Align D-mannose isomerase (EC 5.3.1.7) (characterized)
to candidate N515DRAFT_1920 N515DRAFT_1920 Mannose or cellobiose epimerase, N-acyl-D-glucosamine 2-epimerase family
Query= reanno::BFirm:BPHYT_RS02050 (427 letters) >FitnessBrowser__Dyella79:N515DRAFT_1920 Length = 404 Score = 507 bits (1306), Expect = e-148 Identities = 235/394 (59%), Positives = 293/394 (74%), Gaps = 11/394 (2%) Query: 22 FRSRDFLLSHVQDTLRFYAPNVFDPSGGFFHFFRDDGSVYDKTTRHLVSSCRYVFNYAMA 81 FRS FL H+ T+ FY P+ DP+GGFFH+++DDG++YD++ RHLVSS R++FNYAMA Sbjct: 6 FRSERFLREHIAHTMAFYHPHAIDPAGGFFHYYKDDGTIYDRSHRHLVSSTRFIFNYAMA 65 Query: 82 YRQFGDP--QHLEYARHGLRFLREAHWDAQHEGYDWEIEWRDGKKRTLDATRHCYGLAFV 139 R+F D ++L+ ARHGLR+LRE H DA GY W I RDGK D T H YG+AFV Sbjct: 66 AREFEDKRAEYLDAARHGLRYLREVHRDASSGGYAWTI--RDGKPE--DRTYHAYGVAFV 121 Query: 140 LLAYSHAAMAGIEEAKPMIGATFELMEHRFWDAAAGLYADEASPDWRVSSYRGQNANMHT 199 LLAYS A AGI+E +P + T+EL+E R+WDA GLY DEA W S YRGQNANMH Sbjct: 122 LLAYSTALKAGIDEVRPWMDETWELLEKRYWDAGFGLYRDEADEHWNFSGYRGQNANMHM 181 Query: 200 TEALLAAHEATRHLVYLDRAERVASNITLRQAKLSQGLVWEHFHADWSVDWHYNEEDSSN 259 EA+LAA++A+ YL+RA +A ++T RQA ++GLVWEH+ +W++DW YN ++ + Sbjct: 182 CEAMLAAYQASDEPRYLERALTLADHMTRRQAAKAEGLVWEHYDVEWNIDWKYNLDNPKH 241 Query: 260 IFRPWGFQPGHQTEWAKLLLI-----LERFRPLPWLLPRAIELFDAAMAHAWDEDHGGLY 314 +FRPWGFQPGHQTEWAKLLLI LER R WL+P A LFD A+ +WD+ +GG+ Sbjct: 242 LFRPWGFQPGHQTEWAKLLLILEPLLLERNREEKWLVPTAQHLFDVALDRSWDQQYGGMA 301 Query: 315 YGFGPDGTVCDHDKYFWVQAETFATAALLGKRTGNERFWDWYDEIWRYSWAHFVDHEYGA 374 YGF PDGTVCD DKYFWVQAE+ A AALL RTG ++ +WY ++W YSW HFVDH+YGA Sbjct: 302 YGFAPDGTVCDDDKYFWVQAESLAAAALLHARTGEAKYDEWYQKLWAYSWEHFVDHKYGA 361 Query: 375 WYRILTCDNRKYSDEKSPAGKTDYHTMGACYEVL 408 W+RILT DNRKY DEKSPAGK DYHTMGACYEV+ Sbjct: 362 WFRILTRDNRKYDDEKSPAGKVDYHTMGACYEVM 395 Lambda K H 0.322 0.135 0.456 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: 821 Number of extensions: 51 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: 427 Length of database: 404 Length adjustment: 31 Effective length of query: 396 Effective length of database: 373 Effective search space: 147708 Effective search space used: 147708 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 (21.9 bits) S2: 50 (23.9 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