Align phosphogluconate dehydratase (characterized)
to candidate HSERO_RS16705 HSERO_RS16705 dihydroxy-acid dehydratase
Query= CharProtDB::CH_024239 (603 letters) >FitnessBrowser__HerbieS:HSERO_RS16705 Length = 578 Score = 185 bits (469), Expect = 5e-51 Identities = 158/528 (29%), Positives = 251/528 (47%), Gaps = 60/528 (11%) Query: 68 IAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQDGME-LSL 126 I I +Y+++ + + E ++ + EA GG P ++ G+ + ++ Sbjct: 46 IGICNTYSELTPCNSHFRALAEQVKIGIWEA-------GGFPLEFPVMSLGETLLRPTAM 98 Query: 127 LSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLP 186 L R + +M + N DG + L CDK P L M A S +P + V GPM SG Sbjct: 99 LYRNLASMDVEESIRANPLDGVVLLMGCDKTTPALLMGAASVD-VPTIGVSGGPMLSG-- 155 Query: 187 NKEKVRIRQLYA------------EGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVV 234 K R R+L + GK+ + E+E+ + + G C GTA+T +V Sbjct: 156 ---KYRGRELGSGTGVWQMSEDVRAGKMTQEEFFEAESCMHRSHGHCMTMGTASTMASMV 212 Query: 235 EFMGMQLPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVAL 294 E +G+ LP ++ + R+ L A R++ +M E + + K++ + N I Sbjct: 213 EALGVGLPHNAAIPAVDARRNVLARNAGRRIVQMV---EEDLVLSKILTRQAFENAIRVN 269 Query: 295 LATGGSTNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVP 354 A GGSTN +HL+A+A GI+++ D+ D+ +P + L P+G + F AGG+P Sbjct: 270 AAIGGSTNAVIHLLAIAGRIGIKLDLKDWDDIGQQLPCLLDLQPSGKFLMEDFYYAGGLP 329 Query: 355 VLVRELLKAGLLHEDVNTVAGFGLSRYTLEPWLNNGEL-DWREGAEKSLDSNVIASFEQP 413 ++R+L ++ + T G L W N + +W E VI SF++P Sbjct: 330 AVIRQL--ESVIDKTALTANGKTL-------WENCQDAPNWNE--------EVIRSFDKP 372 Query: 414 FSHHGGTKVLSGNLG--RAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRD-- 469 F G +L GNL AV+K SA AVVFE+ D+ + LD D Sbjct: 373 FKEAAGIAILKGNLAPDGAVIKPSAATPALLKHRGRAVVFENSDDLHKRIDDENLDVDET 432 Query: 470 CVVVVRHQGPKA-NGMPELHKLMPPLGVLLDRCFKIALVTDGRLSG-ASGKVPSAIHVTP 527 CV+V+++ GPK GM E + P +L + V+D R+SG A G V +HV+P Sbjct: 433 CVLVLKNCGPKGYPGMAEAGNMPLPPKILRKGITDMVRVSDARMSGTAYGTV--VLHVSP 490 Query: 528 EAYDGGLLAKVRDGDIIRVNGQTGELTLLVDEAELAAR-----EPHIP 570 EA GG LA V++GD I ++ + +L L V + ELA R +P +P Sbjct: 491 EAAAGGPLAVVQNGDFIELDVEARKLHLDVSDEELARRRAQWQKPELP 538 Lambda K H 0.318 0.134 0.392 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: 792 Number of extensions: 44 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 603 Length of database: 578 Length adjustment: 37 Effective length of query: 566 Effective length of database: 541 Effective search space: 306206 Effective search space used: 306206 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: 53 (25.0 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