Align D-mannose isomerase (EC 5.3.1.7) (characterized)
to candidate RR42_RS28130 RR42_RS28130 N-acylglucosamine 2-epimerase
Query= reanno::acidovorax_3H11:Ac3H11_2078 (424 letters) >FitnessBrowser__Cup4G11:RR42_RS28130 Length = 379 Score = 72.4 bits (176), Expect = 2e-17 Identities = 78/261 (29%), Positives = 101/261 (38%), Gaps = 28/261 (10%) Query: 92 FLDPATGGYAWLIDWQDGRATVQDTTRHCYGMAFVMLAYARAYE-AGVPEARVWLAEAFD 150 F D GG+ + ID Q DTT+ Y AFV+ A A ++ +G +AR L A Sbjct: 98 FADGGQGGFIYSIDAQ---GQPLDTTKDLYTHAFVVFACAAYFKRSGSAQARALLDGATR 154 Query: 151 TAEQHFWQPAAGLYADEASPDWQ-LTSYRGQNANMHACEAMISAFRATGERRYIERAEQL 209 E F A GLY + D++ L QN MH EA ++AF TGER Y +R + Sbjct: 155 LIEARF-ATADGLYHAALAQDFRPLGGPPQQNPIMHLTEAYLAAFEVTGERFYADRLAGI 213 Query: 210 AQGICQRQAALSDRTHAPAAEGWVWEHFHADWSVDWDYNRHDRSNIFRPWGYQVGHQTEW 269 A + T A G + E D NR + GHQ EW Sbjct: 214 AAAVLA--------TFVDPATGCIAE---LPMCTDRAGNR-----------VEPGHQFEW 251 Query: 270 AKLLLQLDALLPADWHLPCAQRLFDTAVERGWDAEHGGLYYGMAPDGSICDDGKYHWVQA 329 LL AL R F A++ G D G+ + DGS D + W Q Sbjct: 252 FSLLASAPALFEDSGLAQALARAFGFAMQHGVDTSTMGVAAALHLDGSPRDPIQRIWAQT 311 Query: 330 ESMAAAAVLAVRTGDARYWQW 350 E A AV A W Sbjct: 312 EFARALAVRGDSVALAHLQAW 332 Score = 27.7 bits (60), Expect = 6e-04 Identities = 36/144 (25%), Positives = 55/144 (38%), Gaps = 19/144 (13%) Query: 69 YRTTGEARYQVGMRHALEFLRTAFLDPATGGYAWLIDWQDGRATVQDTTRHCYGMAFVML 128 + TGE Y + + F+DPATG A L D + + + Sbjct: 198 FEVTGERFYADRLAGIAAAVLATFVDPATGCIAELPMCTDRAGNRVEPGHQFEWFSLLAS 257 Query: 129 AYARAYEAGVPEARVWLAEAFDTAEQH-----FWQPAAGLYADEASPD-----WQLTSY- 177 A A ++G+ +A LA AF A QH AA L+ D + D W T + Sbjct: 258 APALFEDSGLAQA---LARAFGFAMQHGVDTSTMGVAAALHLDGSPRDPIQRIWAQTEFA 314 Query: 178 -----RGQNANMHACEAMISAFRA 196 RG + + +A + A+ A Sbjct: 315 RALAVRGDSVALAHLQAWLKAYPA 338 Score = 25.4 bits (54), Expect = 0.003 Identities = 18/58 (31%), Positives = 24/58 (41%) Query: 289 AQRLFDTAVERGWDAEHGGLYYGMAPDGSICDDGKYHWVQAESMAAAAVLAVRTGDAR 346 A RLF + R D GG Y + G D K + A + A A R+G A+ Sbjct: 87 AARLFASLGGRFADGGQGGFIYSIDAQGQPLDTTKDLYTHAFVVFACAAYFKRSGSAQ 144 Lambda K H 0.324 0.135 0.460 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: 484 Number of extensions: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 424 Length of database: 379 Length adjustment: 31 Effective length of query: 393 Effective length of database: 348 Effective search space: 136764 Effective search space used: 136764 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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