GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proP in Burkholderia phytofirmans PsJN

Align proline porter II (characterized)
to candidate BPHYT_RS08740 BPHYT_RS08740 membrane protein

Query= CharProtDB::CH_024324
         (500 letters)



>FitnessBrowser__BFirm:BPHYT_RS08740
          Length = 427

 Score =  266 bits (681), Expect = 8e-76
 Identities = 145/415 (34%), Positives = 229/415 (55%), Gaps = 19/415 (4%)

Query: 22  KLRKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPL 81
           K+ + I AAS+GNA+EWFD  VYGF A  + K+FFP    ++ ++  L TF + ++IRPL
Sbjct: 17  KVHRIILAASIGNALEWFDLVVYGFFAVTIAKLFFPARTEAISLMLTLGTFGISYMIRPL 76

Query: 82  GGLFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSV 141
           GGL  G L D+ GR+  L ++I +M + T  I ++P Y  IG+WAP  +++ ++ QGFS 
Sbjct: 77  GGLVLGSLADRAGRKASLLLSIALMMVGTLTIAVMPPYAAIGLWAPAGIMLSRLVQGFSA 136

Query: 142 GGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWR 201
           GGE+  ++ F+ E++P+R RGFMGSW         +L +G   L+++ +  A    WGWR
Sbjct: 137 GGEFGASTAFLVEHAPER-RGFMGSWQFASQGMATLLASGFGALLTSQLTSAQLESWGWR 195

Query: 202 IPFFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSL 261
           +PF   L +G +G Y+R  ++E   F       E   R  L+D          T+  R L
Sbjct: 196 VPFLFGLAIGPVGFYIRRYVDEGAEF-----NAEPKARTPLRD-------LFGTQKVRML 243

Query: 262 LTCIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQPVMGLLSDR 321
           L    L+I+T   Y +L  YMP+Y    LH     G    +A  + +  + P  G LSDR
Sbjct: 244 LAVGSLIISTAANYMIL--YMPTYAIKQLHLPASTGFAATLATGVVLTVLTPFAGHLSDR 301

Query: 322 FGRRPFVLLGSVALFVLAIPAFILINS--NVIGLIFAGLLMLAVILNCFTGVMASTLPAM 379
            GR   +   +V + V   PAF+ +N+  + + ++ A L+ + V+   + G + + +  +
Sbjct: 302 LGRIRIMATAAVLMLVTVYPAFVYMNAHPSFVTMLLA-LIWIGVLKATYFGALPALMSEI 360

Query: 380 FPTHIRYSALAAAFNISVLV-AGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLI 433
           FPT  R + LA ++NI V V  G  P +  WL+++S N + P +YLM  AV  L+
Sbjct: 361 FPTQTRATGLAVSYNIGVTVFGGFAPFVITWLIDASGNKLAPGFYLMFCAVASLL 415


Lambda     K      H
   0.327    0.142    0.429 

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: 575
Number of extensions: 28
Number of successful extensions: 6
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: 500
Length of database: 427
Length adjustment: 33
Effective length of query: 467
Effective length of database: 394
Effective search space:   183998
Effective search space used:   183998
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: 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