GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolJ in Desulfovibrio vulgaris Hildenborough

Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate 207620 DVU2143 fructose-1,6-bisphosphate aldolase, class II

Query= SwissProt::P42420
         (290 letters)



>MicrobesOnline__882:207620
          Length = 307

 Score =  198 bits (503), Expect = 1e-55
 Identities = 118/301 (39%), Positives = 169/301 (56%), Gaps = 28/301 (9%)

Query: 1   MAFVSMKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGF 60
           M     +E+   A RE +A+G FN+N ++  + I+QA  +E++P+I   S     Y G  
Sbjct: 1   MPLTGPREMFARAYREGHAVGAFNVNNMEIIQGIMQAGAEERAPLILQVSAGARKYAGQN 60

Query: 61  KTIAAMVGALIEDMAITVPVVLHLDHGSSAERCRQAIDAGFSSVMIDGSHQPIDENIAMT 120
             I  +  AL++     +PVVLHLDHG   + C+  ID GF+SVMIDGSH   +ENIA+T
Sbjct: 61  YIIKLIEAALLDT---DLPVVLHLDHGQDFDICKSCIDGGFTSVMIDGSHLSYEENIAVT 117

Query: 121 KEVTDYAAKHGVSVEAEVGTVGGMEDGLVGGVR-YADITECERIVKETNIDALAAALGSV 179
           + V +YA   GV VEAE+G + G+ED +      Y D  +    V+ T  D+LA A+G+ 
Sbjct: 118 RRVVEYAHDKGVWVEAELGQLAGVEDEVSAEHSVYTDPDQAVEFVQRTGCDSLAIAIGTS 177

Query: 180 HG--KYQGEPNLGFKEMEAISRM-TDIPLVLHGAS---------------------GIPQ 215
           HG  K+ G+  L F  +E I++M  D PLVLHGAS                     G+P+
Sbjct: 178 HGAYKFTGDAKLDFARLETITKMLPDYPLVLHGASSVPQEFVEMANAYGGKVGGARGVPE 237

Query: 216 DQIKKAITLGHAKININTECMVAWTDETRRMFQENSDLYEPRGYLTPGIEAVEETVRSKM 275
           D ++KA T G  KINI+T+  +A T   R+ F EN   ++PR YL P  EAV+  V+ K+
Sbjct: 238 DLLRKAATFGVCKINIDTDIRLAMTATIRKHFIENPGDFDPRAYLKPAREAVKNMVQHKI 297

Query: 276 R 276
           R
Sbjct: 298 R 298


Lambda     K      H
   0.316    0.132    0.372 

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: 227
Number of extensions: 10
Number of successful extensions: 6
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: 290
Length of database: 307
Length adjustment: 27
Effective length of query: 263
Effective length of database: 280
Effective search space:    73640
Effective search space used:    73640
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 (21.6 bits)
S2: 48 (23.1 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