Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate WP_086509098.1 BZY95_RS06185 altronate dehydratase
Query= reanno::WCS417:GFF829 (517 letters) >NCBI__GCF_002151265.1:WP_086509098.1 Length = 547 Score = 244 bits (624), Expect = 4e-69 Identities = 183/526 (34%), Positives = 249/526 (47%), Gaps = 58/526 (11%) Query: 12 SIRLHERDNVVIVVNDQGVPAGTEFPDG---LVTVDFIPQSHKVTLEDIPEGGQIIRYGQ 68 S+R+H DNV + + D +PAG DG L + I HK L D+ +I YG Sbjct: 15 SLRVHHADNVRVALKD--LPAGHAVDDGERRLHLAEAIRHKHKFALHDLAPDDAVIMYGV 72 Query: 69 TIGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEA-----QAP----LEGFTFEG 119 T+G A PIP G+ + D TA T VP+A QAP G TF+G Sbjct: 73 TVGRATRPIPAGAAITTDNTAHSTA---------TSVPQARRGEWQAPDVAAFAGATFDG 123 Query: 120 YRNADGTVGTRNILGITTTV-----------QCVTGVLDHA----VKRIKDELLPK---- 160 Y +G VGT N+ + V QCV L KR+ ELL Sbjct: 124 YHRPNGQVGTANVWLVVPLVFCENRNIEVLRQCVADALGEDPYRDYKRMARELLHGSSGT 183 Query: 161 ----------YPHVDDVVALTHSYGCGVAITATDAYIPIRTVRNLARNPNLGGEALVISL 210 +P+VD V LTH+ GCG T DA R + +PN+ G A V+SL Sbjct: 184 AAVEPPGERLFPNVDGVRFLTHTLGCGG--TDDDALALCRLLAGYICHPNVAG-ATVLSL 240 Query: 211 GCEKLQAGQVMHDNDSSVDLS--EPWLYRLQDSSHGFTEMIEQIMALAETRLKKLDQRRR 268 GC+K Q +++ + D P Y Q S +I + + L + ++ R Sbjct: 241 GCQKAQI-EMLQTAVAERDPCGLRPVHYLEQQGSQSEEALIREALTTIFDGLSEANRTPR 299 Query: 269 ETVPASELILGMQCGGSDAFSGITANPALGYASDLLLRAGATVMFSEVTEVRDAIYLLTS 328 P S L LG++CGGSD FSG++ANP +G D L+ G + + SE E+ + L + Sbjct: 300 TPAPLSALTLGVECGGSDGFSGLSANPLVGAVVDRLVALGGSGILSEFPELCGVEHELIA 359 Query: 329 RAENTQVAQELVREMDWYDRYLAKGEADRSANTTPGNKKGGLSNIVEKSLGSIVKSGSSA 388 R + VA+ M+ Y R+ A+ AD S N +PGN + GL KS G+ K G S Sbjct: 360 RCRDDAVAERFRTLMEAYQRHAARVGADFSMNPSPGNIRDGLITDAMKSAGAAKKGGDSP 419 Query: 389 INGVLGPGERFKGKGLIFCATPASDFVCGTLQLAAGMNLHVFTTGRGTPYGLAMAPVVKV 448 + VL E GL TP +D T +G NL +FTTG GTP G + PV+K+ Sbjct: 420 VVDVLDYAEPHTRAGLSLLCTPGNDVESTTALAGSGANLILFTTGLGTPTGNPVTPVLKI 479 Query: 449 STRTELAQRWPDLIDIDAGRIATGRATIEELGWELFHFYLDVASGR 494 S+ +ELA R D+ID DAG I G +I+EL L LD ASGR Sbjct: 480 SSNSELAARMGDVIDFDAGPIIRGEVSIDELAERLLRLCLDTASGR 525 Lambda K H 0.318 0.135 0.401 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: 748 Number of extensions: 49 Number of successful extensions: 7 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: 517 Length of database: 547 Length adjustment: 35 Effective length of query: 482 Effective length of database: 512 Effective search space: 246784 Effective search space used: 246784 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 24 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