GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ltaE in Pedobacter sp. GW460-11-11-14-LB5

Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate CA265_RS02210 CA265_RS02210 threonine aldolase

Query= BRENDA::Q9X266
         (343 letters)



>FitnessBrowser__Pedo557:CA265_RS02210
          Length = 341

 Score =  284 bits (727), Expect = 2e-81
 Identities = 154/333 (46%), Positives = 203/333 (60%), Gaps = 2/333 (0%)

Query: 2   IDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMG 61
           +D RSDTVTKPT  M  AM  A+VGDDV+GED T++ LE   A  F  EA LF PSGTM 
Sbjct: 6   LDFRSDTVTKPTAGMLDAMMNAKVGDDVFGEDETVHALETKLASIFNMEAGLFCPSGTMT 65

Query: 62  NQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRP 121
           NQ++I   TQ  DEVI +  +H++ YE+G +A  SG     + G  G + P+ +   I  
Sbjct: 66  NQIAIKCFTQPMDEVICDQTAHVYRYEIGGIAYHSGASVRLLYGDRGILTPELIEPEINE 125

Query: 122 RNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGV 181
            NIH+P +SL+ +ENT N+ GG    L  I  I  +    G+ +H+DGARIFNA +A+G 
Sbjct: 126 DNIHYPNSSLVVLENTVNKGGGSCYTLSQIAPIHHLCNIKGLKLHLDGARIFNALVATGD 185

Query: 182 PVKEYAGYADSVMFCLSKGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGI 241
              EY  Y D +  CLSKGL APVGSV++G +  I +ARK RK  GGGMRQAG LAAAGI
Sbjct: 186 QASEYGKYFDGISVCLSKGLGAPVGSVLLGSKQMIHKARKIRKAFGGGMRQAGFLAAAGI 245

Query: 242 IALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALR 301
            AL   V RLK+DH +A+ LA  L    Y  +   V+TN+VI   +  K +A   +   +
Sbjct: 246 YALDHHVTRLKDDHAHAQALANALASTKYVKSVMPVETNIVIFEVE--KGSAEKIVHQFK 303

Query: 302 NSGVLANAVSDTEIRLVTHKDVSRNDIEEALNI 334
             G+  N  S + IRLVTH D+S   I++A+ I
Sbjct: 304 EKGLHCNTTSASTIRLVTHLDLSTEMIDQAIEI 336


Lambda     K      H
   0.319    0.135    0.384 

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: 301
Number of extensions: 9
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: 343
Length of database: 341
Length adjustment: 29
Effective length of query: 314
Effective length of database: 312
Effective search space:    97968
Effective search space used:    97968
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 (21.7 bits)
S2: 49 (23.5 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