Align Mannose-6-phosphate isomerase ManA; Phosphohexomutase; Phosphomannose isomerase; PMI; EC 5.3.1.8 (characterized)
to candidate WP_009120604.1 BUB52_RS12575 mannose-6-phosphate isomerase
Query= SwissProt::O31646 (315 letters) >NCBI__GCF_900129655.1:WP_009120604.1 Length = 324 Score = 187 bits (474), Expect = 4e-52 Identities = 106/309 (34%), Positives = 170/309 (55%), Gaps = 16/309 (5%) Query: 5 PLFFKPVFKERIWGGTALADFGY---TIPSQRTGECWAFAAHQNGQSVVQNGMYKGFTLS 61 PL F+P+ K+ +WGG + F + T+P+ GE W +A + +SVV NG KG+TL Sbjct: 3 PLKFEPILKQTLWGGDKIIPFKHLDETLPN--VGESWEVSAVEGSESVVANGADKGYTLP 60 Query: 62 ELWEHHR-HLFGQLE----GDRFPLLTKILDADQDLSVQVHPNDEYANIHENGELGKTEC 116 E+ ++ L G+ G++FPLL K +DA DLS+QVHP DE A N GK E Sbjct: 61 EMVRKYKDELVGEANYARFGNKFPLLIKFIDAKLDLSIQVHPGDELAKKRHNS-FGKNEM 119 Query: 117 WYIIDCQKDAEIIYGHNAT-TKEELTTMIERGEWDELLRRVKVKPGDFFYVPSGTVHAIG 175 WY+I K A++I G + T +E + G + E+L+ ++PGD FYVP+G VH IG Sbjct: 120 WYVIAADKGAKLISGFSEEITPKEYKDRVHNGTFAEVLQTCTIEPGDAFYVPAGRVHGIG 179 Query: 176 KGILALETQQNSDTTYRLYDYDRKDAEGKLRELHLKKSIEVIEVPSIPERHTVHHEQIED 235 G E QQ SD TYR++DY+RKD +GK R+LH ++++ I + + +E+I + Sbjct: 180 AGAFVAEIQQTSDITYRIFDYNRKDKDGKSRDLHTSQAMDAINFSDVQDDFRTEYERIRN 239 Query: 236 LLTTTLIECAYFSVGKWNLSG--SASLKQQKPFLLISVIEGEGRMI-SGEYVYPFKKGDH 292 ++ YF+ ++++ + + F++ +EG R+ + + G+ Sbjct: 240 -EPVEMVASPYFTTSVYDMTEEITCDYSELDSFVIFICVEGSCRLTDDNQNEITLRAGET 298 Query: 293 MLLPYGLGE 301 +LLP + E Sbjct: 299 VLLPAAVQE 307 Lambda K H 0.319 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: 315 Number of extensions: 17 Number of successful extensions: 5 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: 315 Length of database: 324 Length adjustment: 28 Effective length of query: 287 Effective length of database: 296 Effective search space: 84952 Effective search space used: 84952 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: 48 (23.1 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