GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapM in Pseudomonas fluorescens FW300-N2E3

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 AO353_04605 AO353_04605 amino acid ABC transporter permease

Query= TCDB::Q52814
         (384 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_04605 AO353_04605 amino acid
           ABC transporter permease
          Length = 365

 Score =  389 bits (999), Expect = e-113
 Identities = 200/376 (53%), Positives = 255/376 (67%), Gaps = 15/376 (3%)

Query: 11  TSILAAEPPPPGER-GAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAVWS 69
           T I   + PPPG R G +AW+R ++ ++  + +LT+ A  LI   VP +++W  + A W 
Sbjct: 3   THIFKPDMPPPGTRIGILAWMREHMFSSWINTLLTLFAFYLIYLVVPPILHWAILDANWV 62

Query: 70  GPDRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGILFILLLV 129
           G  R  C              GACW FI  ++ QF++G YP   RWR  +   L ++ + 
Sbjct: 63  GTTRADCTK-----------EGACWVFIQQRFGQFMYGYYPPELRWRVDLTVWLAVIGVA 111

Query: 130 PMLIPSAPRKGLNAILLFAVLPVIAFWLLHGGF-GLEVVETPLWGGLMVTLVLSFVGIAV 188
           P+ I   PRK +  +    + P++A+ LLHG   GL  V T  WGGLM+TLV++ VGI  
Sbjct: 112 PLFISRFPRKAVYGLSFLVLYPIVAYILLHGDILGLTNVATSQWGGLMLTLVIATVGIVG 171

Query: 189 SLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLL 248
           +LP+GI+LALGRRS +P IR++CVTFIE  RGVPLITVLFM+SVMLPLFLP G N DKLL
Sbjct: 172 ALPLGIMLALGRRSNLPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLL 231

Query: 249 RALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSI 308
           RALIGV +F SAY+AEV+RGGLQAIPKGQ+E A ++GLGYW+   L+I+PQA+KLVIP I
Sbjct: 232 RALIGVILFQSAYVAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGI 291

Query: 309 VNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMS 368
           VNTFI  FKDTSLV IIG+FDLL  VK   +D  W    T   G +FA  +FW+FCFGMS
Sbjct: 292 VNTFIALFKDTSLVIIIGLFDLLNSVKQAAADPKWLGMAT--EGYVFAALVFWIFCFGMS 349

Query: 369 RYSGFMERHLDTGHKR 384
           RYS  +ER LDTGHKR
Sbjct: 350 RYSMHLERKLDTGHKR 365


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: 576
Number of extensions: 27
Number of successful extensions: 5
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: 365
Length adjustment: 30
Effective length of query: 354
Effective length of database: 335
Effective search space:   118590
Effective search space used:   118590
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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