GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Marinobacter adhaerens HP15

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate GFF1119 HP15_1097 branched-chain amino acid ABC transporter, ATP-binding protein

Query= TCDB::Q8DQH8
         (254 letters)



>FitnessBrowser__Marino:GFF1119
          Length = 255

 Score =  188 bits (478), Expect = 8e-53
 Identities = 98/251 (39%), Positives = 156/251 (62%), Gaps = 7/251 (2%)

Query: 3   LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62
           +LE + L+KH+GG+ A+ D++L+  +  L G++GPNGAGK+TL N+L G  +P+ G +  
Sbjct: 6   ILETESLSKHWGGIKALDDISLQFQDKHLHGVVGPNGAGKSTLLNMLCGTLKPTSGCIFH 65

Query: 63  DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122
            G  + G  P++    G+GR+FQ   ++ D+T L+N  IA      Q  FT    L A  
Sbjct: 66  KGDQIEGMKPWEFVHRGIGRSFQKTNIYVDVTCLENCAIA-----AQRRFTGSFNLFASR 120

Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182
            S K ++  A + L    L+    T+A  +SYG+QR+LE+   LAT+P IL LDEP AGM
Sbjct: 121 HSNKLVREGAEKALCQVGLENRVHTVAAEISYGEQRQLELAMVLATDPCILLLDEPMAGM 180

Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKTN 242
             +E+  + EL+ ++K  +  +I+L+EHDM+ + E+++++ VL+ G  +  GT DE++ +
Sbjct: 181 GHEESQRIIELMNQLKQTY--SIVLVEHDMDAIFELSDQLTVLDNGTHLITGTVDEVRND 238

Query: 243 KRVIEAYLGGE 253
            RV EAYLG E
Sbjct: 239 TRVKEAYLGKE 249


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: 154
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: 254
Length of database: 255
Length adjustment: 24
Effective length of query: 230
Effective length of database: 231
Effective search space:    53130
Effective search space used:    53130
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 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