Align D-mannose isomerase (EC 5.3.1.7) (characterized)
to candidate WP_057508916.1 ABB28_RS12325 AGE family epimerase/isomerase
Query= reanno::BFirm:BPHYT_RS02050 (427 letters) >NCBI__GCF_001431535.1:WP_057508916.1 Length = 395 Score = 520 bits (1340), Expect = e-152 Identities = 238/387 (61%), Positives = 291/387 (75%), Gaps = 4/387 (1%) Query: 22 FRSRDFLLSHVQDTLRFYAPNVFDPSGGFFHFFRDDGSVYDKTTRHLVSSCRYVFNYAMA 81 FRS+DFL H+ T+ FY P DP GGFFH+FRDDGSVYD T RHLVSS R+VF+YAMA Sbjct: 7 FRSQDFLRGHIAHTMAFYHPRCIDPQGGFFHYFRDDGSVYDATHRHLVSSTRFVFDYAMA 66 Query: 82 YRQFGDPQHLEYARHGLRFLREAHWDAQHEGYDWEIEWRDGKKRTLDATRHCYGLAFVLL 141 YR+FGD +L+ +HG+R+LRE H + GY W + RDG D T HCYG+AFVLL Sbjct: 67 YREFGDAAYLDGVQHGVRYLREVHRNPATGGYAWTL--RDGVVE--DDTNHCYGVAFVLL 122 Query: 142 AYSHAAMAGIEEAKPMIGATFELMEHRFWDAAAGLYADEASPDWRVSSYRGQNANMHTTE 201 AYS A AGIE+A+ + T++L+E RF++ A GLY DEA W S YRGQNANMH E Sbjct: 123 AYSCALKAGIEDARGWMDETWQLLETRFYEPAHGLYRDEADAQWNFSGYRGQNANMHMCE 182 Query: 202 ALLAAHEATRHLVYLDRAERVASNITLRQAKLSQGLVWEHFHADWSVDWHYNEEDSSNIF 261 A+LAA E++ YLDRA ++A +T RQA + GLVWEH+ ++W++DW YN +D ++F Sbjct: 183 AMLAAFESSGEQRYLDRALQLADIMTRRQAAKADGLVWEHYDSEWNIDWKYNLDDPKHLF 242 Query: 262 RPWGFQPGHQTEWAKLLLILERFRPLPWLLPRAIELFDAAMAHAWDEDHGGLYYGFGPDG 321 RPWGFQPGHQTEWAKLLLIL+R WL+P A LFD A+ +WD GGLYYGF PDG Sbjct: 243 RPWGFQPGHQTEWAKLLLILDRHVQAEWLVPMARHLFDVAVERSWDAQRGGLYYGFAPDG 302 Query: 322 TVCDHDKYFWVQAETFATAALLGKRTGNERFWDWYDEIWRYSWAHFVDHEYGAWYRILTC 381 +VCD DKYFWVQAE+ ATAA+L +RTG+ +WDWY+ +W Y+W HFVDH+YGAW+RIL Sbjct: 303 SVCDDDKYFWVQAESLATAAVLAQRTGDAVYWDWYERLWAYAWEHFVDHQYGAWFRILDA 362 Query: 382 DNRKYSDEKSPAGKTDYHTMGACYEVL 408 DNRKYSDEKSPAGK DYHTMGACYEVL Sbjct: 363 DNRKYSDEKSPAGKVDYHTMGACYEVL 389 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: 814 Number of extensions: 39 Number of successful extensions: 6 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: 395 Length adjustment: 31 Effective length of query: 396 Effective length of database: 364 Effective search space: 144144 Effective search space used: 144144 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 24 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