARAVADHFRRDIHPEVLADYPNVDGVVALSHSAGCAVDPSGEALGLL 187 Query: 177 RTMLQNMVRHPNAGAVLVIGLGCENNQVAAFRETLGDIDPERVHFMICQQ---QDDEIEA 233 R L HPN AVL+IGLGCE NQ+ ET G ++ Q I A Sbjct: 188 RRTLAGYAVHPNFAAVLIIGLGCETNQIETLLETQGLQASAQLRAFTIQGIGGTSKTIAA 247 Query: 234 GIEHLHQLYNVMRNDKREPGKLSELKFGLECGGSDGLSGITANPMLGRFSDYVIANGGTT 293 GI + L +R+P L GL+CGGSDG SGITANP LG D ++A GGT Sbjct: 248 GIAQVKALLAEANQVRRQPVSARHLVVGLQCGGSDGYSGITANPALGNAVDRLVAAGGTA 307 Query: 294 VLTEVPEMFGAEQLLMDHCRDEATFEKLVTMVNDFKQYFIAHDQPIYENPSPGNKAGGIT 353 +L+E PE++GAE LL EKLV + ++ Y + + NPS GNKAGG+T Sbjct: 308 ILSETPEIYGAEHLLTRRAVSREVGEKLVARIRWWEDYCQRMNAELNNNPSAGNKAGGLT 367 Query: 354 TLEDKSLGCTQKAGSSVVVDVLRYGERLKTPGLNLLSAPGNDAVATSALAGAGCHMVLFS 413 T+ +KSLG KAGSS +VDV +Y + ++ GL + PG D V+ + G +++ F+ Sbjct: 368 TILEKSLGAVAKAGSSNLVDVYQYAQAVRAQGLVFMDTPGYDPVSATGQVAGGANLIAFT 427 Query: 414 TGRGTPYG-GFVPTVKIATNSELAAKKKHWIDFDAGQLIHGKAMPQLLEEFI-DTIVEFA 471 TGRG+ YG P++K+ATN+ + ++ +D + G + G + FI + ++ A Sbjct: 428 TGRGSAYGCAPAPSIKLATNNRVFEHQQEDMDVNCGGIADGSTSIEERGAFIFEQMLRIA 487 Query: 472 NGKQTCNERNDF 483 +G+++ +E++ + Sbjct: 488 SGERSKSEQHGY 499 Lambda K H 0.319 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: 644 Number of extensions: 38 Number of successful extensions: 6 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: 495 Length of database: 513 Length adjustment: 34 Effective length of query: 461 Effective length of database: 479 Effective search space: 220819 Effective search space used: 220819 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 (21.7 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