GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pgmA in Phaeobacter inhibens BS107

Align Phosphomannomutase/phosphoglucomutase; PMM / PGM; EC 5.4.2.2; EC 5.4.2.8 (uncharacterized)
to candidate GFF2403 PGA1_c24340 phosphomannomutase/phosphoglucomutase AlgC

Query= curated2:Q88C93
         (463 letters)



>lcl|FitnessBrowser__Phaeo:GFF2403 PGA1_c24340
           phosphomannomutase/phosphoglucomutase AlgC
          Length = 498

 Score =  224 bits (571), Expect = 5e-63
 Identities = 152/452 (33%), Positives = 240/452 (53%), Gaps = 21/452 (4%)

Query: 14  FRAYDIRGVVGKTLHAETAYWIGRAIGAQSLAQGEPQV-SVGRDGRLSGPMLVEQLIKGL 72
           FR YD R    + ++      +G  +G Q   +G P V +V  D R     +   LI GL
Sbjct: 26  FREYDARWKYPEEINLPGMTALGLGLGTQMHKRGIPPVIAVANDYRDYSVAIKHALIIGL 85

Query: 73  VDAGCNVSDVGLVPTPALYYAANVLAGKSGVMLTGSHNPSDYNGFKIVIAGDTLANEQIQ 132
           + AG  V D+G   +P  Y+A   L   +  M+T SHNP+ + G K+             
Sbjct: 86  MQAGIEVRDIGPALSPMAYFAQFHLDVPAVAMVTASHNPNGWTGVKMGFERPLTHGPDEM 145

Query: 133 ALLTRLKTNDLTLAQ--GRVEKVE-ILDRYFKQIVGDVKLAKKLKVVVDCGNGAAGVVAP 189
             L  +  N   +A+  G  + V+ + + Y   +VGD K+++ LKVV   GNG A   AP
Sbjct: 146 GELRDIVLNGEGVARPGGSYQFVDGVKEAYLDDLVGDFKMSRPLKVVCATGNGTASAFAP 205

Query: 190 QLIEALGCEVIPLFCEVDGNFPNHHPDPGKPENLEDLIAKVKETGADIGLAFDGDGDRVG 249
           +L E +G EV+     +D  FP+++P+P   E L D+ A VK +GAD+ L FDGDGDR G
Sbjct: 206 ELFERMGVEVVDSHNALDYTFPHYNPNPEAMEMLHDMSASVKASGADMALGFDGDGDRCG 265

Query: 250 VVTNTGSIVYPDRLLMLFAQDVLSRNPGAEIIFDVKCTRRLT--PLIEQHGGRALMWKTG 307
           VV + G  ++ D++ ++ A+D+    P +  + DVK T      P ++ +G  A  WKTG
Sbjct: 266 VVDDEGEEIFADKVGVIMARDLSKLYPNSTFVADVKSTGLFASDPELKANGVTADYWKTG 325

Query: 308 HSLIKKKMKQTGSLLAGEMSGHIFIKER-WYGFDDGIYSAARLLEILSKT-EQSAENLFA 365
           HS +K+++K+ G+L   E SGH F+ E    G+D G+  A  + +++ +  ++S  +L  
Sbjct: 326 HSHMKRRVKEIGALAGFEKSGHYFLAEPVGRGYDCGMRVAVEICKLMDRNPDKSMSDLRK 385

Query: 366 AFPNDISTPEINIDVTDEGKFSIID----ALQRDADWGEA-------NLTTIDGVRVDYA 414
           A P   +TP ++    D  K+++++     L   A+ GE         + T++G RV   
Sbjct: 386 ALPKTWATPTMSPYCADTEKYTVLERLVAKLVAKAEAGETLADRPIKEVVTVNGARVILD 445

Query: 415 NG-WGLVRASNTTPVLVLRFE-ADSDAELQRI 444
           NG WGLVRAS+ TP LV+  E ++S+AEL+ I
Sbjct: 446 NGSWGLVRASSNTPNLVVVCESSESEAELREI 477


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: 575
Number of extensions: 39
Number of successful extensions: 7
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: 498
Length adjustment: 34
Effective length of query: 429
Effective length of database: 464
Effective search space:   199056
Effective search space used:   199056
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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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