Align Altronate dehydratase; EC 4.2.1.7; D-altronate hydro-lyase (uncharacterized)
to candidate Pf1N1B4_1107 D-galactarate dehydratase (EC 4.2.1.42)
Query= curated2:O34673 (497 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1107 Length = 517 Score = 258 bits (658), Expect = 5e-73 Identities = 172/495 (34%), Positives = 256/495 (51%), Gaps = 34/495 (6%) Query: 4 FIKIHKQDNVLLALRD--IQKGERLHAYGVSIEVKDDIKRGHKIALQSIKENDSIVKYGF 61 +I++H++DNV++ + D + G V++ D + + HK+ L+ I E +++YG Sbjct: 12 YIRLHERDNVVIVVNDQGVPAGTEFPDGLVTV---DFVPQSHKVTLEDIPEGGQVIRYGQ 68 Query: 62 PIGHASQDISIGEHIHVHNTKTNLSDIQLYSYTPRFDENPYSNE---------NRTFKGF 112 IG+A Q I G + + + P D P S E TF+G+ Sbjct: 69 TIGYALQPIPRGSWVKEDQLRMPTA--------PPLDSLPLSTEVPAAQAPLEGFTFEGY 120 Query: 113 RRENGDAGVRNELWIVPTVGCVNGIAEKMLQRFVRETGDIAP-FDNVLVLKHQYGCSQL- 170 R +G G RN L I TV CV G+ + ++R E P D+V+ L H YGC Sbjct: 121 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPNVDDVVALTHSYGCGVAI 180 Query: 171 -GDDHENTKQILLNAIRHPNAGG-VLVLGLGCENNELARMKEA------LQDVNLKRVKF 222 D + + N R+PN GG LV+ LGCE + ++ L D L R++ Sbjct: 181 TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHENDSSVDLSDPWLYRLQD 240 Query: 223 LESQSVTDEMEAGVALLKEIHEAAKGDKREDIPLSELKIGLKCGGSDGFSGITANPLLGR 282 S T+ +E +AL + + +RE +P SEL +G++CGGSD FSGITANP LG Sbjct: 241 -SSHGFTEMIEQIMALAETRLKKLDLRRRETVPASELILGMQCGGSDAFSGITANPALGY 299 Query: 283 FSDYLIAQGGSTVLTEVPEMFGAETILMQRAANEEVFHKIVDLINDFKQYFIKHDQPVYE 342 SD L+ G + + +EV E+ A +L RA EEV ++V ++ + +Y K + Sbjct: 300 ASDLLLRAGATVMFSEVTEVRDAIYLLTSRAETEEVAQELVREMDWYDRYLAKGEADRSA 359 Query: 343 NPSPGNKAGGISTLEDKSLGCTQKAGISPVTDVLKYGEVLKTKGLTLLSAPGNDLIASSA 402 N +PGNK GG+S + +KSLG K+G S + VL GE K KGL + P +D + + Sbjct: 360 NTTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKRKGLIFCATPASDFVCGTL 419 Query: 403 LAAAGCQIVLFTTGRGTPFG-TFVPTVKVATNTELYEAKPHWIDFNAGLLAEDDVHEEYV 461 AAG + +FTTGRGTP+G P VKV+T TEL + P ID +AG +A E + Sbjct: 420 QLAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRASIEEL 479 Query: 462 LREFIHYMIEVASGQ 476 E HY ++VASG+ Sbjct: 480 GWELFHYYLDVASGK 494 Lambda K H 0.317 0.137 0.394 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: 610 Number of extensions: 25 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: 497 Length of database: 517 Length adjustment: 34 Effective length of query: 463 Effective length of database: 483 Effective search space: 223629 Effective search space used: 223629 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 (21.6 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