GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Cup4G11:RR42_RS14410 RR42_RS14410
           leucine/isoleucine/valine transporter ATP-binding
           subunit
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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