Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate PP_5288 PP_5288 Phosphomannomutase/phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >FitnessBrowser__Putida:PP_5288 Length = 463 Score = 733 bits (1891), Expect = 0.0 Identities = 355/455 (78%), Positives = 405/455 (89%) Query: 9 LPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQL 68 LP SIFRAYDIRGVVG TL AETAYWIGRAIG++SLA+GEP V+VGRDGRLSGP LV+QL Sbjct: 9 LPDSIFRAYDIRGVVGKTLHAETAYWIGRAIGAQSLAQGEPQVSVGRDGRLSGPMLVEQL 68 Query: 69 IQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLAN 128 I+GLVD GC VSDVG+VPTP LYYAANVL GKSGVMLTGSHNP DYNGFKIV+AG+TLAN Sbjct: 69 IKGLVDAGCNVSDVGLVPTPALYYAANVLAGKSGVMLTGSHNPSDYNGFKIVIAGDTLAN 128 Query: 129 EQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGVIA 188 EQIQAL R++ NDL G VE+V+IL RYFKQI D+ +AK +KVVVDCGNG AGV+A Sbjct: 129 EQIQALLTRLKTNDLTLAQGRVEKVEILDRYFKQIVGDVKLAKKLKVVVDCGNGAAGVVA 188 Query: 189 PQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDRV 248 PQLIEALGC VIPL+CEVDGNFPNHHPDPGKPENL+DLIAKVK AD+GLAFDGDGDRV Sbjct: 189 PQLIEALGCEVIPLFCEVDGNFPNHHPDPGKPENLEDLIAKVKETGADIGLAFDGDGDRV 248 Query: 249 GVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTGH 308 GVVTNTG+I+YPDRLLMLFA+DV+SRNPGA+IIFDVKCTRRL LI +GGR +MWKTGH Sbjct: 249 GVVTNTGSIVYPDRLLMLFAQDVLSRNPGAEIIFDVKCTRRLTPLIEQHGGRALMWKTGH 308 Query: 309 SLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAFP 368 SLIKKKMK+TG+LLAGEMSGH+F KERW+GFDDGIYSAARLLEILS+ ++ +E++F+AFP Sbjct: 309 SLIKKKMKQTGSLLAGEMSGHIFIKERWYGFDDGIYSAARLLEILSKTEQSAENLFAAFP 368 Query: 369 SDISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLVRASNTTPV 428 +DISTPEINI VT++ KF+II+ALQRDA WGE N+TT+DGVRVDY GWGLVRASNTTPV Sbjct: 369 NDISTPEINIDVTDEGKFSIIDALQRDADWGEANLTTIDGVRVDYANGWGLVRASNTTPV 428 Query: 429 LVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463 LVLRFEAD++ EL+RIK VFR QL V+ L +PF Sbjct: 429 LVLRFEADSDAELQRIKDVFRTQLLRVEPELQLPF 463 Lambda K H 0.319 0.138 0.410 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: 740 Number of extensions: 18 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: 463 Length of database: 463 Length adjustment: 33 Effective length of query: 430 Effective length of database: 430 Effective search space: 184900 Effective search space used: 184900 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