Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate Ac3H11_2215 Phosphomannomutase (EC 5.4.2.8)
Query= BRENDA::P26276 (463 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2215 Length = 462 Score = 509 bits (1310), Expect = e-149 Identities = 258/439 (58%), Positives = 324/439 (73%), Gaps = 8/439 (1%) Query: 12 SIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQG 71 +IF+AYDIRG+V TL E A +GRA G+ + A G+ VAVGRDGRLSGP + LIQG Sbjct: 6 AIFKAYDIRGIVPSTLNEEVALGLGRAFGTAARAEGQTTVAVGRDGRLSGPAMSAALIQG 65 Query: 72 LVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLANEQI 131 LV+ G +V DVG+V TP+LY+AA+ L SG+ +TGSHNP DYNGFK+V+ G + E+I Sbjct: 66 LVEAGIEVIDVGLVTTPLLYFAASTL-CNSGIQVTGSHNPKDYNGFKMVLNGRAIYGEEI 124 Query: 132 QALRERIEKND--LASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGVIAP 189 Q LR +E+ LA G GSV VD+LP Y ++I D+ +A+PMK+VVDCGNG+AG AP Sbjct: 125 QGLRRTMEQESWQLAPG-GSVRHVDVLPTYRERIVGDVKLARPMKIVVDCGNGIAGASAP 183 Query: 190 QLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDRVG 249 + ALGC VI L+ EVDGNFPNHHPDP KPENL+DLI +KA +A+LGLAFDGDGDR+G Sbjct: 184 AIFRALGCEVIELFSEVDGNFPNHHPDPSKPENLRDLIDALKASDAELGLAFDGDGDRLG 243 Query: 250 VVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTGHS 309 +VT GT I+PDR +MLFA+DV+SR PG +IIFDVKCT+RL I+ GG PVM+KTGHS Sbjct: 244 IVTKDGTNIFPDRQMMLFAQDVLSRVPGGEIIFDVKCTQRLAPAIAAAGGVPVMFKTGHS 303 Query: 310 LIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAFPS 369 LIK +MKET + L GEMSGH+FFKERW+GFDDG Y+ RLLEILS+ Q D V +A P+ Sbjct: 304 LIKARMKETNSPLGGEMSGHIFFKERWYGFDDGTYAGCRLLEILSKSQ-DPSAVLNALPT 362 Query: 370 DISTPEINITVTEDSKF---AIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLVRASNTT 426 STPE+N+ E A ++AL ++T+DG+RVD+P G+GL+RASNTT Sbjct: 363 SFSTPELNVACAEGEPHRLTAELQALAAGQFAAPATVSTIDGLRVDWPDGFGLIRASNTT 422 Query: 427 PVLVLRFEADTEEELERIK 445 PVLVLRFE T E L RI+ Sbjct: 423 PVLVLRFEGHTPEALARIE 441 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: 630 Number of extensions: 23 Number of successful extensions: 5 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: 462 Length adjustment: 33 Effective length of query: 430 Effective length of database: 429 Effective search space: 184470 Effective search space used: 184470 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