GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Persephonella marina EX-H1

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_012676070.1 PERMA_RS08615 ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b20002
         (358 letters)



>NCBI__GCF_000021565.1:WP_012676070.1
          Length = 224

 Score =  114 bits (286), Expect = 2e-30
 Identities = 66/203 (32%), Positives = 108/203 (53%), Gaps = 9/203 (4%)

Query: 16  LEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTIDDVRMNDVDPSK- 74
           ++ +KG+DL+I  GE V  +GPSG GKSTLL +I G++  + G + I    +  ++  + 
Sbjct: 22  IDALKGIDLEIYEGEMVALMGPSGSGKSTLLHLIGGIDIPTEGKVFIHGTDIFSLNEKRL 81

Query: 75  -----RGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGALLDR 129
                  I  VFQ + L P  T  EN+ F ++     + + E++  E    L L   ++ 
Sbjct: 82  ARFRNENIGFVFQFHYLLPEFTALENVMFPVQIYS--KGDAEEKAREILERLGLSHRINH 139

Query: 130 KPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLATTIVY 189
           KP Q+SGG++QRVAI RAIV  P I + DEP  NLD+     +      ++ +   TI+ 
Sbjct: 140 KPSQMSGGEQQRVAIARAIVNRPSIIIADEPTGNLDSRNTETVMKIFREMNDKDNVTIII 199

Query: 190 VTHDQVEAMTLADKIVVMRAGVV 212
            THD+ +      + + +R G++
Sbjct: 200 ATHDK-DVANYCKRTIYLRDGIL 221


Lambda     K      H
   0.321    0.139    0.396 

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: 173
Number of extensions: 7
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: 358
Length of database: 224
Length adjustment: 26
Effective length of query: 332
Effective length of database: 198
Effective search space:    65736
Effective search space used:    65736
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 Apr 09 2024. 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