GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Echinicola vietnamensis KMM 6221, DSM 17526

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Echvi_1582 Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component

Query= TCDB::Q8DQH8
         (254 letters)



>FitnessBrowser__Cola:Echvi_1582
          Length = 225

 Score =  121 bits (303), Expect = 1e-32
 Identities = 82/238 (34%), Positives = 124/238 (52%), Gaps = 27/238 (11%)

Query: 1   MALLEVKQLTKHFGG----LTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPS 56
           M +L ++ ++K +      LT + D+ L +  G+ + ++GP+G+GKTTL  L  G+   S
Sbjct: 1   MDILSIENVSKIYQSGSRTLTVLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGLDSAS 60

Query: 57  EGTVTLDGHLLNGKSPYK---IASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFT 113
            G+V L+GH L G S  +   + S  +G  FQN +L   LT L+NV++            
Sbjct: 61  SGSVALNGHRLEGLSEDQRAAVRSQEIGFIFQNFQLLPTLTALENVMV------------ 108

Query: 114 SFLRLPAFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKIL 173
                P   K  K+ K KA ELL+   L          LS G+Q+R+ I RA A EPKIL
Sbjct: 109 -----PLELKKRKDAKQKATELLQQVGLGDRMTHYPTQLSGGEQQRVSIARAFANEPKIL 163

Query: 174 FLDEPAAGMNPQETAELTE-LIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRL 230
           F DEP   ++  ET EL E LI  +      T++L+ HD +L  + T RI  ++ G++
Sbjct: 164 FADEPTGNLD-TETGELIETLIFDLNKALGTTLILVTHDTDLAAK-TNRIIHIKGGKI 219


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: 131
Number of extensions: 7
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: 225
Length adjustment: 23
Effective length of query: 231
Effective length of database: 202
Effective search space:    46662
Effective search space used:    46662
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: 46 (22.3 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