Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_048080780.1 EI99_RS04680 hypothetical protein
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000746075.1:WP_048080780.1 Length = 431 Score = 249 bits (636), Expect = 1e-70 Identities = 146/434 (33%), Positives = 227/434 (52%), Gaps = 21/434 (4%) Query: 10 VRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALISGLLSVG 69 +RG+ N +IT EFA +G G + R G+K V+VGRD +M+K ++ +G+L+ G Sbjct: 8 IRGVVNSEITNEFASNLGNIIGNFV-RSGKK---VIVGRDINDPSQMIKRSITAGILAAG 63 Query: 70 CDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKEREAIVE 129 DVID GIAP P V + +N D ITASH PE IK+ + + L + Sbjct: 64 IDVIDFGIAPIPTVHYGADLYNTDVLVTITASHMNPEEIDIKVFSNHEIPLTQRHA---- 119 Query: 130 ELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVEAIKKRKPFVVVDTSNGAGSL 188 ++ W ++G++ D + Y+ A+ + I R P VV+D +NG+ Sbjct: 120 --------EKVSWDKVGQLSYVHDYVDKYLNAVLENTEKNVISSRAPKVVIDCANGSAVQ 171 Query: 189 TLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGVAQDGDADR 248 LP +L LGC VI QP + EP E++ +V A+GAD G+A D D DR Sbjct: 172 FLPEILSRLGCDVILFGCQPTNVSTKKFAEPTPESVSLVSNLVNAVGADMGIAMDNDGDR 231 Query: 249 AVFIDENGRFIQGDKTFALVADAVLKEKGGGLLVTTVATSNLLDDIAKKHGAKVMRTKVG 308 +FIDE G I+ A++A L E G +V++V S LD+I G K+++ + Sbjct: 232 VIFIDEKGNVIRDQTVLAILAREALIENPEGTIVSSVTASMSLDEIVSDQGGKLLKAPMN 291 Query: 309 DLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKKFSELIDELP 368 V + +N GG+++G +FP+ D K++EI K K FS L++E+P Sbjct: 292 --CVLDEIIKNKAVFGGDDSGMYVFPQFQECFDAIFAAVKMLEIICKHNKTFSTLVNEIP 349 Query: 369 KYYQIKTKRHVEGD-RHAIVNKVAEMARERGYTVDTTDGAKIIFEDGWVLVRASGTEPII 427 +Y + + E D + ++ + E +E G +DTT+G K+ ED +VLVR S EP++ Sbjct: 350 EYPRTVFSVNCEHDEKQKVLTNLEENLKENG-EIDTTEGIKMQEEDSFVLVRPSRFEPLL 408 Query: 428 RIFSEAKSKEKAQE 441 R++ EAKS K Q+ Sbjct: 409 RVYVEAKSSGKLQK 422 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: 477 Number of extensions: 24 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: 431 Length adjustment: 32 Effective length of query: 423 Effective length of database: 399 Effective search space: 168777 Effective search space used: 168777 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