Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_012473876.1 CPHAMN1_RS02145 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000020545.1:WP_012473876.1 Length = 471 Score = 252 bits (643), Expect = 2e-71 Identities = 157/451 (34%), Positives = 235/451 (52%), Gaps = 21/451 (4%) Query: 9 GVRGIANEKITPEFAMKIGMAFGTLL--------KREGRKKPLVVVGRDTRVSGEMLKEA 60 G+RG+ E ++P AF + + E P +V+GRDTR +GE + + Sbjct: 6 GIRGVVGESLSPAVLTSFTQAFAAWVHTKSNVEERTEKNALPKIVIGRDTRPTGEAVSDL 65 Query: 61 LISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGL 120 + L GC V+D+GIA TP V+ AT +ADGG +ITASHNP E+N +KLL NG L Sbjct: 66 VAGTLALSGCRVVDLGIATTPTVEIATTEEHADGGIIITASHNPVEWNALKLLNRNGEFL 125 Query: 121 KKEREAIVEELFFKEDFDRAKWYEIGEVRREDIIKP-YIEAI--KSKVDVEAIKKRKPFV 177 + + +F E F A W +G + + +I+ I S +D+++I +++ V Sbjct: 126 NETELQELLNIFRTEQFTPADWAHVGSSEKNSLYDTLHIDRILALSSIDIDSIAEQRFRV 185 Query: 178 VVDTSNGAGSLTLPYLLRELG-CKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGA 236 +VD GAGS +P L R LG +V T+ G FP RNPEP ENL +EI+K Sbjct: 186 LVDAVEGAGSSVVPELCRRLGVSQVETIFCNGSGIFP-RNPEPLPENLTSTVEILKDKAC 244 Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKGGGLLVTTVATSNLLDDIAK 296 DF + D DADR I E+G + + + AD L+ K G +V +++S L DIA+ Sbjct: 245 DFAIVVDPDADRLALICEDGSMFGEEYSLVVCADFYLRHKKGA-VVNNLSSSRALRDIAE 303 Query: 297 KHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIF--- 353 KHG VG+ V + E N IGGE NGG+I PE GRD +A +++ F Sbjct: 304 KHGQSFFSANVGEANVVDLMKEKNAVIGGEGNGGIILPELHYGRDALAGIALMLQAFTDW 363 Query: 354 ---AKSGKKFSELIDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYT-VDTTDGAKI 409 + + S P Y+ K K + + E++R V+ DG K+ Sbjct: 364 REKSSQNRTLSGFRKCFPDYFMAKHKIRLAERPENFDSIFTEISRAHPEAEVNREDGLKL 423 Query: 410 IFEDGWVLVRASGTEPIIRIFSEAKSKEKAQ 440 F + WV +R S TEP++RI++EAK++++A+ Sbjct: 424 DFPEEWVHIRPSNTEPVLRIYTEAKNRKRAE 454 Lambda K H 0.317 0.138 0.391 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: 487 Number of extensions: 20 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: 455 Length of database: 471 Length adjustment: 33 Effective length of query: 422 Effective length of database: 438 Effective search space: 184836 Effective search space used: 184836 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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