GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Rhodobacter viridis JA737

Align Fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate WP_110804301.1 C8J30_RS02965 fructose bisphosphate aldolase

Query= curated2:Q8RGH3
         (295 letters)



>NCBI__GCF_003217355.1:WP_110804301.1
          Length = 294

 Score =  340 bits (871), Expect = 3e-98
 Identities = 177/290 (61%), Positives = 219/290 (75%), Gaps = 3/290 (1%)

Query: 5   LEKMRNGKGFIAALDQSGGSTPKALKLYGVNENEYSNDKEMFDLIHKMRTRIIKSPAFNE 64
           +E MR G+GFIAALDQSGGSTPKAL+LYG+ E+ YSN+ EM+DLIH MR RIIKS AF  
Sbjct: 6   MEHMRKGEGFIAALDQSGGSTPKALRLYGITEDAYSNETEMYDLIHAMRARIIKSSAFTG 65

Query: 65  SKILGAILFEQTMDSKIDGKYTADFLWEEKKVLPFLKIDKGLNDLDADGVQTMKPNPTLA 124
            K++GAILFEQTMD  IDG  TA +LWE++ V+PFLKIDKGL + + +G Q +K  PTL 
Sbjct: 66  DKVVGAILFEQTMDRDIDGIPTATYLWEKRGVVPFLKIDKGLEE-EKNGCQMLKAMPTLD 124

Query: 125 DLLKRANERHIFGTKMRSVIKKASPAGIARVVEQQFEVAAQVVAAGLIPIIEPEVDINNV 184
            LL+RA E  IFGTK RSVI  A P GIA VV QQFEV  QV+ AG++PI+EPEV I+  
Sbjct: 125 ALLERAAEAGIFGTKERSVISAADPMGIASVVAQQFEVGEQVLGAGMVPILEPEVTISIA 184

Query: 185 DKVQCEEILRDEIRKHLNALPETSNVMLKLTLPTVENLYEEFTKHPRVVRVVALSGGYSR 244
           DK+  E +LRD +   L  +  +S VMLKL+LPT++N Y    +HP V++VVALSGGY+R
Sbjct: 185 DKIDAEAMLRDALLAGLETV--SSPVMLKLSLPTIDNFYLPLVEHPNVIKVVALSGGYAR 242

Query: 245 EKANDILSKNKGVIASFSRALTEGLSAQQTDEEFNKTLAASIDGIYEASV 294
             AN IL++NKG+IASFSRALTEGL+AQ TD EF+  L  +ID IY AS+
Sbjct: 243 NDANAILARNKGMIASFSRALTEGLTAQMTDAEFDAALGEAIDSIYRASI 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: 265
Number of extensions: 6
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: 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 24 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