GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_04605
          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 (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