GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltK in Rhizorhabdus wittichii RW1

Align Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit

Query= TCDB::Q9I404
         (222 letters)



>NCBI__GCF_000016765.1:WP_012048835.1
          Length = 374

 Score = 84.3 bits (207), Expect = 3e-21
 Identities = 63/205 (30%), Positives = 102/205 (49%), Gaps = 4/205 (1%)

Query: 17  GMLMTLKLMVLGVLGGVALGTVLALMRLSHSKLLSNIAGFYVNYFRSIPLLLVITWFYFA 76
           G+  T   M++ VLGG+ L  + A     H   L  +          I L L +      
Sbjct: 168 GITGTALPMIVTVLGGLTLTLITAWRGHLHKASLCTLGTIVAGSALWIVLDLGLAR---D 224

Query: 77  VPFILRW-ITGEDTPVGAFTSCLVAFMMFEAAYYCEIVRAGIQAIPKGQMGAAQALGMTY 135
           VP   R+  TG  T    F + L   +++ +A+  EIVR G+  +P+GQ  A++ALG++ 
Sbjct: 225 VPHFDRFNFTGGLTLTPEFVAVLWGSVIYASAFAAEIVRGGLDGVPRGQWEASRALGLSK 284

Query: 136 GQTMRLVILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLMDFLNSARSRGDIIGQANEFL 195
            Q++RLVI+PQA R + P +  Q I + ++++L   VG  D    A +  +  GQ  E +
Sbjct: 285 RQSLRLVIVPQALRMIVPPMNSQFITILKNSTLALVVGYPDLNFVANTAINHTGQGLEGV 344

Query: 196 IFAGLVYFVVSFTASFAVKRLQKRL 220
               LV+F ++   S A+ RL  R+
Sbjct: 345 AILMLVFFTLASAISLAMNRLNARV 369



 Score = 33.9 bits (76), Expect = 4e-06
 Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 4/61 (6%)

Query: 14  LWEGMLMTLKLMVLGVLGGVALGTVLALMRLSHSKLLSNIAGFYVNYFRSIPLLLVITWF 73
           L   + +TL ++VL  + GV +    AL R S   L   +AG +V+  R++PL++ + ++
Sbjct: 79  LGNSIALTLLIIVLSTMAGVPI----ALARHSGHMLARTLAGGFVDLVRNVPLVVQLLFW 134

Query: 74  Y 74
           Y
Sbjct: 135 Y 135


Lambda     K      H
   0.331    0.143    0.426 

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: 169
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 222
Length of database: 374
Length adjustment: 26
Effective length of query: 196
Effective length of database: 348
Effective search space:    68208
Effective search space used:    68208
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 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