GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msdB2 in Phyllobacterium leguminum ORS 1419

Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate WP_110753066.1 C7477_RS13715 carbohydrate ABC transporter permease

Query= uniprot:A3DE71
         (289 letters)



>NCBI__GCF_003217235.1:WP_110753066.1
          Length = 274

 Score =  159 bits (403), Expect = 5e-44
 Identities = 94/280 (33%), Positives = 160/280 (57%), Gaps = 17/280 (6%)

Query: 17  KDTIANIILAILVVLTLGPIVFMV--LTSLMDHNAIARGKW---IAPTRF--SNYVEVFQ 69
           K  ++ +  A+LV + + P +F    + SL     I  G +   + P RF  SNY ++F 
Sbjct: 4   KSILSKLGTALLVFVIVSPAIFFFVWMLSLSLKYEIDNGAYPPILIPERFAWSNYTQIFA 63

Query: 70  KLPFGIYFRNSLIVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQLLPGMMFL 129
           +  F +YF NSL+V  +  ++AL++   AGY +A+ K   S    ++I+  ++ PG+ +L
Sbjct: 64  ENDFLLYFWNSLLVTGMATLLALLVGVPAGYGIARLKAHKSA---VVIMIARMTPGLSYL 120

Query: 130 LPLYLDFVKIKQATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFASIPGELEEAARIDG 189
           +PL+L F    Q  G  L+ ++   +I++    VP  IWI+ G+F + P ELEEAA+IDG
Sbjct: 121 IPLFLLF----QTLG--LLGTLWPQIIIHLVVTVPIVIWIMIGYFEATPMELEEAAQIDG 174

Query: 190 CNKFTAFLRVMLPLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVTTIPAGIRGFIAYT 249
            N +  F  V LP+A PGIV + I   + +W+  +F  ++L   +  T+P  +   +++ 
Sbjct: 175 ANAWQVFRLVALPIAKPGIVVSLILAVIFSWNNFVFG-IVLASRETRTLPVAVYNMLSFE 233

Query: 250 TARYDLLMAAGTIVTIPVLIMFFTMQKKFISGMTAGAVKG 289
              +  L AA  +VT+PVL++    Q++ ++G+TAGAVKG
Sbjct: 234 QVSWGPLAAAALVVTLPVLLLTVLAQRQIVAGLTAGAVKG 273


Lambda     K      H
   0.332    0.145    0.434 

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: 247
Number of extensions: 13
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: 289
Length of database: 274
Length adjustment: 26
Effective length of query: 263
Effective length of database: 248
Effective search space:    65224
Effective search space used:    65224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 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