GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Williamsia sterculiae CPCC 203464

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_083710258.1 BW971_RS17380 ABC transporter ATP-binding protein

Query= TCDB::Q8DQH7
         (236 letters)



>NCBI__GCF_900156495.1:WP_083710258.1
          Length = 263

 Score =  273 bits (699), Expect = 2e-78
 Identities = 139/235 (59%), Positives = 182/235 (77%), Gaps = 2/235 (0%)

Query: 3   VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62
           VL++ ++ +HYG I+A+  +S  V+ GE+V+L+GANGAGK+T +R +SGL + +SG IEF
Sbjct: 27  VLQIRDMVIHYGRIEALHGISLTVDAGELVTLLGANGAGKSTTMRGISGLKQLTSGSIEF 86

Query: 63  LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKK--NREENQANLKKVF 120
           LGQ+I +MPA K V  G+ QVPEGR VFPG+TV ENL+MG + +K  +R E +  +  V+
Sbjct: 87  LGQDITRMPAAKRVIEGIVQVPEGRRVFPGMTVAENLDMGCYGRKFGSRAEQKTTVDYVY 146

Query: 121 SRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQ 180
             FPRL ER++Q   T+SGGEQQMLA+GRALM+ PKLLLLDEPSMGLAP+ IQ+IF II 
Sbjct: 147 ELFPRLAERRSQLGGTMSGGEQQMLAIGRALMARPKLLLLDEPSMGLAPMVIQQIFRIIA 206

Query: 181 DIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235
            I +QGTT+LL+EQNA +AL+ SDRGYVLETG I   G GKEL + + VR+AYLG
Sbjct: 207 TINEQGTTILLVEQNAQQALSRSDRGYVLETGTITREGPGKELLADDAVREAYLG 261


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: 206
Number of extensions: 7
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: 263
Length adjustment: 24
Effective length of query: 212
Effective length of database: 239
Effective search space:    50668
Effective search space used:    50668
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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