GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Stutzerimonas stutzeri A1501

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA

Query= TCDB::Q9X272
         (328 letters)



>NCBI__GCF_000013785.1:WP_011911265.1
          Length = 279

 Score =  137 bits (344), Expect = 4e-37
 Identities = 81/261 (31%), Positives = 147/261 (56%), Gaps = 19/261 (7%)

Query: 11  KPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPD 70
           +P+++   + K + +    L  ++G+ ++++EGE + ++G SG GKSTL R ++ L   D
Sbjct: 23  QPMVRFASVTKRYGE----LTVLEGLDLDVQEGEKVAIIGPSGSGKSTLLRVLMTLEGID 78

Query: 71  GGKIFFEGKDITNLND----------KEMKPYRKKMQIIFQDPLGSLNPQMT-VGRIIED 119
            G I  +G+ +T++ D          + ++  R K+ ++FQ    +L P M  +  ++E 
Sbjct: 79  DGLIEVDGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQS--FNLFPHMNALQNVMEA 136

Query: 120 PLIIHKIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIV 179
           P+ +  + +K+E R+R EELL MVG+  + +  FP + SGGQQQR+ IARALA+ PK ++
Sbjct: 137 PVQVLGL-SKREARERAEELLAMVGL-EDKLEHFPAQLSGGQQQRVAIARALAMRPKVML 194

Query: 180 CDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYG 239
            DE  SALD  +  +++ ++  + +   ++ L + H +      + +V   + G+I E G
Sbjct: 195 FDEVTSALDPELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQG 254

Query: 240 DVDKIFLNPIHPYTRALLKSV 260
             D +F NP    TR  L +V
Sbjct: 255 SPDALFNNPQEDRTREFLSAV 275


Lambda     K      H
   0.321    0.142    0.417 

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: 224
Number of extensions: 13
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: 328
Length of database: 279
Length adjustment: 27
Effective length of query: 301
Effective length of database: 252
Effective search space:    75852
Effective search space used:    75852
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 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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