GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Rhizorhabdus wittichii RW1

Align AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit

Query= TCDB::Q52813
         (400 letters)



>NCBI__GCF_000016765.1:WP_012048835.1
          Length = 374

 Score =  210 bits (534), Expect = 6e-59
 Identities = 122/366 (33%), Positives = 198/366 (54%), Gaps = 15/366 (4%)

Query: 33  QILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFSSDSTYARAL 92
           Q+  ++ L G V  VA   + N+ R +     GFLR  A F I +S + ++   T A A 
Sbjct: 16  QVALLLALAGLVLVVARTVSDNMERQDMVLSLGFLRSTAEFPIAESFLAYAPGDTIAWAF 75

Query: 93  LVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFFWY 152
           +VG+ N++ + +  I  +T+ G  I + R S + L   L   +V++ RN+P ++ + FWY
Sbjct: 76  VVGLGNSIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRNVPLVVQLLFWY 135

Query: 153 LGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVASI---IIAR 209
             +L   P  R +      ++L NRG+     +   G+    + +++ ++  +   +I  
Sbjct: 136 GVILMAFPPARAAAQPLPGLFLTNRGIT----VTTVGITGTALPMIVTVLGGLTLTLITA 191

Query: 210 WAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGSVVGPEF 269
           W      A+     T+    AL        ++V    L  DVP   +FN TGG  + PEF
Sbjct: 192 WRGHLHKASLCTLGTIVAGSAL--------WIVLDLGLARDVPHFDRFNFTGGLTLTPEF 243

Query: 270 MSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIIIPP 329
           +++      Y ++F AEIVRGG+ GVP+GQ EA+ ALGL      RLV+VPQALR+I+PP
Sbjct: 244 VAVLWGSVIYASAFAAEIVRGGLDGVPRGQWEASRALGLSKRQSLRLVIVPQALRMIVPP 303

Query: 330 LTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSILTSLFMN 389
           + SQ++ + KNS+LA+ +G+ DL  V  T +N +GQ +E V I  +V+ +L+   SL MN
Sbjct: 304 MNSQFITILKNSTLALVVGYPDLNFVANTAINHTGQGLEGVAILMLVFFTLASAISLAMN 363

Query: 390 WFNAKM 395
             NA++
Sbjct: 364 RLNARV 369


Lambda     K      H
   0.327    0.141    0.432 

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: 391
Number of extensions: 16
Number of successful extensions: 2
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: 400
Length of database: 374
Length adjustment: 30
Effective length of query: 370
Effective length of database: 344
Effective search space:   127280
Effective search space used:   127280
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 (21.7 bits)
S2: 50 (23.9 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