GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Cupriavidus basilensis 4G11

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate RR42_RS20235 RR42_RS20235 metal-dependent hydrolase

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__Cup4G11:RR42_RS20235
          Length = 247

 Score =  203 bits (517), Expect = 2e-57
 Identities = 115/244 (47%), Positives = 155/244 (63%), Gaps = 8/244 (3%)

Query: 1   MSDLLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLT---P 57
           MS +L VKD+   Y   V  + G N  +  G++VTVIGPNGAGKST+   I G L     
Sbjct: 1   MSLILEVKDLHVRY-GKVEAVHGANLKVEAGKIVTVIGPNGAGKSTMLNAIMGALPVSGS 59

Query: 58  SQGEIIFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQ--GPTQTL 115
           S G + + G ++ GL ++  V RGMC VP+   +FGS++VA+NL +GA+  +  G    L
Sbjct: 60  STGAVTYLGHDLAGLPAEGRVARGMCLVPEKRELFGSMSVADNLVLGAYRRKRAGEKNFL 119

Query: 116 KDR--IYTMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVK 173
                +Y +FP+L +R  Q AGTLSGGERQMLA+GRALM  P LL+LDEPS  L+P++VK
Sbjct: 120 DQMEVVYGLFPRLKERAKQDAGTLSGGERQMLAVGRALMAKPQLLMLDEPSLGLAPLIVK 179

Query: 174 DVFAQIKAINATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELY 233
           ++F  I  +  TG A +L+EQNA+ AL +AD GYV+E G   +EG    L  +P V E Y
Sbjct: 180 EIFHIINDLRKTGVATLLIEQNARAALQVADYGYVIETGDMAMEGPAGELAANPKVIETY 239

Query: 234 LGAA 237
           LG A
Sbjct: 240 LGLA 243


Lambda     K      H
   0.320    0.139    0.393 

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: 177
Number of extensions: 8
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: 240
Length of database: 247
Length adjustment: 23
Effective length of query: 217
Effective length of database: 224
Effective search space:    48608
Effective search space used:    48608
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: 46 (22.3 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