GapMind for catabolism of small carbon sources

 

Aligments for a candidate for citA in Cupriavidus basilensis 4G11

Align Citrate:H+ symporter (characterized)
to candidate RR42_RS07835 RR42_RS07835 membrane protein

Query= TCDB::P16482
         (444 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS07835 RR42_RS07835 membrane
           protein
          Length = 434

 Score =  298 bits (762), Expect = 3e-85
 Identities = 161/427 (37%), Positives = 244/427 (57%), Gaps = 6/427 (1%)

Query: 3   TARCSMRASSTAPVRMMATAGGARIGAILRVTSGNFLEQFDFFLFGFYATYIAHTFFPAS 62
           TA  +  +S++      A A      A++  + GN LE FD  ++GF+A  I+  FFP  
Sbjct: 2   TAVSASGSSNSGAAASAAPASRHPWRAVISASIGNALEWFDLVVYGFFAVTISALFFPNH 61

Query: 63  SEFASLMMTFAVFGAGFLMRPIGAIVLGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSY 122
            E  SL++T   FG  F MRP+GA+V+G Y D+ GRR  L +++ +M  GT +I L+P+Y
Sbjct: 62  DENTSLLLTLGTFGVSFFMRPLGAVVIGVYADRKGRRAALTLSILLMMVGTLIIALLPTY 121

Query: 123 QTIGLWAPLLVLIGRLLQGFSAGAELGGVSVYLAEIATPGRKGFYTSWQSGSQQVAIMVA 182
             IG+ AP+ +++ R++QGFSAG E G  + +LAE A P R+GFY+S+Q  SQ +  ++A
Sbjct: 122 AAIGVMAPIGIVLARMIQGFSAGGEFGSATAFLAEHA-PNRRGFYSSFQVASQGLTTLLA 180

Query: 183 AAMGFALNAVLEPSAISDWGWRIPFLFGVLIVPFIFILRRKLEETQEF-TARRHHLAMRQ 241
           A  G  L   L P  +  WGWR+PFLFG+LI P  + +RR ++ET EF  A      +R 
Sbjct: 181 AGFGAVLTTTLTPDQMQSWGWRVPFLFGLLIGPVAYYIRRHVDETPEFLQAETTDTPLRD 240

Query: 242 VFATLLANWQVVIAGMMMVAMTTTAFYLITVYAPTFGKKVLMLSASDSLLVTLLVAISNF 301
              TL    + ++  M +V + T + YL+ +Y PT+  K L L  S +   TL   +   
Sbjct: 241 ---TLSHQKERLLLAMGVVIVATVSTYLV-LYMPTYAVKQLGLPPSAAFAATLATGVVQM 296

Query: 302 FWLPVGGALSDRFGRRSVLIAMTLLALATAWPALTMLANAPSFLMMLSVLLWLSFIYGMY 361
            + P+ G  SDR+GR   +    LL L + WP   +L++ P F +ML+V + L  +  +Y
Sbjct: 297 LFAPLVGHWSDRYGRIPPMRLAALLLLVSIWPLFWLLSHYPGFGVMLAVQVVLGLMMTLY 356

Query: 362 NGAMIPALTEIMPAEVRVAGFSLAYSLATAVFGGFTPVISTALIEYTGDKASPGYWMSFA 421
            GA+    +EI P + R  G SL+Y++A  +FGGF P I T LI  TG K +P +++   
Sbjct: 357 FGALPALASEIFPVKTRTTGLSLSYNIAVTLFGGFAPFILTWLISATGSKLAPSFYLMVC 416

Query: 422 AICGLLA 428
           A+  L A
Sbjct: 417 AVVSLAA 423


Lambda     K      H
   0.329    0.139    0.421 

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: 545
Number of extensions: 26
Number of successful extensions: 5
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: 444
Length of database: 434
Length adjustment: 32
Effective length of query: 412
Effective length of database: 402
Effective search space:   165624
Effective search space used:   165624
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 (21.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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