Align D-mannose isomerase (EC 5.3.1.7) (characterized)
to candidate H281DRAFT_02117 H281DRAFT_02117 Mannose or cellobiose epimerase, N-acyl-D-glucosamine 2-epimerase family
Query= reanno::BFirm:BPHYT_RS02050 (427 letters) >FitnessBrowser__Burk376:H281DRAFT_02117 Length = 427 Score = 849 bits (2194), Expect = 0.0 Identities = 393/427 (92%), Positives = 403/427 (94%) Query: 1 MTQSDPLHPANGAAAAPPVESFRSRDFLLSHVQDTLRFYAPNVFDPSGGFFHFFRDDGSV 60 MT S ANGA P V SFRSR+FLLSHV+DTLRFYAPNVFD SGGFFHFFRDDGSV Sbjct: 1 MTLSATPPSANGAPVVPAVASFRSREFLLSHVEDTLRFYAPNVFDSSGGFFHFFRDDGSV 60 Query: 61 YDKTTRHLVSSCRYVFNYAMAYRQFGDPQHLEYARHGLRFLREAHWDAQHEGYDWEIEWR 120 YDKTTRHLVSSCRYVFNYAMAYRQFGDP+HLEYARHGL+FLR+AHWD QHEGYDWEIEW Sbjct: 61 YDKTTRHLVSSCRYVFNYAMAYRQFGDPKHLEYARHGLQFLRDAHWDGQHEGYDWEIEWS 120 Query: 121 DGKKRTLDATRHCYGLAFVLLAYSHAAMAGIEEAKPMIGATFELMEHRFWDAAAGLYADE 180 DG+KRTLDATRHCYGLAFVLLAYSHAAMAGIEEAKPMIGATFELMEHRFWDAAAGLYADE Sbjct: 121 DGRKRTLDATRHCYGLAFVLLAYSHAAMAGIEEAKPMIGATFELMEHRFWDAAAGLYADE 180 Query: 181 ASPDWRVSSYRGQNANMHTTEALLAAHEATRHLVYLDRAERVASNITLRQAKLSQGLVWE 240 ASP+WRVSSYRGQNANMHTTEALLAAHEAT HLVYLDRAERVASNITLRQAKLSQGLVWE Sbjct: 181 ASPEWRVSSYRGQNANMHTTEALLAAHEATGHLVYLDRAERVASNITLRQAKLSQGLVWE 240 Query: 241 HFHADWSVDWHYNEEDSSNIFRPWGFQPGHQTEWAKLLLILERFRPLPWLLPRAIELFDA 300 HFHADWSVDWHYNEEDSSNIFRPWGFQPGHQTEWAKLLLILER+RPLPWLLPRAIELFDA Sbjct: 241 HFHADWSVDWHYNEEDSSNIFRPWGFQPGHQTEWAKLLLILERYRPLPWLLPRAIELFDA 300 Query: 301 AMAHAWDEDHGGLYYGFGPDGTVCDHDKYFWVQAETFATAALLGKRTGNERFWDWYDEIW 360 AM HAWDEDHGGLYYGFGPDGTVCDHDKYFWVQAETFATAALLGKRTGNERFWDWYDEIW Sbjct: 301 AMTHAWDEDHGGLYYGFGPDGTVCDHDKYFWVQAETFATAALLGKRTGNERFWDWYDEIW 360 Query: 361 RYSWAHFVDHEYGAWYRILTCDNRKYSDEKSPAGKTDYHTMGACYEVLAHALPDGAAAAP 420 RYSWAHFVDH+YGAWYRILTCDNRKYSDEKSPAGKTDYHTMGACYEVL HAL DG+ AA Sbjct: 361 RYSWAHFVDHKYGAWYRILTCDNRKYSDEKSPAGKTDYHTMGACYEVLTHALADGSTAAA 420 Query: 421 ESAEQTK 427 S E K Sbjct: 421 VSTEHAK 427 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: 1001 Number of extensions: 44 Number of successful extensions: 1 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: 427 Length adjustment: 32 Effective length of query: 395 Effective length of database: 395 Effective search space: 156025 Effective search space used: 156025 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: 51 (24.3 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