Align Mannokinase (EC 2.7.1.7) (characterized)
to candidate SMc02880 SMc02880 hypothetical protein
Query= reanno::Smeli:SMc03109 (298 letters) >FitnessBrowser__Smeli:SMc02880 Length = 303 Score = 120 bits (302), Expect = 3e-32 Identities = 91/266 (34%), Positives = 133/266 (50%), Gaps = 26/266 (9%) Query: 47 VASAESTAGERGS----IGIGIPGSPNPRTGIVRNSNAVLINGKPLGRDLAAALGREVRL 102 V + ES E G + I I G +P T ++ +N I+G+ L +L AAL V + Sbjct: 40 VEAMESVLDEAGGLPERVAISITGVIDPETRRIKCANIPCIDGRELVAELEAALHLPVVI 99 Query: 103 ANDANCLAVSEAVDGAGKDAGVVFGVIVGTGHGGGLAI-GKKVHA--GYQG-------VA 152 ANDA+C A++EA GAG+ +VFG I+GTG GGGL I G+ ++A G+ G VA Sbjct: 100 ANDADCFALAEAGVGAGRGHRIVFGAILGTGVGGGLVIDGRLINADGGFAGEWGHGPAVA 159 Query: 153 AEIGHYPLPWMTKDEYPGHRCWCGKLGCLDMYACGTGLELDYRMTTGTDRRGRDIIEAKR 212 A GH P+ P C CG+ C+D GLE + G DIIE + Sbjct: 160 AAAGHPPI------AIPAFPCGCGQSRCVDTVGGARGLERLHETVHGKALSSHDIIEGWQ 213 Query: 213 AGDPVAIGVYGRFVDRLARSLALLTNIVDPDVFVLGGGMSNVDEIYGELPASITRYLFGD 272 G+ A FVD ++ LAL+ NI + +GGG+SN + + E+ ++ + Sbjct: 214 NGNAEAARTIDVFVDLVSSPLALVINITGATIVPVGGGLSNAEALLAEIDRAVRARIL-R 272 Query: 273 SFETPIRKAVHGD---SSGVRGAAWL 295 F+ P+ V G+ G+ GAA L Sbjct: 273 RFDRPL--VVRGECRVEPGLIGAALL 296 Lambda K H 0.319 0.140 0.436 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: 244 Number of extensions: 12 Number of successful extensions: 2 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: 298 Length of database: 303 Length adjustment: 27 Effective length of query: 271 Effective length of database: 276 Effective search space: 74796 Effective search space used: 74796 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 (21.7 bits) S2: 48 (23.1 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