GapMind for catabolism of small carbon sources

 

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

Align KguT (characterized, see rationale)
to candidate Pf6N2E2_1312 4-hydroxyphenylacetate symporter, major facilitator superfamily (MFS)

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1312
          Length = 434

 Score =  200 bits (508), Expect = 8e-56
 Identities = 126/423 (29%), Positives = 205/423 (48%), Gaps = 19/423 (4%)

Query: 4   DRLAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYF 63
           DR      W +MP++ + Y  A+LDR N GFA    M+ DL  +  +      LFF+ Y 
Sbjct: 16  DRTHATITWRLMPLLLVCYLFAHLDRINIGFAKMQ-MSADLQFSDTVYGFGAGLFFIAYA 74

Query: 64  FFQVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAM 123
            F VP  +  ++   ++ I   +++WG L++   ++ S +    +RFLLGV EA   P +
Sbjct: 75  LFGVPSNMALDRVGPRRWIATLMVVWGALSSGMFLIDSAAGFYVLRFLLGVAEAGFFPGI 134

Query: 124 LIYLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHF-------DWRWMFIIEGL 176
           L++L  W+    R++      +  P+  +    +SG +++HF        W+WMF+IEGL
Sbjct: 135 LVFLNRWYPARRRAQVTALFAIAVPMAGVIGGPLSGGILEHFHDVGGLRGWQWMFVIEGL 194

Query: 177 PAVLWAFIWWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIIL 236
           P +L   +  + + D  E   WL    K  LRE L+ E+Q  K + ++     +P+V +L
Sbjct: 195 PVILLGLVVLKCLPDDFETVKWLTPHAKQQLREQLSLEEQR-KSITSFSAILNNPQVWLL 253

Query: 237 SLQYFCWSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQK 296
              YF   + V     W+P+++  A        G LSAVPYL     M+G   +SDR ++
Sbjct: 254 VAVYFAVMLAVNTLAFWMPTLIHGAGIGSDGKVGLLSAVPYLAGCFFMIGCGRSSDRHRE 313

Query: 297 RKRFVWPPLLIAALAFYGSYILGTEHFWWSYTL--LVIAGACMYAPYGPFFAIVPELLPS 354
           R+  +  PLL+AAL   G  + G         L  L++AG    A    F+ + P  L +
Sbjct: 314 RRWHLCVPLLMAAL---GIAVTGLSPGNPILVLSGLIVAGMGASAALPMFWQLPPAFLSN 370

Query: 355 NVAGGAMALINSMGALGSFSGSWLVGYLNGVTGGP-----GASYLFMCGALLVAVALTAV 409
                 +ALI+S G++ SF   +L+G++   T          + L   G LLV     A+
Sbjct: 371 GTQAAGIALISSFGSIASFFAPYLIGWMRDTTQSASLALYALALLIALGGLLVLRTHAAI 430

Query: 410 LNP 412
           +NP
Sbjct: 431 VNP 433


Lambda     K      H
   0.328    0.140    0.457 

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: 584
Number of extensions: 29
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 425
Length of database: 434
Length adjustment: 32
Effective length of query: 393
Effective length of database: 402
Effective search space:   157986
Effective search space used:   157986
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: 51 (24.3 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