GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Paraburkholderia phymatum STM815

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_012403750.1 BPHY_RS22455 ABC transporter ATP-binding protein

Query= TCDB::Q8DQH7
         (236 letters)



>NCBI__GCF_000020045.1:WP_012403750.1
          Length = 237

 Score =  199 bits (506), Expect = 4e-56
 Identities = 106/238 (44%), Positives = 154/238 (64%), Gaps = 11/238 (4%)

Query: 3   VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62
           +LKVE L+ +YG    + DVS EV  GEVV+L+G NGAGK+T ++++ GL+    G + F
Sbjct: 5   MLKVERLNAYYGRAHILFDVSLEVGRGEVVALMGRNGAGKSTTMKSIMGLLPRREGTVHF 64

Query: 63  LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANL-----K 117
              +I  +P  +I   GL  VPE R VF GLTVMENL+ G      R+ ++A       +
Sbjct: 65  NSADISALPPHRIARMGLGYVPENRRVFAGLTVMENLDTG------RQPSRAGAPSWTPE 118

Query: 118 KVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFD 177
           K+F  FP L E   +    +SGGEQQML + R LM  P L+LLDEPS G+AP+ ++++ +
Sbjct: 119 KLFKLFPNLGEMPKRRGDQMSGGEQQMLTVSRTLMGNPYLVLLDEPSEGVAPVVVEQMAN 178

Query: 178 IIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235
           +I +++++G ++LL EQN + A  +SDR YVLE G+I  SGT +ELA  + VR+A+LG
Sbjct: 179 MILELKREGLSILLSEQNVHFAELVSDRAYVLEKGQIRFSGTMRELAQDDVVRRAHLG 236


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: 176
Number of extensions: 3
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: 237
Length adjustment: 23
Effective length of query: 213
Effective length of database: 214
Effective search space:    45582
Effective search space used:    45582
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 Apr 09 2024. 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