GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Azospirillum brasilense Sp245

Align AapM, 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 AZOBR_RS08665 AZOBR_RS08665 amino acid ABC transporter permease

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__azobra:AZOBR_RS08665
          Length = 367

 Score =  336 bits (862), Expect = 5e-97
 Identities = 183/379 (48%), Positives = 237/379 (62%), Gaps = 19/379 (5%)

Query: 9   VRTSILAAEPPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAVW 68
           V T  +  E PP    G VAW+R NL  T  + +LTIL   L+  A+P L++WL   A  
Sbjct: 5   VHTGSIPDERPPANTVGPVAWLRNNLFNTWYNALLTILIAWLLFKAIPPLLDWLIFSANS 64

Query: 69  SGPDRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGILFILLL 128
            G     C              GACW F+S K    +FG +P  E+WRP I     I+++
Sbjct: 65  FGTPPQVCRQE----------GGACWTFVSEKLRFVMFGTFPYDEQWRPLIT----IVII 110

Query: 129 VPMLIPSAPR---KGLNAILLFAVLPVIAFWLLHGGFGLEVVETPLWGGLMVTLVLSFVG 185
           + +++ S  R   K   A++  A L  +   +  G  GL  VE  LWGGL +TL+LS VG
Sbjct: 111 IALVLASCDRRFWKPWLALVWIAGLTAVGVLMWGGVLGLTYVENTLWGGLPLTLMLSVVG 170

Query: 186 IAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVD 245
           ++V+ P  +LLALGRRS++P IR++ VT+IE+IRGVPLI++LFMASVM PLFLPTG N D
Sbjct: 171 LSVAFPASVLLALGRRSQLPAIRVISVTYIELIRGVPLISLLFMASVMFPLFLPTGVNFD 230

Query: 246 KLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVI 305
           KLLRA I   +F +AYMAE IRGGLQAIPKGQ+E AD+LGL YWQ    II+PQA+ + I
Sbjct: 231 KLLRAQIAFIMFAAAYMAEAIRGGLQAIPKGQYEAADALGLNYWQAMGKIILPQALAISI 290

Query: 306 PSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCF 365
           P +VNTFI  FKDTSLV IIG++DLLG  K   SD  W          +F G I+W+FC+
Sbjct: 291 PPLVNTFISFFKDTSLVIIIGLYDLLGTAKAALSDPAWRGFYR--EAYLFIGVIYWVFCY 348

Query: 366 GMSRYSGFMERHLDTGHKR 384
            MS+YS  +ER L  GH+R
Sbjct: 349 SMSKYSQKLERDLRRGHRR 367


Lambda     K      H
   0.330    0.145    0.469 

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: 515
Number of extensions: 28
Number of successful extensions: 4
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: 384
Length of database: 367
Length adjustment: 30
Effective length of query: 354
Effective length of database: 337
Effective search space:   119298
Effective search space used:   119298
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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