GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5405 in Hippea jasoniae Mar08-272r

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_035587918.1 EK17_RS04610 phosphate ABC transporter ATP-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



>NCBI__GCF_000744435.1:WP_035587918.1
          Length = 252

 Score =  134 bits (337), Expect = 2e-36
 Identities = 82/246 (33%), Positives = 137/246 (55%), Gaps = 12/246 (4%)

Query: 14  IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEE-----HQQ 68
           +I ++ +N +YG   VLKDINL++ + +   L GPSG GK+T +RC NR+ +       +
Sbjct: 6   LISVEHLNFYYGNNQVLKDINLSIYKNKITALIGPSGCGKTTFLRCFNRMHDLYKNNRYE 65

Query: 69  GRIVVDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEE 128
           G+I+  G  +    + IE +R ++GMVFQ    FP ++I  N            K +  E
Sbjct: 66  GKIIYQGENILTTKRIIE-LRGKIGMVFQKPTPFP-MSIFDNVAYGLKLKGVKNKEEIRE 123

Query: 129 IAMHYLERV----RIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEM 184
                L++      + ++  +    LSGGQQQR+ IAR L ++P I+LFDEPTSALDP +
Sbjct: 124 RVEKALKQAALWDEVKDKLFESGLSLSGGQQQRLVIARVLAVEPDIILFDEPTSALDP-I 182

Query: 185 VKEVLDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDR 244
               ++ ++   ++  T+L VTH M  A  +++   F+ KGE++E +     F NP+ + 
Sbjct: 183 ATAKIEELVSELKNITTILIVTHNMQQAARISDFTAFLFKGELIEFSETEKLFTNPEKEL 242

Query: 245 TKLFLS 250
           T+ +++
Sbjct: 243 TERYIT 248


Lambda     K      H
   0.322    0.137    0.407 

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: 162
Number of extensions: 8
Number of successful extensions: 4
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: 254
Length of database: 252
Length adjustment: 24
Effective length of query: 230
Effective length of database: 228
Effective search space:    52440
Effective search space used:    52440
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 (21.9 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