GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Phyllobacterium brassicacearum STM 196

Align ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized)
to candidate WP_106713295.1 CU102_RS22265 carbohydrate ABC transporter permease

Query= BRENDA::P68183
         (296 letters)



>NCBI__GCF_003010955.1:WP_106713295.1
          Length = 281

 Score =  109 bits (272), Expect = 8e-29
 Identities = 93/289 (32%), Positives = 137/289 (47%), Gaps = 25/289 (8%)

Query: 15  ITHLLLLLFIAAIMFPLLMVVAISLRQGNFATGSLIPEQISW--DHWKLA----LGFSVE 68
           + HL  L+ +  I+ P++ +  +S+     +T  LI + + W  D   L+    L  SV 
Sbjct: 11  LVHLAALVLLVVILAPVVWLFVMSIS----STPDLIAKPLHWWPDTVDLSRYGVLLSSVA 66

Query: 69  QADGRITPPPFPVLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKGMLIF 128
            + G         +  L+NS+KVAG++ +  VAL      A+A  R P     L  ++  
Sbjct: 67  NSAGEA------FVASLFNSIKVAGMATV--VALIVAVPSAWAVSRTPSVGWSLYAVIAT 118

Query: 129 QMFPAVLSLVALYALFDRLGEYIPFIGLNTHGGVIFAYLGGIA-LHVWTIKGYFETIDSS 187
            M P V   V LY      G       LN   G+   YL  +A    W IK  F++I   
Sbjct: 119 YMLPPVALAVPLYMTLAWAGL------LNNVFGLALVYLTILAPFTTWLIKSGFDSIPRE 172

Query: 188 LEEAAALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAV 247
           +E AA LDGA   Q  RL+ LPL+ P++A   + +F+ A  E   A L   D  + TL V
Sbjct: 173 IESAATLDGARLDQILRLITLPLAAPVMATAALFAFLLAWDEFFYALLFTSDQRAKTLTV 232

Query: 248 GMQQYLNPQNYLWGDFAAAAVMSALPITIVFLLAQRWLVNGLTAGGVKG 296
            +      +   +G  A A V++ALP  +V L  QR L+ GLT+GGVKG
Sbjct: 233 AIADLAGGRVSDYGLIATAGVLAALPPLLVGLFMQRALIAGLTSGGVKG 281


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: 230
Number of extensions: 15
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: 281
Length adjustment: 26
Effective length of query: 270
Effective length of database: 255
Effective search space:    68850
Effective search space used:    68850
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: 48 (23.1 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