Align Phosphomannomutase/phosphoglucomutase; PMM / PGM; EC 5.4.2.2; EC 5.4.2.8 (uncharacterized)
to candidate SM_b21081 SM_b21081 phosphoglucomutase phosphomannomutase
Query= curated2:Q88C93 (463 letters) >FitnessBrowser__Smeli:SM_b21081 Length = 515 Score = 256 bits (653), Expect = 2e-72 Identities = 169/474 (35%), Positives = 255/474 (53%), Gaps = 29/474 (6%) Query: 14 FRAYDIRGVVGKT-------LHAETAYWIGRAIGAQSLAQGE-PQVSVGRDGRLSGPMLV 65 FR YD R G++ L+ A +G +G G P++ G D R + Sbjct: 36 FREYDARWWFGRSDCGKAPELNLMGAQALGMGLGTFIQRSGAGPEIVTGHDFRSYSLGIK 95 Query: 66 EQLIKGLVDAGCNVSDVGLVPTPALYYAANVLAGKSGVMLTGSHNPSDYNGFKIVIAGDT 125 L+ GL+ AG V D+GL +P Y+A L S M+T SHN + + G K+ +A Sbjct: 96 LALVCGLMAAGARVRDIGLALSPMAYFAQFALDVPSVAMVTASHNENGWTGVKMGMARPL 155 Query: 126 LANEQIQALLTRLKTN---DLTLAQGRVEKV-EILDRYFKQIVGDVKLAKKLKVVVDCGN 181 Q A L R+ DLT G E V + RY + ++ +KLKVV CGN Sbjct: 156 TFGPQEMAELRRIVLEADFDLT-GGGAYEFVPDFRRRYIDDLTRGRRIGRKLKVVAACGN 214 Query: 182 GAAGVVAPQLIEALGCEVIPLFCEVDGNFPNHHPDPGKPENLEDLIAKVKETGADIGLAF 241 G AG AP +++ +GCEVIPL C++D +FP ++P+P + L + KV E+GAD+GL F Sbjct: 215 GTAGAFAPDVLQRIGCEVIPLDCDLDHSFPRYNPNPEDLKMLHAIRDKVLESGADVGLGF 274 Query: 242 DGDGDRVGVVTNTGSIVYPDRLLMLFAQDVLSRNPGAEIIFDVKCTRRLT--PLIEQHGG 299 DGDGDR GVV N GS ++ D++ ++ A+D+ + NPG+ + DVK T P+++ +G Sbjct: 275 DGDGDRCGVVDNEGSEIFADKIGVMLARDISASNPGSVFVVDVKSTGLFASDPVLKANGA 334 Query: 300 RALMWKTGHSLIKKKMKQTGSLLAGEMSGHIFIK-ERWYGFDDGIYSAARLLEILSKT-E 357 R WKTGHS IK+++ + G++ E SGH F G+DDG+ +A + E+L ++ Sbjct: 335 RTDYWKTGHSYIKRRVAELGAIAGFEKSGHFFFNAPLGRGYDDGLITAISICEMLDRSPN 394 Query: 358 QSAENLFAAFPNDISTPEINIDVTDEGKFSIID-------ALQRD----ADWGEANLTTI 406 +S ++ A P S+P ++ DE K+++ + A+QRD A A+L T+ Sbjct: 395 RSIAEIYRALPMTWSSPTMSPHCADEVKYAVAERVVERFRAMQRDGVPVAGQMIADLVTV 454 Query: 407 DGVRVDYANG-WGLVRASNTTPVLVLRFEADSDAELQRIKDVFRTQLLRVEPEL 459 +GVRV +G WGLVRAS+ P LV+ E+ QR +LR PE+ Sbjct: 455 NGVRVVTEDGTWGLVRASSNKPELVVVVESPVSEARQRAMFEAVDCVLRENPEV 508 Lambda K H 0.319 0.138 0.406 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: 608 Number of extensions: 41 Number of successful extensions: 6 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: 463 Length of database: 515 Length adjustment: 34 Effective length of query: 429 Effective length of database: 481 Effective search space: 206349 Effective search space used: 206349 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 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