GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Sphingomonas koreensis DSMZ 15582

Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate Ga0059261_4235 Ga0059261_4235 ABC-type multidrug transport system, ATPase component

Query= TCDB::P0A9S7
         (255 letters)



>FitnessBrowser__Korea:Ga0059261_4235
          Length = 310

 Score =  102 bits (254), Expect = 9e-27
 Identities = 76/237 (32%), Positives = 114/237 (48%), Gaps = 23/237 (9%)

Query: 6   LSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLR 65
           +SV GL  RFG    V+ V+LE+    I   +GPNG+GKTT    + G   P GG   + 
Sbjct: 7   ISVEGLTKRFGNRTVVDTVSLEVGRGRICGFLGPNGSGKTTTLRMICGLLIPDGGGGEVL 66

Query: 66  DQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENL-LVAQHQQLKTGLFSGLLKTPSFR 124
              L  L  +++ +  +    Q   LF ++T+ ENL  VA    L               
Sbjct: 67  GMDL--LTQRELIKRRIGYMTQRFGLFEDLTIRENLAFVADAYGL--------------- 109

Query: 125 RAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAGL 184
               E + R    LER+GL   A + A  L+ G ++RL +A C++  PEIL+LDEP AG+
Sbjct: 110 ---DEKMKRVDAALERLGLETRAGQLAGTLSGGWKQRLALAACVLHDPEILLLDEPTAGV 166

Query: 185 NPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQI 241
           +P   +E  + +  + +   TT+L+  H M       D  Y+   G  LA GT ++I
Sbjct: 167 DPLARREFWDQV-HMLSAEGTTVLVSTHYMDEAERCHDIAYIA-YGVLLARGTADEI 221


Lambda     K      H
   0.320    0.137    0.395 

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: 196
Number of extensions: 6
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: 310
Length adjustment: 26
Effective length of query: 229
Effective length of database: 284
Effective search space:    65036
Effective search space used:    65036
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: 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