GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Sinorhizobium meliloti 1021

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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