GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguT in Burkholderia phytofirmans PsJN

Align KguT (characterized, see rationale)
to candidate BPHYT_RS30610 BPHYT_RS30610 major facilitator transporter

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__BFirm:BPHYT_RS30610
          Length = 429

 Score =  230 bits (586), Expect = 7e-65
 Identities = 137/404 (33%), Positives = 205/404 (50%), Gaps = 16/404 (3%)

Query: 12  WYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAI 71
           W ++P +   Y  AYLDR N GFA    M  DL  + A   +   +FF+GY  F++P  +
Sbjct: 22  WRLLPFLVTCYMFAYLDRVNVGFAKLQ-MQTDLGFSDAAYGVGAGIFFIGYVLFELPSNL 80

Query: 72  YAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWF 131
              K   ++     L+LWG  +     V+SV    A+RFLLGV EA   P M+ YL  W+
Sbjct: 81  MLPKVGARRTFSRILVLWGITSACMLFVRSVPAFYAMRFLLGVFEAGFAPGMIYYLSCWY 140

Query: 132 TRAERSRANTFL--------ILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVLWAF 183
             A  +RA   +        I+G PV+   M+ +SG +     W+WMF++EGLP +    
Sbjct: 141 GPARMARAIALVFVAGPLGGIVGGPVSAWLMTSLSG-VGGLAGWQWMFLVEGLPCIALGL 199

Query: 184 IWWRLVDDRPEQASWLKAQEKTAL-REALAAEQQGIKPVKNYREAFRSPKVIILSLQYFC 242
           +  R++ DRPEQA WL   EK  L RE    E +      +++   +SP+V +L+  YF 
Sbjct: 200 LTLRVLSDRPEQARWLNDDEKLLLGRETAPTEHR----ADSFKAVLKSPRVYVLAFAYFS 255

Query: 243 WSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVW 302
               +Y    WLP++LK+    D +  GW SA+PY+ A + M     +SDR+ +R+    
Sbjct: 256 IIFPIYAISFWLPTLLKEQGVSDTIRLGWYSAIPYVVAAVCMYLAGRSSDRVGERRYHCA 315

Query: 303 PPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMA 362
            P L AA+    + I    +   + T L +  AC++  Y  F+AI  +L+    A G +A
Sbjct: 316 IPALGAAICLIAA-IFADGNVMLTLTALTLGTACLWMAYTVFWAIPSQLVEGTAAAGGIA 374

Query: 363 LINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVAL 406
           LIN++G  G F GS +VG+    TG   A    M GA  +A  L
Sbjct: 375 LINTVGLSGGFWGSAVVGWAKASTGSMHAGLFVMAGAAALAAIL 418


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: 606
Number of extensions: 34
Number of successful extensions: 7
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: 425
Length of database: 429
Length adjustment: 32
Effective length of query: 393
Effective length of database: 397
Effective search space:   156021
Effective search space used:   156021
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