Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate 5210100 Shew_2544 phosphoglucomutase/phosphomannomutase alpha/beta/subunit (RefSeq)
Query= BRENDA::C6L2F4 (596 letters) >FitnessBrowser__PV4:5210100 Length = 584 Score = 327 bits (839), Expect = 6e-94 Identities = 217/595 (36%), Positives = 322/595 (54%), Gaps = 47/595 (7%) Query: 13 LEAAVNFWRSVDRREETQKETLELLKNLTEDELAKLFLARLEFGTAGLRGRMGAGFSRMN 72 ++A + W S+D +++ E L+ ++EL F RL FGTAG+RG +GAG RMN Sbjct: 5 IQARIKHWLSLDSDAKSRAEIQALVDQGAQEELVARFAGRLTFGTAGIRGVVGAGPMRMN 64 Query: 73 DVTIQQTTQGYCAFLVDVFGEDGKDRGVVIGFDARHNSRRFAQLTAAVFLSKGFRVQLFS 132 + +QQT++G +L E+ RGVVIG+D RH+S++FA+ A+V + GF+V L S Sbjct: 65 RLVVQQTSKGVAEYLKAQV-ENAVSRGVVIGYDGRHDSKQFAEDAASVLTAAGFKVFLTS 123 Query: 133 DIVHTPMVPYTVVAANCIAGIMITASHNPKADNGYKVYAANGAQIIPPMDSEISAFINSN 192 + TP+V + V+ AGI++TASHNP NGYKVY NGAQIIPP D+ I+A I Sbjct: 124 KVAPTPLVAFGVLHLGAAAGIVVTASHNPPQYNGYKVYWGNGAQIIPPHDTGIAARI--E 181 Query: 193 LDFWSDVDEYFDSKTGMLTEKAANSSLLEDPLNTYVDAYIKDIA-ADLCVAEQQGSDLKF 251 L S VD +T + T K +LE+ Y AY + + A++ + + + Sbjct: 182 LAANSPVD-MLPLETAVETGKLV---MLEE---DYYQAYRQGVLNAEVLQSPARPELVSL 234 Query: 252 MYTAMHGVGTPMVKKMLAAFGFNDNLLTVDAQCTPDPEFPTVAFPNPEEKGALDLAFQEA 311 YTAMHGVG M + +L G + +V AQ PD +FPTV FPNPEE GA+ L EA Sbjct: 235 AYTAMHGVGAEMAETLLKDIGVT-QVYSVAAQREPDGDFPTVNFPNPEEAGAMVLVMAEA 293 Query: 312 DSHGLTLVIANDPDADRFAAA--------EKCDGRWYQ-FTGDELGAILGAYAIKLREGQ 362 HG L ANDPDADRFA A E YQ TGD++G +LG Y + Sbjct: 294 HKHGAMLACANDPDADRFAVAVRKPAATPEMLASEAYQMLTGDQVGVLLGHYLL-----S 348 Query: 363 GISKSKMALICSAVSSRMLQKIAKENGCTFAETMTGFKWMENKAIEMEAEGLIPVFVYEE 422 S + L C+ VSS +L +I++ G T+TGFKW+ N + + + +F YEE Sbjct: 349 HASDDQRLLCCTIVSSSLLTRISEACGARCETTLTGFKWLTNVGMSKQTQENRFLFAYEE 408 Query: 423 ALGYALSQRVRDKDGVSAAAVWMQMAIDLYSRGQTVMDFLMSLRKRYGYFVTRN-SYFIC 481 ALGY + V DKDG+SA ++Q+ +L ++G+T+ D L ++ ++YGY++ R S + Sbjct: 409 ALGYTVGSMVWDKDGLSALVAFVQLTAELAAKGETLWDRLETIYRQYGYYLNRQVSIALS 468 Query: 482 PDP------RLIQGLFKDFANGGNYPKQLGPFTIRRIRDVGRGY----DSEEQCSFPSNC 531 +P ++ L P ++ + + D+ G D E+ Sbjct: 469 GEPGAPTIGEQLRAL---------DPSEIAGRALVSVDDISLGVRRFADGREETIDLPRS 519 Query: 532 EMLTVYLDNGAVVTLRGSGTEPKLK-YYAETSSTDPEQGLAELAKVIAAVISDFV 585 ++L L A V +R SGTEPK+K YY ++GLA++ + A +++FV Sbjct: 520 DVLIYRLQGNARVIVRPSGTEPKVKCYYEVVEPFGEQEGLADVQRRAEAAMAEFV 574 Lambda K H 0.320 0.135 0.398 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: 767 Number of extensions: 34 Number of successful extensions: 8 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: 596 Length of database: 584 Length adjustment: 37 Effective length of query: 559 Effective length of database: 547 Effective search space: 305773 Effective search space used: 305773 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 (21.8 bits) S2: 53 (25.0 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