GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Acidovorax sp. GW101-3H11

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Ac3H11_3213 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)

Query= TCDB::Q8DQH7
         (236 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3213
          Length = 236

 Score =  213 bits (541), Expect = 3e-60
 Identities = 116/232 (50%), Positives = 156/232 (67%), Gaps = 3/232 (1%)

Query: 4   LKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEFL 63
           L V+NL+  Y   Q ++D+S +   G  V ++G NGAGKTT+L+ L+GL+ P +G +   
Sbjct: 6   LTVQNLTTGYHGFQVLQDLSLQAAPGITV-IVGPNGAGKTTLLKALAGLL-PRTGTVALD 63

Query: 64  GQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFSRF 123
           G ++  M A   V  GL+ V EGR +FP +TV ENLE+G +L  +R      L + F  F
Sbjct: 64  GSDLPAMNATACVQRGLALVAEGRQLFPQMTVTENLELGGWLVPSRTRAD-RLAQAFEDF 122

Query: 124 PRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQDIQ 183
           PRL+ER  Q A T+SGGEQQM+A+ RALMS P+LL+LDEPS+GLAP  + E+  I+Q I 
Sbjct: 123 PRLKERATQLAGTMSGGEQQMVAVARALMSGPRLLMLDEPSLGLAPRMVDELLAIVQRIA 182

Query: 184 KQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235
            QG TVL++EQN  KAL I+ RGYVLE G+IV SG   +L  S+ VR+AYLG
Sbjct: 183 AQGVTVLMVEQNVRKALQIAQRGYVLERGRIVASGAASDLLQSDVVRQAYLG 234


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: 166
Number of extensions: 6
Number of successful extensions: 4
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: 236
Length adjustment: 23
Effective length of query: 213
Effective length of database: 213
Effective search space:    45369
Effective search space used:    45369
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