Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate 16156 b2048 phosphomannomutase (NCBI)
Query= BRENDA::Q8PGN7 (450 letters) >FitnessBrowser__Keio:16156 Length = 456 Score = 520 bits (1338), Expect = e-152 Identities = 261/451 (57%), Positives = 325/451 (72%), Gaps = 7/451 (1%) Query: 5 LPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAGLR 64 L FKAYDIRG++ +ELNED+A RIG A L +VLG DVRL S L+ AL+ GL+ Sbjct: 4 LTCFKAYDIRGKLGEELNEDIAWRIGRAYGEFLKPKTIVLGGDVRLTSETLKLALAKGLQ 63 Query: 65 ASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDTGL 124 +G DV+DIG+ GTEE+YF T +L GG+ VTASHNPMDYNGMKLVRE ARPIS DTGL Sbjct: 64 DAGVDVLDIGMSGTEEIYFATFHLGVDGGIEVTASHNPMDYNGMKLVREGARPISGDTGL 123 Query: 125 FAIRDTVAADTAAPGEPT--ASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGGAG 182 ++ A+ P + T Q + AY++HL Y++ L PLKLV+N+GNG AG Sbjct: 124 RDVQRLAEANDFPPVDETKRGRYQQINLRDAYVDHLFGYINVKNLTPLKLVINSGNGAAG 183 Query: 183 LIVDLLAPHL-----PFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIA 237 +VD + P E ++V + PDGNFPNGIPNPLLPE RD T AV +GAD GIA Sbjct: 184 PVVDAIEARFKALGAPVELIKVHNTPDGNFPNGIPNPLLPECRDDTRNAVIKHGADMGIA 243 Query: 238 WDGDFDRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGI 297 +DGDFDRCF FD G+FIEGYY+VGLLA+A L K PG K++HDPRL+WNTV+ V AGG Sbjct: 244 FDGDFDRCFLFDEKGQFIEGYYIVGLLAEAFLEKNPGAKIIHDPRLSWNTVDVVTAAGGT 303 Query: 298 PVLCKSGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLA 357 PV+ K+GHAFIKE+MR E+A+YGGEMSAHHYFR+FAY DSGMIPWLL+AELV ++L Sbjct: 304 PVMSKTGHAFIKERMRKEDAIYGGEMSAHHYFRDFAYCDSGMIPWLLVAELVCLKDKTLG 363 Query: 358 DLVEARMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQWRFNLRS 417 +LV RM FP SGEIN K+A ++ RV +H++ + +D TDGIS F WRFNLR+ Sbjct: 364 ELVRDRMAAFPASGEINSKLAQPVEAINRVEQHFSREALAVDRTDGISMTFADWRFNLRT 423 Query: 418 SNTEPLLRLNVETRGDAALLETRTQEISNLL 448 SNTEP++RLNVE+RGD L+E RT+ + LL Sbjct: 424 SNTEPVVRLNVESRGDVPLMEARTRTLLTLL 454 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: 634 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