Align Mannose-6-phosphate isomerase ManA; Phosphohexomutase; Phosphomannose isomerase; PMI; EC 5.3.1.8 (characterized)
to candidate 349901 BT0373 mannose-6-phosphate isomerase (NCBI ptt file)
Query= SwissProt::O31646 (315 letters) >FitnessBrowser__Btheta:349901 Length = 323 Score = 181 bits (459), Expect = 2e-50 Identities = 106/302 (35%), Positives = 167/302 (55%), Gaps = 13/302 (4%) Query: 5 PLFFKPVFKERIWGGTALADFGYTIPSQR-TGECWAFAAHQNGQSVVQNGMYKGFTLSEL 63 PL F+P+ K+ +WGG + F + + GE W + ++ +SVV NG KG TL+++ Sbjct: 3 PLKFEPILKQTLWGGDKIIPFKHLNSDLKGVGESWEISGVEDNESVVANGPDKGLTLADM 62 Query: 64 WEHHRH-LFGQLE----GDRFPLLTKILDADQDLSVQVHPNDEYANIHENGELGKTECWY 118 +R L G+ G++FPLL K +DA QDLS+QVHP D+ A N +GKTE WY Sbjct: 63 VRKYREELVGEANYARFGNKFPLLIKFIDAKQDLSIQVHPADDLAKKRHNS-MGKTEMWY 121 Query: 119 IIDCQKDAEIIYGHNAT-TKEELTTMIERGEWDELLRRVKVKPGDFFYVPSGTVHAIGKG 177 ++D K A++ G + T +E + ++L+ ++KPGD F++P+G VH+IG G Sbjct: 122 VVDADKGAKLRSGFSEQITPKEYKERVLNNTITDVLQEYEIKPGDVFFLPAGRVHSIGAG 181 Query: 178 ILALETQQNSDTTYRLYDYDRKDAEGKLRELHLKKSIEVIEVPSIPERHTVHHEQIEDLL 237 E QQ SD TYR+YD++RKDA GK RELH + E I + + T +E ++D Sbjct: 182 AFIAEIQQTSDITYRIYDFNRKDANGKTRELHTDLAREAINYEVLDDYRT-KYEAVKD-E 239 Query: 238 TTTLIECAYFSVGKWNLSG--SASLKQQKPFLLISVIEGEGRMISGE-YVYPFKKGDHML 294 L+ C YF+ ++++ S + F++ +EG ++ E G+ +L Sbjct: 240 PVELVACPYFTTSVYDMTEEISCDYSELDSFVIFICMEGACKIKDNEGNELKVGAGESIL 299 Query: 295 LP 296 LP Sbjct: 300 LP 301 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: 293 Number of extensions: 18 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: 323 Length adjustment: 28 Effective length of query: 287 Effective length of database: 295 Effective search space: 84665 Effective search space used: 84665 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 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