Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate 3608505 Dshi_1900 Phosphomannomutase (RefSeq)
Query= BRENDA::Q8PGN7 (450 letters) >FitnessBrowser__Dino:3608505 Length = 456 Score = 474 bits (1221), Expect = e-138 Identities = 245/450 (54%), Positives = 308/450 (68%), Gaps = 7/450 (1%) Query: 5 LPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAGLR 64 L FKAYD+RGR+ D L+ ++A+ +G A+A L VV+G D+R +SPAL EAL AGLR Sbjct: 4 LACFKAYDVRGRIGDTLDTEIAQDVGRAVAEVLGARCVVVGRDIRDSSPALCEALGAGLR 63 Query: 65 ASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDTGL 124 A+G DV DIGLCGTEEVYF TD+L A GVMVTASHNP+DYNG K+V ARP+ D Sbjct: 64 AAGADVRDIGLCGTEEVYFATDHLDACAGVMVTASHNPIDYNGFKIVGRGARPLP-DAQF 122 Query: 125 FAIRDTVAADT-AAPGEPTASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGGAG- 182 AI A AAP + + + AY+ + S+VD + L P+ +V NAGNG AG Sbjct: 123 RAIERLAATRAFAAPTAQSGTHLEADTRAAYVARVCSFVDPAALGPVHVVANAGNGCAGS 182 Query: 183 ----LIVDLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAW 238 +I L A E R+ H PD FPNGIPNPLLPEN+ AT+ A+ GAD GIAW Sbjct: 183 TFDAVIAALEAGGAKIEVTRLHHAPDARFPNGIPNPLLPENQPATSAAITRAGADLGIAW 242 Query: 239 DGDFDRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIP 298 DGDFDRCFFFD TG FI G ++VGLLA+AIL + PG +V+DPR+ WNT VE AGG Sbjct: 243 DGDFDRCFFFDETGAFIPGEFVVGLLAEAILEQTPGASIVYDPRVVWNTRRIVEAAGGAA 302 Query: 299 VLCKSGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLAD 358 VL K+GH +K+ MR +A YGGEMSAHHYFR+F + DSGMIPWLL+ E +S+SGR L+ Sbjct: 303 VLSKTGHVLVKDTMRRNDAAYGGEMSAHHYFRDFMFCDSGMIPWLLMLERLSKSGRPLSA 362 Query: 359 LVEARMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQWRFNLRSS 418 V ++ P SGEINF+V+DA +A + +HYA + +D DG+S +F WRFNLR+S Sbjct: 363 AVAEMRRRHPSSGEINFRVSDAARVMATLRQHYADSAEHIDTLDGVSMEFADWRFNLRAS 422 Query: 419 NTEPLLRLNVETRGDAALLETRTQEISNLL 448 NTEPLLRLNVET AALL+ R EI +++ Sbjct: 423 NTEPLLRLNVETLESAALLDRRVGEIRSMI 452 Lambda K H 0.319 0.136 0.404 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: 574 Number of extensions: 17 Number of successful extensions: 3 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: 450 Length of database: 456 Length adjustment: 33 Effective length of query: 417 Effective length of database: 423 Effective search space: 176391 Effective search space used: 176391 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