GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Pseudomonas fluorescens FW300-N2E2

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate Pf6N2E2_1423 Gamma-aminobutyrate permease

Query= TCDB::Q2VQZ4
         (536 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1423
          Length = 466

 Score =  223 bits (567), Expect = 2e-62
 Identities = 140/400 (35%), Positives = 212/400 (53%), Gaps = 13/400 (3%)

Query: 30  NGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLAL 89
           NG L Q  K RH+ M++I G IGAGLFVGSG A+   GPA +L  YL  G++++     L
Sbjct: 10  NGHLAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPAVML-AYLFSGLLVVLVMRML 68

Query: 90  AEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDIN 149
            EMAV  P  G+F TY  + +    GF +GW Y   W+ V+P E +AA   +  W   I+
Sbjct: 69  GEMAVANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVLNQWFPAID 128

Query: 150 MAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIG 209
             ++ SV +V+L    +F V  YGE EF  ++ K+ A +GFI LG  +  G + ++   G
Sbjct: 129 AWLFASVSIVLLAVTNLFSVSKYGEFEFWFAMAKVVAIIGFISLGFAVLMGWIPEREASG 188

Query: 210 V-KYWRDPGAFTSFKGFCAV---FVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFW 265
           + +   + G F    G  AV   F+   FSF GTE V +AAAES NP ++I  A++ V W
Sbjct: 189 LSRLMEEHGGFAP-NGLSAVVGAFITIMFSFIGTEAVTIAAAESDNPAQNIAKATRSVIW 247

Query: 266 RIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVA 325
           RI +FY+L++F+V  ++P NDP L            +  A++   I     +++ V+ +A
Sbjct: 248 RIGVFYLLSIFVVISVVPWNDPLL-------ASVGSYQRALELMNIPHAKFLVDMVVLIA 300

Query: 326 VLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQG 385
           V S  NS  + ++R + ++  R  AP   K   S G P   VI     G    + +    
Sbjct: 301 VASCMNSSIYIASRMLYSLGRRGDAPKALKVTSSAGVPRSAVIASTVLGAGVTLFSYFMP 360

Query: 386 MEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINL 425
             +F +LLA +G   L V+  I ++ +RMR  ++ Q I L
Sbjct: 361 AGLFQFLLASSGAIALLVYLVIAISQLRMRRMLQRQNIEL 400


Lambda     K      H
   0.327    0.142    0.442 

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: 561
Number of extensions: 28
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: 536
Length of database: 466
Length adjustment: 34
Effective length of query: 502
Effective length of database: 432
Effective search space:   216864
Effective search space used:   216864
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: 52 (24.6 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