GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Chryseobacterium arthrosphaerae CC-VM-7

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_065398591.1 BBI00_RS09790 ATP-binding cassette domain-containing protein

Query= TCDB::Q8DQH8
         (254 letters)



>NCBI__GCF_001684965.1:WP_065398591.1
          Length = 342

 Score =  127 bits (320), Expect = 2e-34
 Identities = 81/264 (30%), Positives = 137/264 (51%), Gaps = 33/264 (12%)

Query: 3   LLEVKQLTKHFG----GLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEG 58
           ++E++ ++K F        A+  V+L + +G++VG+IG +GAGK+TL   +  +  P EG
Sbjct: 1   MIEIRNISKTFHQKNQSFKALDKVSLNIEKGDIVGIIGFSGAGKSTLIRTVNLLERPDEG 60

Query: 59  TVTLDGHLLNGKSPYKIASLGL-------GRTFQNIRLFKDLTVLDNVLIAFGNHHKQHV 111
            +     ++NGK   K+ S  L       G  FQ+  L    TV DNV +     H    
Sbjct: 61  QI-----IINGKDFTKLNSRQLAEERKKIGMIFQHFNLLSSRTVFDNVALPLELDHT--- 112

Query: 112 FTSFLRLPAFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPK 171
                        ++++  K  ELLKI  L+  A    ++LS GQ++R+ I RALA +P 
Sbjct: 113 ------------GKEQINRKVNELLKIVGLEEKANDYPRSLSGGQKQRVAIARALANDPH 160

Query: 172 ILFLDEPAAGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLI 231
           +L  DE  + ++P  T  + +L+R I     ITI+LI H+M ++  V   + V++ G+L+
Sbjct: 161 LLLCDEATSALDPATTQSILQLLRDINQRLGITILLITHEMEVIKTVCNHVAVIDKGKLL 220

Query: 232 AQGTPDEIKTNKR--VIEAYLGGE 253
            +GT  EI ++K   VI  ++  +
Sbjct: 221 TKGTLSEIISDKEHPVIRQFINSD 244


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: 190
Number of extensions: 11
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: 342
Length adjustment: 26
Effective length of query: 228
Effective length of database: 316
Effective search space:    72048
Effective search space used:    72048
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: 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