GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Sphingomonas koreensis DSMZ 15582

Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Ga0059261_2668 Ga0059261_2668 Enoyl-CoA hydratase/carnithine racemase

Query= metacyc::MONOMER-15953
         (257 letters)



>FitnessBrowser__Korea:Ga0059261_2668
          Length = 256

 Score =  152 bits (383), Expect = 9e-42
 Identities = 99/245 (40%), Positives = 128/245 (52%), Gaps = 2/245 (0%)

Query: 14  VRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGS-RKAFAAGADIKEMAE 72
           V  ITL RP  LNAL  ++   L A ++        R VV+TG+  KAF+AG+DI  +  
Sbjct: 13  VATITLNRPAKLNALTPEMAAALIASVSACNSSDAVRCVVITGAGEKAFSAGSDITTLDG 72

Query: 73  RDLVGILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFGQPEI 132
                   + R  +   + A  KP++AA+NG+ LGGG E AM ADI IA  +ARF  PEI
Sbjct: 73  YATPWDFRN-RDDYCDALRACRKPVVAAINGYALGGGLETAMAADIRIASTNARFAAPEI 131

Query: 133 NLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIERALAI 192
            LG + G G    L  ++G S A  M+ +G  IDA  A   GLVSEV  P+  + RA  I
Sbjct: 132 KLGWIGGGGMAAGLTYSMGASNAALMLFTGDMIDAEKALAWGLVSEVVAPDALLARAQEI 191

Query: 193 ARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAFQEKRRP 252
           AR IA +AP+A   AK  L  A        + +ER    +   T D  EG  AF EKR P
Sbjct: 192 ARTIASRAPIAAETAKLNLRAAHTMPWDKAIEYERDLQAICFATDDAKEGRAAFAEKRAP 251

Query: 253 EFTGR 257
            F  R
Sbjct: 252 VFRRR 256


Lambda     K      H
   0.320    0.134    0.374 

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: 169
Number of extensions: 9
Number of successful extensions: 3
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: 257
Length of database: 256
Length adjustment: 24
Effective length of query: 233
Effective length of database: 232
Effective search space:    54056
Effective search space used:    54056
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 (21.8 bits)
S2: 47 (22.7 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