GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Sinorhizobium meliloti 1021

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate SMc03119 SMc03119 ABC transporter ATP-binding protein

Query= TCDB::Q8DQH7
         (236 letters)



>FitnessBrowser__Smeli:SMc03119
          Length = 233

 Score =  174 bits (440), Expect = 2e-48
 Identities = 91/233 (39%), Positives = 141/233 (60%), Gaps = 4/233 (1%)

Query: 3   VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62
           +LKV  L+  YG    +  V   V EGE+V+L+G NG GKTT LR + G+VR   G+I F
Sbjct: 4   LLKVAGLNAWYGESHVLHGVDMTVGEGEMVTLLGRNGVGKTTTLRAIMGIVRERRGEISF 63

Query: 63  LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFSR 122
            G+++ ++P  ++   GL  VPE R +F  LTV ENL +   + K        + ++F  
Sbjct: 64  AGEDLMRVPLHRVAHRGLGFVPEERGIFSTLTVYENLLLPPAVAKGG----MTIDEIFEL 119

Query: 123 FPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQDI 182
           FP L ER+N     LSGGEQQMLA+ R L +  +++LLDEP+ GLAP+ +Q I ++++ +
Sbjct: 120 FPNLHERRNSAGTKLSGGEQQMLAIARILRTGVRMMLLDEPTEGLAPVIVQRIGEVLKKL 179

Query: 183 QKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235
           +++G TVLL+EQN   A  ++DR Y+++ G++       EL+   ++    LG
Sbjct: 180 KERGMTVLLVEQNFRFASKVADRFYLMDHGRVAGEFPVSELSGRMDMLHDVLG 232


Lambda     K      H
   0.315    0.134    0.358 

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: 148
Number of extensions: 8
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: 236
Length of database: 233
Length adjustment: 23
Effective length of query: 213
Effective length of database: 210
Effective search space:    44730
Effective search space used:    44730
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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