GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Phyllobacterium leguminum ORS 1419

Align ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized)
to candidate WP_110753066.1 C7477_RS13715 carbohydrate ABC transporter permease

Query= BRENDA::P68183
         (296 letters)



>NCBI__GCF_003217235.1:WP_110753066.1
          Length = 274

 Score =  127 bits (318), Expect = 4e-34
 Identities = 87/285 (30%), Positives = 146/285 (51%), Gaps = 27/285 (9%)

Query: 16  THLLLLLFIAAIMFPLLMVVAISLRQGNFATGS----LIPEQISWDHWKLALGFSVEQAD 71
           T LL+ + ++  +F  + ++++SL+      G+    LIPE+ +W ++      +     
Sbjct: 12  TALLVFVIVSPAIFFFVWMLSLSLKY-EIDNGAYPPILIPERFAWSNYTQIFAEN----- 65

Query: 72  GRITPPPFPVLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMF 131
                     LL+ WNS+ V G++ +  + +     Y  AR++    A ++   +I +M 
Sbjct: 66  --------DFLLYFWNSLLVTGMATLLALLVGVPAGYGIARLKAHKSAVVI---MIARMT 114

Query: 132 PAVLSLVALYALFDRLGEYIPFIGLNTHGGVIFAYLGGIALHVWTIKGYFETIDSSLEEA 191
           P +  L+ L+ LF  LG     +G      +I   +  + + +W + GYFE     LEEA
Sbjct: 115 PGLSYLIPLFLLFQTLG----LLG-TLWPQIIIHLVVTVPIVIWIMIGYFEATPMELEEA 169

Query: 192 AALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQ 251
           A +DGA  WQ FRLV LP++ P + V  IL+ I +     V  ++L    + TL V +  
Sbjct: 170 AQIDGANAWQVFRLVALPIAKPGIVVSLILAVIFSWNNF-VFGIVLASRETRTLPVAVYN 228

Query: 252 YLNPQNYLWGDFAAAAVMSALPITIVFLLAQRWLVNGLTAGGVKG 296
            L+ +   WG  AAAA++  LP+ ++ +LAQR +V GLTAG VKG
Sbjct: 229 MLSFEQVSWGPLAAAALVVTLPVLLLTVLAQRQIVAGLTAGAVKG 273


Lambda     K      H
   0.328    0.141    0.435 

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: 259
Number of extensions: 20
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: 296
Length of database: 274
Length adjustment: 26
Effective length of query: 270
Effective length of database: 248
Effective search space:    66960
Effective search space used:    66960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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