GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TAT in Cupriavidus basilensis 4G11

Align tryptophan permease (characterized)
to candidate RR42_RS05070 RR42_RS05070 amino acid permease

Query= CharProtDB::CH_091156
         (592 letters)



>FitnessBrowser__Cup4G11:RR42_RS05070
          Length = 466

 Score =  202 bits (515), Expect = 2e-56
 Identities = 129/394 (32%), Positives = 202/394 (51%), Gaps = 14/394 (3%)

Query: 78  LKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLGEI 137
           L R+LKP  L MIAIGG+IGTGLF+GSG AI   GP GV++ +AI     +  +  L E+
Sbjct: 8   LHRSLKPAQLAMIAIGGAIGTGLFMGSGFAIGFAGP-GVLLSYAIGALVTLLLMGCLAEM 66

Query: 138 TVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDPVI 197
           TV  P  G+F  Y   ++ P   F+V   Y       +  E+ A A+ + YW   +    
Sbjct: 67  TVAHPTSGSFGAYAEHYVSPLAGFLVRYAYWASIVLAVGTEVTAVALYMGYWFPQVPAWF 126

Query: 198 WVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICG--GGPDHEFIGA 255
           W+  F A ++ INL GV  FG  E+ FS +K + +  FI++   ++ G  G       GA
Sbjct: 127 WIVSFSAALILINLVGVGIFGAVEYLFSMVKIVAIVAFILVAAYIVFGAPGSTGSGAAGA 186

Query: 256 KYWH---DPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGET-DP-KGLPSAIKQVFWR 310
            + H     G L NG  G+   ++V+ +S   IEM  +A+GE  DP + +  A +    R
Sbjct: 187 GFHHYTAHGGFLPNGLWGMWVAVIVSIFSYLSIEMIAVAAGEAQDPERAVLQAFRSTMIR 246

Query: 311 ILFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISVLS 370
           +  F+L++L L+  +VP+        +    SPFV  ++  H+    +I+N V+LI+ LS
Sbjct: 247 LGLFYLLTLALMLAIVPWNQ------AGAQKSPFVQVMEAIHVPGAAAIINFVVLIAALS 300

Query: 371 VGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMSEV 430
             NS ++ ++RT+ S+A  G  P  FG + + G P+  ++ +S+   LA  +        
Sbjct: 301 AMNSQLYITTRTMFSLARAGQAPRSFGEVSKRGIPVRALLLSSIGIALATGLNVFYPGNA 360

Query: 431 FNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQG 464
           F  +MAI+       W  I ++H RFR    A G
Sbjct: 361 FLLMMAISMFGALFTWFMIFVTHYRFRRQWAAAG 394


Lambda     K      H
   0.326    0.141    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: 679
Number of extensions: 40
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: 592
Length of database: 466
Length adjustment: 35
Effective length of query: 557
Effective length of database: 431
Effective search space:   240067
Effective search space used:   240067
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 (21.6 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