GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Dinoroseobacter shibae DFL-12

Align Fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate 3608764 Dshi_2156 Fructose-bisphosphate aldolase (RefSeq)

Query= curated2:Q8RGH3
         (295 letters)



>FitnessBrowser__Dino:3608764
          Length = 294

 Score =  343 bits (880), Expect = 3e-99
 Identities = 176/291 (60%), Positives = 222/291 (76%), Gaps = 1/291 (0%)

Query: 4   KLEKMRNGKGFIAALDQSGGSTPKALKLYGVNENEYSNDKEMFDLIHKMRTRIIKSPAFN 63
           K +++R+G GFIAALDQSGGSTPKAL+LYG+ E+ Y  D EMFDLIH+MR+RI+ +PAF 
Sbjct: 3   KADQIRSGHGFIAALDQSGGSTPKALRLYGIEEDAYGTDAEMFDLIHQMRSRIVAAPAFT 62

Query: 64  ESKILGAILFEQTMDSKIDGKYTADFLWEEKKVLPFLKIDKGLNDLDADGVQTMKPNPTL 123
             K++GAILFE TMD +  GK    +LWE+K V+PFLKIDKGL + +A+GVQ MKP P L
Sbjct: 63  GEKVIGAILFEMTMDREFAGKSAPAYLWEDKGVVPFLKIDKGL-EAEANGVQLMKPMPGL 121

Query: 124 ADLLKRANERHIFGTKMRSVIKKASPAGIARVVEQQFEVAAQVVAAGLIPIIEPEVDINN 183
            DLL RA    IFGTK RSVI  A+P GI  +V QQFE+ AQV+A GL+PI+EPEV I  
Sbjct: 122 DDLLSRAAAMGIFGTKERSVISAANPKGIKAIVAQQFEIGAQVLAHGLVPILEPEVTITI 181

Query: 184 VDKVQCEEILRDEIRKHLNALPETSNVMLKLTLPTVENLYEEFTKHPRVVRVVALSGGYS 243
            DK + E++L  EI  HL+ +PE   +MLKL+LP+  N Y    +H +V++VVALSGGYS
Sbjct: 182 ADKAEAEDMLLAEILAHLDTVPEGLQIMLKLSLPSKPNQYLPLVEHAKVMKVVALSGGYS 241

Query: 244 REKANDILSKNKGVIASFSRALTEGLSAQQTDEEFNKTLAASIDGIYEASV 294
           RE+AN  L++N GVIASFSRALTEGLSAQQ+D EFN T+AA+ID I+ AS+
Sbjct: 242 REEANAKLAENTGVIASFSRALTEGLSAQQSDAEFNATIAATIDSIHAASI 292


Lambda     K      H
   0.314    0.132    0.362 

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: 255
Number of extensions: 2
Number of successful extensions: 2
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: 295
Length of database: 294
Length adjustment: 26
Effective length of query: 269
Effective length of database: 268
Effective search space:    72092
Effective search space used:    72092
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: 42 (22.0 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