GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Amycolatopsis halophila YIM 93223

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_034276702.1 AMYHA_RS10540 ABC transporter ATP-binding protein

Query= TCDB::Q8DQH8
         (254 letters)



>NCBI__GCF_000504245.1:WP_034276702.1
          Length = 269

 Score =  199 bits (505), Expect = 6e-56
 Identities = 104/260 (40%), Positives = 160/260 (61%), Gaps = 9/260 (3%)

Query: 3   LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62
           LL+V  +T  FGG+TA+ DV+  + +G +  +IGPNGAGK++L N L+G+Y P  G+ TL
Sbjct: 7   LLDVSGITLRFGGITALDDVSFRVTQGHVHAVIGPNGAGKSSLLNCLSGLYRPQHGSATL 66

Query: 63  ---------DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFT 113
                      H L    P++IA+LG+ R+FQNI LF+ LTVLDN+++    H +  +  
Sbjct: 67  RTRTEDSSVTTHDLVRMKPHRIAALGVARSFQNIELFRHLTVLDNLMLGRHVHMRHRLLP 126

Query: 114 SFLRLPAFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKIL 173
           S        + E E +    E++ +  +     T    L+YG Q+R+E+ RAL  +P +L
Sbjct: 127 SLAWYGPARRQEIEHRELVEEVIDLLQIQAVRHTPVGALAYGFQKRVELGRALCLQPALL 186

Query: 174 FLDEPAAGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQ 233
            LDEP AGMN +E  ++   I  + +   +T+MLIEHDMN+VM+++ R+ VL++G LIA 
Sbjct: 187 LLDEPMAGMNAEEKEDMARYILDVHELAGVTVMLIEHDMNVVMDISNRVSVLDFGALIAD 246

Query: 234 GTPDEIKTNKRVIEAYLGGE 253
           G+P E+ ++  VI+AYLG E
Sbjct: 247 GSPAEVSSDPDVIKAYLGEE 266


Lambda     K      H
   0.319    0.139    0.385 

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: 168
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: 254
Length of database: 269
Length adjustment: 25
Effective length of query: 229
Effective length of database: 244
Effective search space:    55876
Effective search space used:    55876
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: 47 (22.7 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