Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_077280100.1 B1C78_RS15640 phosphomannomutase
Query= BRENDA::Q8PGN7 (450 letters) >NCBI__GCF_002000365.1:WP_077280100.1 Length = 518 Score = 514 bits (1325), Expect = e-150 Identities = 275/509 (54%), Positives = 326/509 (64%), Gaps = 61/509 (11%) Query: 1 MPMTLPAFKAYDIRGRVPDELNEDLARRIGVALAAQLD-QGPVVLGHDVRLASPALQEAL 59 M LP FKAYDIRGR+PDELN DLA RIG A A + +GPV +G D+RL SP L EA+ Sbjct: 4 MSDALPCFKAYDIRGRIPDELNADLAWRIGRAYAEVIQPRGPVAVGQDMRLTSPELAEAV 63 Query: 60 SAGLRASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPIS 119 GL G D +GLCGTE VY GG+MVTASHNP+DYNGMKLVRE+A P+S Sbjct: 64 IRGLNEGGIDTRSLGLCGTEIVYHAASLPGMGGGIMVTASHNPIDYNGMKLVREEAIPVS 123 Query: 120 SDTGLFAIRDTVAADTAAPGEPTASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNG 179 D+GL I V ++ + Y+ +LS VD ++LKPL LVVNAGNG Sbjct: 124 GDSGLGEIERLVREGHWPAATARGNDAPLDVMSGYVRRVLSLVDVASLKPLHLVVNAGNG 183 Query: 180 GAGLIVDLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWD 239 AG + D +A HLPF R+ HEPDG FPNGIPNPLLPENR+ TA AV++ GAD GIAWD Sbjct: 184 AAGPVFDAIAEHLPFRITRIHHEPDGRFPNGIPNPLLPENREVTASAVREQGADLGIAWD 243 Query: 240 GDFDRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPV 299 GD+DRCF FD GRFIEGYYLVGLLA+ +LAK PG K++HDPRLTWNT+EQV AGGIPV Sbjct: 244 GDYDRCFLFDADGRFIEGYYLVGLLAEVMLAKYPGAKIIHDPRLTWNTIEQVTAAGGIPV 303 Query: 300 LCKSGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELV--------SQ 351 + K+GHAFIKE+MR E+AVYGGEMSAHHYFR+FAY DSGMIPWLLIAEL+ S Sbjct: 304 MSKTGHAFIKERMRLEDAVYGGEMSAHHYFRDFAYCDSGMIPWLLIAELMCKAASVHSSS 363 Query: 352 SG-----RSL--------ADLVEARMQKFPCSG--------------------------- 371 SG RSL + VE ++ P G Sbjct: 364 SGEERVQRSLSAEQSVHPSPSVEQQVHPSPSGGQPVHPSPSGGGAGEGVVSAPITPLAAL 423 Query: 372 ------------EINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQWRFNLRSSN 419 EINF+V ++AR+ HY P +D TDG+S F WRFNLR SN Sbjct: 424 VNERMTAYPCSGEINFRVDSVPDTIARIEAHYLPHDPAVDRTDGLSMAFDTWRFNLRGSN 483 Query: 420 TEPLLRLNVETRGDAALLETRTQEISNLL 448 TEP++RLNVETR DAAL+E +T EIS L+ Sbjct: 484 TEPVIRLNVETRHDAALMEEKTTEISRLI 512 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: 721 Number of extensions: 29 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 450 Length of database: 518 Length adjustment: 34 Effective length of query: 416 Effective length of database: 484 Effective search space: 201344 Effective search space used: 201344 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: 52 (24.6 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