GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Sinorhizobium meliloti 1021

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate SMa0796 SMa0796 hypothetical protein

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__Smeli:SMa0796
          Length = 487

 Score =  338 bits (867), Expect = 3e-97
 Identities = 200/474 (42%), Positives = 286/474 (60%), Gaps = 12/474 (2%)

Query: 23  FINGEYTAAAENET-FETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPA 81
           +INGE+   A+ E  FE++DP T    A++   +  D++RA+ AAR       WS  +  
Sbjct: 7   YINGEF---ADGEARFESIDPTTGRAWAEMPEAREADVNRAVEAARIALHDQPWSTLTAT 63

Query: 82  KRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGE 141
           +R  +L KLADL+  +A  LA LET DTGK IR +    I   A   R+YA   DK+ G 
Sbjct: 64  QRGKLLYKLADLVAENAGRLAELETRDTGKIIRET-SSQIAYVADYYRYYAGIADKIEGS 122

Query: 142 VATTSSHELAM-IVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSA 200
                  ++ + + REP+GV+A +VPWN  L L+  K+GPALAAG ++++K SE  P   
Sbjct: 123 YLPIDKPDMDVWLRREPIGVVAMVVPWNSQLFLSAVKIGPALAAGCTMVVKASEDGPAPL 182

Query: 201 IRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSN 260
           +  A L   AG P GV+N+VTGFG   G ALSRH  +D IAFTG   T + +++++ + N
Sbjct: 183 LEFARLVHAAGFPAGVVNIVTGFGPSCGAALSRHPQVDHIAFTGGPETARHIVRNSAE-N 241

Query: 261 MKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLA 320
           +    LE GGKS  IVFAD  DL+ AA+A  AGIF   GQ C+AG+RL++E+S+ D FL 
Sbjct: 242 LASTSLELGGKSPFIVFADA-DLESAANAQIAGIFAATGQSCVAGSRLIVEKSVKDRFLQ 300

Query: 321 LLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNA--GLAAA 378
           +LK +A+  + G PL+ +T +G L     ++ V + +    + G  L+ G  A  G    
Sbjct: 301 ILKAKAETIRIGSPLEMSTEVGPLATERQSNHVKTLVARSLAAGAKLVTGGTAPEGAGFY 360

Query: 379 IGPTIFVDVDPNASLSRE-EIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRA 437
             PTI +D D +AS S E E FGPVL V  F +E +AL LANDS++GL A V+T++L+RA
Sbjct: 361 YRPTI-LDCDGSASPSLENEFFGPVLSVLSFETEAEALHLANDSRFGLAAGVFTQNLTRA 419

Query: 438 HRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491
           HR+ + ++AG V+VN Y       PFGG+  SG+GR+  L A   +T  KT+W+
Sbjct: 420 HRLMKGIRAGIVWVNTYRAVSPVAPFGGFGLSGHGREGGLEAALDYTRSKTVWL 473


Lambda     K      H
   0.317    0.133    0.389 

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: 551
Number of extensions: 24
Number of successful extensions: 5
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: 495
Length of database: 487
Length adjustment: 34
Effective length of query: 461
Effective length of database: 453
Effective search space:   208833
Effective search space used:   208833
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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