GapMind for catabolism of small carbon sources

 

Alignments for a candidate for permease in Cupriavidus basilensis 4G11

Align Histidine permease HisP (characterized)
to candidate RR42_RS11100 RR42_RS11100 gamma-aminobutyrate permease

Query= SwissProt::A2RI97
         (477 letters)



>FitnessBrowser__Cup4G11:RR42_RS11100
          Length = 509

 Score =  468 bits (1205), Expect = e-136
 Identities = 228/472 (48%), Positives = 326/472 (69%), Gaps = 6/472 (1%)

Query: 5   NQVKRNLKQRHITMIALGGTIGTGLFLTSGATISQAGPWGAVLAYCFIGIMVYFVMTSLG 64
           + ++R LK RH+TMIA+GG +GTGLF+ SGA+ISQAGP GA+L YC IG+MVY +MTSLG
Sbjct: 16  DDLQRKLKARHLTMIAIGGAVGTGLFVASGASISQAGPGGALLMYCLIGLMVYCLMTSLG 75

Query: 65  EMATYLPTSGSFSDYGGRYVDPAFGFALGWNYWLNGAITIAVDLTTAGLITQFWFPHLPS 124
           E+A ++P +GSF  Y   YV+  FGFALGW+YW + A+TIAV+L  A L+ Q+WFPH+  
Sbjct: 76  ELAVHMPVAGSFVTYSALYVEEGFGFALGWSYWFSLAVTIAVELAAAQLVMQYWFPHVSG 135

Query: 125 WIFSGIATVLIFIINVMAVGAFGETEYWLSTIKVITIVLFLAIGLLTIFGVLGQGNVDVV 184
            ++S    +L+F +N  +V  FGE EYW + IKV TI++FLA GL+ IFG++  G     
Sbjct: 136 VVWSAGFLLLMFGLNAFSVRGFGEAEYWFALIKVATILIFLAAGLMMIFGIMQGGPQSGW 195

Query: 185 ANLTAGNHGFVGGISGFVGVLLIAGFSFQGTEMLGITAGESEDPGKTIPKAMNSIFWRIL 244
            N T G+  FVGGI    GV +IAGFSFQGTE +G+ AGE+ DP +TIP+A+   FWRIL
Sbjct: 196 HNFTLGDAPFVGGIPAMFGVAMIAGFSFQGTETVGVAAGEAADPARTIPRAIRQTFWRIL 255

Query: 245 LFYIFSIIVIAAIINFKDPRLLNPSSTAV-MSPFTIVFKNIGFAVAASVMNAVILTSVIS 303
           LFY+ +I++I  +I + DP LL    T + +SPF +VF++ G A AA +MNAV+LT+++S
Sbjct: 256 LFYVLAILIIGVLIPYTDPSLLRNDVTDIGVSPFALVFRHAGLAFAAGLMNAVVLTALLS 315

Query: 304 SANSVMYASTRILYSLGQEKGAPKFFGRTAKNGIPFYALLATTIICFIAFLTGIFGTQ-I 362
           +  S MYASTRILY L     AP+   R + NG+P+ AL ATT +  + FL+ +FG + +
Sbjct: 316 AGTSSMYASTRILYGLAVSGRAPRALARLSANGVPYVALFATTAVGALCFLSSLFGDKAV 375

Query: 363 YLFLIDLSSLTGFLAWLGISVSHIRFRRAYIAQGKKLEDLPYKAKWFPFGPIVALLMTGA 422
           YL+L++ S +TGF+AWLGI++SH RFRR  + QG K  DL Y++  +PFGP+ A+++   
Sbjct: 376 YLWLLNTSGMTGFIAWLGIAISHYRFRRGLVHQGYKPSDLAYRSPLYPFGPLFAIVLCVV 435

Query: 423 IAINLDPAMLFSE---HWGEGLALYAAIPIFIVLYFGYKWKYNTKIIPLEEV 471
           I +  +    FS+    W E +  Y  +P+F+VL+ GY+    T++I  E++
Sbjct: 436 IVLGQN-YQAFSDVRGRWLEIVGTYIGVPLFLVLWLGYRLVKKTRLIDYEDM 486


Lambda     K      H
   0.327    0.142    0.438 

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: 773
Number of extensions: 51
Number of successful extensions: 4
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: 477
Length of database: 509
Length adjustment: 34
Effective length of query: 443
Effective length of database: 475
Effective search space:   210425
Effective search space used:   210425
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