Align D-mannose isomerase (EC 5.3.1.7) (characterized)
to candidate SMa0058 SMa0058 N-acylglucosamine 2-epimerase
Query= reanno::BFirm:BPHYT_RS02050 (427 letters) >FitnessBrowser__Smeli:SMa0058 Length = 398 Score = 452 bits (1163), Expect = e-132 Identities = 210/393 (53%), Positives = 276/393 (70%), Gaps = 6/393 (1%) Query: 18 PVESFRSRDFLLSHVQDTLRFYAPNVF-DPSGGFFHFFRDDGSVYDKTTRHLVSSCRYVF 76 P+ FRS+DFLL+H+++ + FY P + GG+++ +RDDG + D+ T+HLVS+ R++F Sbjct: 3 PIPDFRSKDFLLAHMREIMDFYHPICLNEEDGGYYNEYRDDGFITDRKTQHLVSTTRFIF 62 Query: 77 NYAMAYRQFGDPQHLEYARHGLRFLREAHWDAQHEGYDWEIEWRDGKKRTLDATRHCYGL 136 NYA A F P E A HG+R+L E H D +H GY W + RD +DAT+HCYG Sbjct: 63 NYATAAVLFERPDFAEAAAHGVRYLDEVHRDPEHGGYYWLMRGRDA----VDATKHCYGH 118 Query: 137 AFVLLAYSHAAMAGIEEAKPMIGATFELMEHRFWDAAAGLYADEASPDWRVSS-YRGQNA 195 AFVLLAY+ A AGI + T++L+E+RFW+ LY DE S DW +S YRGQNA Sbjct: 119 AFVLLAYATAMKAGIPGTGARVSQTWDLLENRFWEPDRELYKDEVSRDWGATSPYRGQNA 178 Query: 196 NMHTTEALLAAHEATRHLVYLDRAERVASNITLRQAKLSQGLVWEHFHADWSVDWHYNEE 255 NMH TEA+LAA+EAT + YLDRAE +A I + A +Q +VWEH+ DWSVDW YN++ Sbjct: 179 NMHMTEAMLAAYEATGEIRYLDRAETLARRICVELAANTQDVVWEHYRQDWSVDWDYNKD 238 Query: 256 DSSNIFRPWGFQPGHQTEWAKLLLILERFRPLPWLLPRAIELFDAAMAHAWDEDHGGLYY 315 D ++FRP+G+QPGH TEW KLLLILER+RP WLLP+A+ L++ A+A + D + GG++Y Sbjct: 239 DPKHLFRPYGYQPGHMTEWTKLLLILERYRPQDWLLPKALLLYETALAKSADLEFGGMHY 298 Query: 316 GFGPDGTVCDHDKYFWVQAETFATAALLGKRTGNERFWDWYDEIWRYSWAHFVDHEYGAW 375 +GP+G + D DKY WV ET A AA L RTG ER+W YD +WRYSW H +DHEYG W Sbjct: 299 SYGPEGKLYDLDKYHWVHCETIAAAAALAGRTGRERYWQDYDRLWRYSWRHLIDHEYGCW 358 Query: 376 YRILTCDNRKYSDEKSPAGKTDYHTMGACYEVL 408 +RIL+ D K SD KSP+GKTDYH GACYE+L Sbjct: 359 FRILSPDGVKQSDIKSPSGKTDYHPFGACYEIL 391 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: 740 Number of extensions: 40 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: 427 Length of database: 398 Length adjustment: 31 Effective length of query: 396 Effective length of database: 367 Effective search space: 145332 Effective search space used: 145332 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