Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate RR42_RS15690 RR42_RS15690 phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >FitnessBrowser__Cup4G11:RR42_RS15690 Length = 461 Score = 507 bits (1306), Expect = e-148 Identities = 250/457 (54%), Positives = 330/457 (72%), Gaps = 6/457 (1%) Query: 12 SIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQG 71 SIF+AYDIRG+V TLT + A IG + G+ + +GE V VGRDGRLSGP+L+ L++G Sbjct: 6 SIFKAYDIRGIVDKTLTRDVARAIGLSFGTAAAEQGERAVVVGRDGRLSGPDLLGGLVEG 65 Query: 72 LVDCGCQVSDVGMVPTPVLYYAANV-LEGK---SGVMLTGSHNPPDYNGFKIVVAGETLA 127 L G V D+GMV TP++Y+ NV L G+ SG+M+TGSHNPPDYNGFK+V+AG+ + Sbjct: 66 LRAAGMDVIDLGMVATPMVYFGTNVELAGRRATSGIMVTGSHNPPDYNGFKMVLAGKAIY 125 Query: 128 NEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGVI 187 EQIQ+LR+RI+ ASG G +QVDI +Y +I DI +A+PMK+ +D GNGVAG Sbjct: 126 GEQIQSLRQRIDAGKFASGAGGYQQVDIRQQYLDRIVGDIELARPMKIALDAGNGVAGAF 185 Query: 188 APQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDR 247 L ALGC V L+CEVDGNFPNHHPDP ENL+DL+ ++ + +LGLAFDGDGDR Sbjct: 186 VGDLFRALGCEVTELFCEVDGNFPNHHPDPAHVENLQDLMQCLRDTDCELGLAFDGDGDR 245 Query: 248 VGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTG 307 +GVVT G +I+PDR LMLFA++++SRNPG II+DVKCT +L I +GG P+MWKTG Sbjct: 246 LGVVTKDGQVIFPDRQLMLFAEEILSRNPGQQIIYDVKCTGKLAPWIREHGGEPLMWKTG 305 Query: 308 HSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAF 367 HSL+K K+KETGA LAGEMSGHVFFK+RW+GFDDG+Y+ ARLLEILS+ D V +A Sbjct: 306 HSLVKAKLKETGAPLAGEMSGHVFFKDRWYGFDDGLYTGARLLEILSK-HADPSAVLNAL 364 Query: 368 PSDISTPEINITVTEDSKFAIIEALQRDAQW-GEGNITTLDGVRVDYPKGWGLVRASNTT 426 P+ TPE+ + E F +++ ++ +A++ G + T+DGVRV+YP G+GL R SNTT Sbjct: 365 PNSNCTPELQLKCAEGEAFTLLDKIRANAKFDGAREVITIDGVRVEYPDGFGLARPSNTT 424 Query: 427 PVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463 PV+V+RFEAD + L RI+ F+ + A +PF Sbjct: 425 PVVVMRFEADNDAALVRIQAEFKRVILAEKPDAQLPF 461 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: 620 Number of extensions: 22 Number of successful extensions: 4 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: 461 Length adjustment: 33 Effective length of query: 430 Effective length of database: 428 Effective search space: 184040 Effective search space used: 184040 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