GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Pseudomonas litoralis 2SM5

Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein

Query= uniprot:A0A159ZWS6
         (255 letters)



>NCBI__GCF_900105005.1:WP_090274680.1
          Length = 378

 Score =  130 bits (326), Expect = 5e-35
 Identities = 75/242 (30%), Positives = 129/242 (53%), Gaps = 18/242 (7%)

Query: 4   EILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTIL 63
           E +K+E +S +F   LAV+ V LT+   ++ AL+G +G+GK+T+   L GF  P+ G +L
Sbjct: 19  EFVKIERVSKQFDDALAVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGFETPSEGRVL 78

Query: 64  LDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAF 123
           LDG+ I  LP H   ++ +   FQ+  LF  MT  +N+                F     
Sbjct: 79  LDGQNITALPPH---KRPINMMFQSYALFPHMTVEQNIA---------------FGLKQD 120

Query: 124 RKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAG 183
           + S  E  E     L  V++ ++A R    L+ GQ++R+ +AR +  RP++L+LDEP   
Sbjct: 121 KLSNTEISERVAEMLKLVHMAKYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGA 180

Query: 184 LNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRD 243
           L+ K    ++  +  + E   VT +++ HD +  M+++  I +++QG  +  GTP  I +
Sbjct: 181 LDKKLRSQMQLELVEIIERVGVTCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDIYE 240

Query: 244 NP 245
           +P
Sbjct: 241 SP 242


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: 216
Number of extensions: 7
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: 255
Length of database: 378
Length adjustment: 27
Effective length of query: 228
Effective length of database: 351
Effective search space:    80028
Effective search space used:    80028
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: 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