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_058859179.1 AS188_RS12835 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>NCBI__GCF_001482365.1:WP_058859179.1
          Length = 275

 Score =  107 bits (266), Expect = 3e-28
 Identities = 70/209 (33%), Positives = 114/209 (54%), Gaps = 12/209 (5%)

Query: 25  RALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFEGRDITRMPTHEIA 84
           RALAGV + + +G+ +++IG+NGAGKST++ TI G+    +G+V  +  D+TR+P H+ A
Sbjct: 20  RALAGVSLRLEEGDFLTVIGSNGAGKSTILNTISGTLIPDSGTVRVDDHDVTRLPEHKRA 79

Query: 85  RL--RIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDV---------EKIFTLFPRL 133
           R   R+ Q P  +   P MTV +N+ +       +     +         EK+ +L   L
Sbjct: 80  RYLSRVFQDPM-KGSSPTMTVEQNMAIAYQRGKSRGLVPGLTGARRTLFREKLASLELGL 138

Query: 134 KERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLNEAE 193
           + R   + G LSGG++Q LS+  A  + P++LLLDE +  L P     +     ++   +
Sbjct: 139 ENRLGAKVGLLSGGQRQALSLLMATFSEPRILLLDEHTAALDPQRADLVSRLTGEIVAEQ 198

Query: 194 GLTVFLVEQNAFAALRLSHRAYVMVNGKV 222
           GLT  +V  N   ALRL +R  +M  G++
Sbjct: 199 GLTTVMVTHNMEQALRLGNRLIMMHEGRI 227


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: 187
Number of extensions: 9
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: 247
Length of database: 275
Length adjustment: 25
Effective length of query: 222
Effective length of database: 250
Effective search space:    55500
Effective search space used:    55500
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: 47 (22.7 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