GapMind for catabolism of small carbon sources

 

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

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_058859405.1 AS188_RS14300 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>NCBI__GCF_001482365.1:WP_058859405.1
          Length = 624

 Score = 90.1 bits (222), Expect = 1e-22
 Identities = 73/237 (30%), Positives = 125/237 (52%), Gaps = 18/237 (7%)

Query: 12  LQVNGVETYYGNIRA-----LAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTG 66
           L + GVE  +G+  A     L G+D+ V  G+ V+++G +G+GKSTL   +  S     G
Sbjct: 361 LVLAGVEAAHGDPAAGAPTVLRGIDLRVPAGQHVAVVGPSGSGKSTLAALLVRSMDPVAG 420

Query: 67  SVVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMG------AGLDNLKHFA 120
           SV  +G D+ R+ +    R  +A   +   +F   +V EN+++G      A ++     A
Sbjct: 421 SVSLDGHDL-RLLSLATVRGSVALLLQDSVLF-HGSVRENIRLGRPGATDAEVEQAARAA 478

Query: 121 EDVEKIFTLFPRLKERHA-QRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIV 179
           +      + FPR  +    +RG T+SGG++Q L+I RAL+    +++LDE + GL P   
Sbjct: 479 Q-AHGFVSAFPRGYDTPVGERGSTVSGGQRQRLAIARALLRDAPVVVLDEATTGLDPEAA 537

Query: 180 KGIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPE 236
           + +  A+R+L    G T   V  +A  AL  + R   + +G++ + G+  ELLA+P+
Sbjct: 538 REVVAALRRL--VRGRTSLAVTHDAALALS-ADRVLWLQDGRILLDGTPAELLADPD 591


Lambda     K      H
   0.320    0.137    0.387 

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: 345
Number of extensions: 16
Number of successful extensions: 3
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: 247
Length of database: 624
Length adjustment: 30
Effective length of query: 217
Effective length of database: 594
Effective search space:   128898
Effective search space used:   128898
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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