GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Sinorhizobium meliloti 1021

Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate SMc04398 SMc04398 enoyl-CoA hydratase

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



>FitnessBrowser__Smeli:SMc04398
          Length = 259

 Score =  149 bits (375), Expect = 7e-41
 Identities = 91/249 (36%), Positives = 130/249 (52%), Gaps = 5/249 (2%)

Query: 11  EQGVRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKEM 70
           E  + ++T+ RPE LNA +  +L  L +     E   + RAV+LTG  KAF+AG DIK  
Sbjct: 11  EGPIAIVTVARPEKLNAFDIDMLKALDSACDTVEARRDLRAVILTGEGKAFSAGGDIKAW 70

Query: 71  AERDLVGILED-PRVAH--WQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARF 127
              +      D  R  H  ++R+A    P+IAA+NG  LGGG ELA  ADI +A +  + 
Sbjct: 71  GGMEPAAFGHDWVRFGHRVFERLATLRMPVIAALNGHALGGGLELAAAADIRLAEKQVKI 130

Query: 128 GQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIE 187
           G PE +LG++PG  GTQRL+   G  +  +MVL G+   A  A+  GL+  V      ++
Sbjct: 131 GLPETSLGMVPGWSGTQRLVARFGAQIVRRMVLGGEMFSAAEARAEGLIDAVVETGAVMQ 190

Query: 188 RALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAFQ 247
            A   A  +A + P A+ ++K  +  A   D   G   E     ++A T D  EG+ AF 
Sbjct: 191 AARDYAARVAGRGPAALEISKLMIASASGED--KGAAVEALGSILVAKTGDLKEGVAAFS 248

Query: 248 EKRRPEFTG 256
           EKR   F G
Sbjct: 249 EKREARFKG 257


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: 201
Number of extensions: 10
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: 259
Length adjustment: 24
Effective length of query: 233
Effective length of database: 235
Effective search space:    54755
Effective search space used:    54755
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.

Links

Downloads

Related tools

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