GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Kocuria flava HO-9041

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_058859430.1 AS188_RS14460 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q8DQH7
         (236 letters)



>NCBI__GCF_001482365.1:WP_058859430.1
          Length = 269

 Score =  105 bits (263), Expect = 7e-28
 Identities = 71/228 (31%), Positives = 122/228 (53%), Gaps = 12/228 (5%)

Query: 6   VENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEFLGQ 65
           VE+L   YG ++ ++ +S  V  G+VV LIG +G+GK+T+LR ++ L  P  G+I     
Sbjct: 23  VEDLHKSYGSLEVLKGISLTVAAGQVVCLIGPSGSGKSTLLRCVNLLETPQKGRITIGDV 82

Query: 66  EIQKMPAQ-KIVAGGLSQVPEGRHVFPGLTVMENLEMGAF--LKKNREENQ----ANLKK 118
           E+    A    +   +  V +  ++FP L+V+EN  +     LK+ + E +    ANL++
Sbjct: 83  EVTDPEADVDRLRRHVGMVFQQFNLFPHLSVLENCTVAQVKVLKREKAEAERIARANLER 142

Query: 119 VFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDI 178
           V      L E+ +     LSGG+QQ +A+ RAL   P L+L DEP+  L P  + ++  I
Sbjct: 143 V-----GLAEKADGYPDQLSGGQQQRVAIARALSMDPSLMLFDEPTSALDPETVGDVLAI 197

Query: 179 IQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASS 226
           ++ +  +G T+L++      A  ++DR   ++ G +V  G   E+  S
Sbjct: 198 MRSLAAEGMTMLVVTHEMEFARDVADRVVFMDGGVVVEEGPAAEVIGS 245


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: 122
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: 269
Length adjustment: 24
Effective length of query: 212
Effective length of database: 245
Effective search space:    51940
Effective search space used:    51940
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.

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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