Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate PP_1777 PP_1777 phosphomannomutase
Query= BRENDA::Q8PGN7 (450 letters) >FitnessBrowser__Putida:PP_1777 Length = 453 Score = 583 bits (1504), Expect = e-171 Identities = 280/450 (62%), Positives = 349/450 (77%), Gaps = 1/450 (0%) Query: 2 PMTLPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSA 61 P+ FKAYDIRG+VP +LNED+A RIG AL A+L V+G D+RL SP L +AL Sbjct: 4 PIQTRCFKAYDIRGQVPADLNEDIAYRIGRALVAELGGRSYVVGRDMRLESPTLSQALMR 63 Query: 62 GLRASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSD 121 GL G DVIDIGLCGTEEVYF T + +A GG+MVTASHNP YNGMKLVREQ+RPIS D Sbjct: 64 GLTEGGADVIDIGLCGTEEVYFATSHYQADGGIMVTASHNPKGYNGMKLVREQSRPISGD 123 Query: 122 TGLFAIRDTVAADTAAPGEPTA-SEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGG 180 TGL IR V + P A S + +DK+AY++HLL+YVD +TLKPLK++ + GNG Sbjct: 124 TGLKDIRQRVESGDLGTAAPAAGSVRLASDKSAYIDHLLTYVDLATLKPLKVLADPGNGA 183 Query: 181 AGLIVDLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWDG 240 G +++LL LP + + EPDGNFPNGIPNPLLPENRD T +AV D GAD GIA+DG Sbjct: 184 VGPVLELLKARLPLKLTVINGEPDGNFPNGIPNPLLPENRDLTRQAVLDTGADMGIAFDG 243 Query: 241 DFDRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPVL 300 DFDRCFFFD+ GRFIEGYY+VGLLA+ +LAK PG K++HDPRLTWNT++QVEEAGG+ + Sbjct: 244 DFDRCFFFDNQGRFIEGYYVVGLLAEMLLAKHPGSKIIHDPRLTWNTIKQVEEAGGMAIQ 303 Query: 301 CKSGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLADLV 360 K+GHAFIKE+MR+E+AVYGGEMSAHHYFR+FAY DSG IPWLL+A+L+S +G+SL LV Sbjct: 304 SKTGHAFIKERMRAEDAVYGGEMSAHHYFRDFAYCDSGNIPWLLVAQLMSVTGKSLGQLV 363 Query: 361 EARMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQWRFNLRSSNT 420 + R+ FPCSGEIN++V D K ++ +++ HY +P +D TDGIS +F WRF+LR SNT Sbjct: 364 DERIAAFPCSGEINYEVEDVKDTIEKILAHYLPRNPSIDRTDGISVEFADWRFSLRGSNT 423 Query: 421 EPLLRLNVETRGDAALLETRTQEISNLLRG 450 EPLLRLNVE+RGD AL+E + +I+ L+RG Sbjct: 424 EPLLRLNVESRGDQALVERQVAQIAGLIRG 453 Lambda K H 0.319 0.136 0.404 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: 691 Number of extensions: 19 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: 450 Length of database: 453 Length adjustment: 33 Effective length of query: 417 Effective length of database: 420 Effective search space: 175140 Effective search space used: 175140 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: 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