GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5405 in Magnetospirillum magneticum AMB-1

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_011384493.1 AMB_RS10565 ABC transporter ATP-binding protein

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



>NCBI__GCF_000009985.1:WP_011384493.1
          Length = 257

 Score =  139 bits (350), Expect = 6e-38
 Identities = 82/243 (33%), Positives = 140/243 (57%), Gaps = 8/243 (3%)

Query: 15  IQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVVD 74
           I++ GV+K +G   VL  I+L+V +GE +V+ G SG+GKS  ++C+  L   + G I +D
Sbjct: 7   IELTGVHKAFGPKVVLDGIDLSVARGESVVVIGGSGTGKSVMLKCILGLLRPESGSIRID 66

Query: 75  GVELTN-DLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHY 133
           G ++     K  + I ++ GM+FQ   LF  L + +N     +  +KM + KA +IA+  
Sbjct: 67  GEDVVGMGPKDRDRIMKKFGMLFQGGALFDSLKVWENVAFGLIQGQKMERAKARDIAIEK 126

Query: 134 LERVRIPEQAHKY-PGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTM 192
           L +V +     +  P +LSGG Q+RV++ARA+   P+I+ FDEPT+ LDP M   + D +
Sbjct: 127 LAQVGLAASTGELSPSELSGGMQKRVSLARAIATNPEIIFFDEPTTGLDPIMADVINDLI 186

Query: 193 IGLAED-GMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLSQ 251
           +   ++ G T L +TH+M  AR +++R+  + KG ++    P    D+  N+    ++ Q
Sbjct: 187 VKCCKEVGATALSITHDMASARKISDRIAMLYKGRLI-WVGPAKDIDHSGNE----YVDQ 241

Query: 252 ILH 254
            +H
Sbjct: 242 FIH 244


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: 167
Number of extensions: 9
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: 257
Length adjustment: 24
Effective length of query: 230
Effective length of database: 233
Effective search space:    53590
Effective search space used:    53590
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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