GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Cupriavidus basilensis 4G11

Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate RR42_RS14635 RR42_RS14635 proline-specific permease

Query= TCDB::P24207
         (458 letters)



>FitnessBrowser__Cup4G11:RR42_RS14635
          Length = 466

 Score =  376 bits (966), Expect = e-109
 Identities = 191/443 (43%), Positives = 274/443 (61%), Gaps = 5/443 (1%)

Query: 15  QEPTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMRQL 74
           Q   L RGL  RHI+ +ALG AIGTGLF G   AIQ AGPAVLL Y + G   +++MR L
Sbjct: 4   QSQGLQRGLSARHIRFMALGSAIGTGLFYGSASAIQTAGPAVLLAYVIGGAAVYMVMRAL 63

Query: 75  GEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPDVP 134
           GEM V  PV+GSF  +A    GP AGFL GW Y    ++V +A++TA GIYM +WFPDVP
Sbjct: 64  GEMAVRNPVAGSFGQYASTGLGPLAGFLLGWTYAFEMIVVCLADVTAFGIYMGFWFPDVP 123

Query: 135 TWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWLLFSGHG----GE 190
            WIW      +I  +NL++V+++GE EFW +L+KV AI+ MIG G+ ++  G G    G 
Sbjct: 124 RWIWVLGIVFLIGGLNLLSVKVFGELEFWLSLLKVGAIVAMIGGGVAIMLFGFGMADGGV 183

Query: 191 KASIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVV 250
              I NLW +GGF   G  G+I S AV+MF+FGG+E+IGITA EARDP++ IP+A+N V 
Sbjct: 184 ATGIHNLWTHGGFMPNGIAGVIASFAVVMFAFGGIEIIGITAGEARDPQRVIPRAINAVP 243

Query: 251 YRILLFYIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNS 310
            RILLFY+ +L VL++LYPW  + S  SPFV IF  L     A+ LN V++ A++S  NS
Sbjct: 244 LRILLFYVLTLAVLMSLYPWHRIGSEGSPFVQIFSRLGIGSAAAVLNIVVISAAVSAINS 303

Query: 311 GVYSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFGLL 370
            ++   RML+G++VQ  AP+    VSR+GVP  ++++        V++NY++P+  F L+
Sbjct: 304 DIFGAGRMLYGMAVQRQAPRIFASVSRKGVPWMTVVVMAFALLAGVVLNYVMPEDVFTLI 363

Query: 371 MALVVATLLLNWIMICLAHLRFRAAM-RRQGRETQFKALLYPFGNYLCIAFLGMILLLMC 429
            ++     +  W+MI L+ +  R  M R +    +F    +P       AF+  I  ++ 
Sbjct: 364 ASIATFATVWVWLMILLSQVALRRRMSRAEVAALKFPVPFWPVAPLAATAFMLFIFGVLG 423

Query: 430 TMDDMRLSAILLPVWIVFLFMAF 452
                R + ++  VW++ L +A+
Sbjct: 424 WFPQTRAALLVGAVWLLLLVVAW 446


Lambda     K      H
   0.329    0.143    0.447 

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: 639
Number of extensions: 30
Number of successful extensions: 3
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: 458
Length of database: 466
Length adjustment: 33
Effective length of query: 425
Effective length of database: 433
Effective search space:   184025
Effective search space used:   184025
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