GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TAT in Cupriavidus basilensis 4G11

Align tryptophan permease (characterized)
to candidate RR42_RS11100 RR42_RS11100 gamma-aminobutyrate permease

Query= CharProtDB::CH_091156
         (592 letters)



>FitnessBrowser__Cup4G11:RR42_RS11100
          Length = 509

 Score =  261 bits (666), Expect = 6e-74
 Identities = 147/440 (33%), Positives = 237/440 (53%), Gaps = 17/440 (3%)

Query: 77  NLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLGE 136
           +L+R LK RHL MIAIGG++GTGLFV SG +I++ GP G ++ + + G  +   +  LGE
Sbjct: 17  DLQRKLKARHLTMIAIGGAVGTGLFVASGASISQAGPGGALLMYCLIGLMVYCLMTSLGE 76

Query: 137 ITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDPV 196
           + V  PV G+F  Y   +++    F +   Y       + +E+ AA + +QYW   +  V
Sbjct: 77  LAVHMPVAGSFVTYSALYVEEGFGFALGWSYWFSLAVTIAVELAAAQLVMQYWFPHVSGV 136

Query: 197 IWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICG---GGPDHEFI 253
           +W A F  ++  +N F VRGFGEAE+ F+ IK  T+  F+   +++I G   GGP     
Sbjct: 137 VWSAGFLLLMFGLNAFSVRGFGEAEYWFALIKVATILIFLAAGLMMIFGIMQGGPQ---- 192

Query: 254 GAKYWHD----PGCLANGFPGVLSVLVVASYSLGGIEMTCLASGE-TDP-KGLPSAIKQV 307
               WH+          G P +  V ++A +S  G E   +A+GE  DP + +P AI+Q 
Sbjct: 193 --SGWHNFTLGDAPFVGGIPAMFGVAMIAGFSFQGTETVGVAAGEAADPARTIPRAIRQT 250

Query: 308 FWRILFFFLISLTLVGFLVPYTNQNLLGGSSVD--NSPFVIAIKLHHIKALPSIVNAVIL 365
           FWRIL F+++++ ++G L+PYT+ +LL     D   SPF +  +   +     ++NAV+L
Sbjct: 251 FWRILLFYVLAILIIGVLIPYTDPSLLRNDVTDIGVSPFALVFRHAGLAFAAGLMNAVVL 310

Query: 366 ISVLSVGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSG 425
            ++LS G S ++AS+R L  +A  G  P     +   G P V + A +  G L FL    
Sbjct: 311 TALLSAGTSSMYASTRILYGLAVSGRAPRALARLSANGVPYVALFATTAVGALCFLSSLF 370

Query: 426 SMSEVFNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQGKSLDELEFVSAVGIWGSAYSA 485
               V+ WL+  +G+   I WL I +SH RFR  +  QG    +L + S +  +G  ++ 
Sbjct: 371 GDKAVYLWLLNTSGMTGFIAWLGIAISHYRFRRGLVHQGYKPSDLAYRSPLYPFGPLFAI 430

Query: 486 LINCLILIAQFYCSLWPIGG 505
           ++  +I++ Q Y +   + G
Sbjct: 431 VLCVVIVLGQNYQAFSDVRG 450


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: 768
Number of extensions: 36
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: 592
Length of database: 509
Length adjustment: 36
Effective length of query: 556
Effective length of database: 473
Effective search space:   262988
Effective search space used:   262988
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: 53 (25.0 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