GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Cupriavidus basilensis 4G11

Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate RR42_RS14410 RR42_RS14410 leucine/isoleucine/valine transporter ATP-binding subunit

Query= uniprot:A0A159ZWS6
         (255 letters)



>FitnessBrowser__Cup4G11:RR42_RS14410
          Length = 259

 Score =  326 bits (835), Expect = 3e-94
 Identities = 155/253 (61%), Positives = 195/253 (77%)

Query: 2   SREILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGT 61
           S E+LKV  L MRFGGLLAV+G+   V+  +V A+IGPNGAGKTTVFNC+ GFY+PT G 
Sbjct: 6   SAELLKVSGLQMRFGGLLAVDGIDFDVRRDEVFAIIGPNGAGKTTVFNCVGGFYKPTAGE 65

Query: 62  ILLDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTP 121
           ++LDG  I  LP H +AR+G+VRTFQN+RLFK +T VENLL+AQH  + +    GLF TP
Sbjct: 66  VMLDGHSIARLPSHQVARRGLVRTFQNIRLFKQLTVVENLLVAQHLQVRSGLLRGLFATP 125

Query: 122 AFRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPA 181
           A+R++EREA+E A  WL+++ L   ANR AGTL+YG QRRLEIARCM+T PR+LMLDEPA
Sbjct: 126 AYRRAEREALERAALWLERMGLRGVANREAGTLSYGHQRRLEIARCMITNPRLLMLDEPA 185

Query: 182 AGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQI 241
           AGLNP+E  +L  LI  LR EH ++VLLIEHDM LVM +SD I+V+  G P+  G P ++
Sbjct: 186 AGLNPQEKVELSQLIDQLRREHKISVLLIEHDMSLVMGVSDRILVMEHGRPILVGKPAEV 245

Query: 242 RDNPEVIKAYLGE 254
           R++P VIKAYLGE
Sbjct: 246 RNDPRVIKAYLGE 258


Lambda     K      H
   0.321    0.138    0.398 

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: 249
Number of extensions: 6
Number of successful extensions: 1
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: 255
Length of database: 259
Length adjustment: 24
Effective length of query: 231
Effective length of database: 235
Effective search space:    54285
Effective search space used:    54285
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: 47 (22.7 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