GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Dechlorosoma suillum PS

Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate Dsui_1115 Dsui_1115 putative acyl-CoA transferase/carnitine dehydratase

Query= SwissProt::Q9HAC7
         (445 letters)



>FitnessBrowser__PS:Dsui_1115
          Length = 388

 Score =  190 bits (483), Expect = 6e-53
 Identities = 127/384 (33%), Positives = 192/384 (50%), Gaps = 24/384 (6%)

Query: 46  KPLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPPFVGTESTYYLS 105
           KPL+GV+ILDLTR+L GP AT++L DLGA+VIK+E  GAGD  RT G    G  S +Y +
Sbjct: 4   KPLQGVRILDLTRLLPGPVATLHLADLGADVIKIEDHGAGDYARTMGDGPEGV-SVFYRA 62

Query: 106 VNRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHIIYC 165
           VNRNK+ + +++K+P+G  + + LAA  DV +E++ PG +  +G+GYE +  + P +++C
Sbjct: 63  VNRNKRGLRLDLKNPEGAALFRRLAAEADVVIESFRPGVMDKLGVGYEALCSLNPRLVFC 122

Query: 166 SITGYGQTGPISQRAGYDAVASAVSGLMHITGPENGDPVRPGVAMTDLATG-LYAYGAIM 224
           +ITGYGQ+GP++  AG+D      +G++   G + G P  P + + DL  G + A   I+
Sbjct: 123 AITGYGQSGPLALAAGHDLNYIGYAGILDQIGVDGGQPAIPNLQIGDLLGGAMSAVMGIL 182

Query: 225 AGLIQKYKTGKGLFIDCNLLSSQVACLSH-----IAANYLIGQKEAKRWGTAHGSIVPYQ 279
           A L    ++G+G F+D   +S   A L+H      A     G  E  R     G    Y 
Sbjct: 183 AALFDARRSGQGRFVD---VSMSDAALAHNLFPLFALQGGAGVAERGR-DMLSGGDAGYG 238

Query: 280 AFKTKDG-YIVVGAGNNQQFATVCKILDLPELIDNSKYKTNHLRVHNRKELIKI-LSERF 337
            + T DG Y+ V     + +   C  L  P      ++K  H         ++  L   F
Sbjct: 239 VYATADGRYMAVAPLERKFWDLFCDTLGQP------RWKARHGATGAEARAMRAELETLF 292

Query: 338 EEELTSKWLYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKISVPGPAVRY 397
             +  S W   F        P+  +    A P     G+  + +      I+  GP VR 
Sbjct: 293 ASQPQSYWTEKFARVDCCVTPVLTVAEALAHPHFQARGMGFQAD-----GITQYGPPVRL 347

Query: 398 SKFKMSEARPPPLLGQHTTHILKE 421
           S   +   RP P  G+H   IL E
Sbjct: 348 SDMPVEPVRPAPAPGEHGQAILAE 371


Lambda     K      H
   0.318    0.137    0.410 

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: 449
Number of extensions: 20
Number of successful extensions: 4
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: 445
Length of database: 388
Length adjustment: 31
Effective length of query: 414
Effective length of database: 357
Effective search space:   147798
Effective search space used:   147798
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: 50 (23.9 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