GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CAT1 in Pedobacter sp. GW460-11-11-14-LB5

Align high affinity cationic amino acid transporter 1 (characterized)
to candidate CA265_RS17395 CA265_RS17395 amino acid transporter

Query= CharProtDB::CH_091324
         (622 letters)



>FitnessBrowser__Pedo557:CA265_RS17395
          Length = 483

 Score =  224 bits (570), Expect = 9e-63
 Identities = 134/409 (32%), Positives = 219/409 (53%), Gaps = 22/409 (5%)

Query: 25  ESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLCY 84
           E  L R L   +L+ +GVG TLGAG++ + G  A  ++GPA+ +SF+IAAL    A LCY
Sbjct: 17  EGSLKRTLGPINLILIGVGLTLGAGLFSITGLAAANHSGPAVTLSFVIAALGCGFAALCY 76

Query: 85  GEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELIGK-- 142
            EF + +P  GSAY YSY T+GEL+A+I GW+L+L Y +G ++VA +WS    + +    
Sbjct: 77  AEFASMIPVAGSAYTYSYATMGELFAWIIGWDLVLEYSVGCATVAISWSQYLTKFLASLH 136

Query: 143 ----PIGEFSRQHMALNAPG-VLAQTPDIFAVIIIIILTGLLTLGVKESAMVNKIFTCIN 197
               P    S    A  A G  +    +I A ++++++T +L  G K SA+VN I   + 
Sbjct: 137 IYLPPQLTLSPFETAKLADGSTVNGIINIPAALVVVLMTAILIRGTKGSAIVNGIIVFLK 196

Query: 198 V-LVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSGAATCF 256
           V +VL FI +          WQ  +      N    +    G F  FG+SGVL GA   F
Sbjct: 197 VGVVLVFIAL---------GWQYIDP----ANYHPYIPENTGTFGQFGWSGVLRGAGLVF 243

Query: 257 YAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPY-FCLDIDSP 315
           + F+GFD +A + +E KNP + +P+GI+ SLL+C + +      +T +  Y    +  +P
Sbjct: 244 FVFIGFDAVAASAQETKNPARDLPIGIIGSLLVCTVLFGLFGHVMTGLANYKEFANSGAP 303

Query: 316 LPGAFKHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKINNRT 375
           +  A +   +     A+ +  L   ++ +L  +    R+ Y++++DGLL K  + ++ + 
Sbjct: 304 VAIAIEKTPYAWLSQAIILAILIGYTSVILIDLMAQSRMFYSISKDGLLPKMFSDVHAKF 363

Query: 376 KTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLR 424
           KTP  + +       + A    +  + ++ SIGTLLA+ +V   +L+LR
Sbjct: 364 KTPYKSNIILCVFIGLFAAFVPMNVVGEMTSIGTLLAFLMVCVGILILR 412



 Score = 69.7 bits (169), Expect = 3e-16
 Identities = 52/143 (36%), Positives = 75/143 (52%), Gaps = 19/143 (13%)

Query: 455 SESQTGFLPVAEKFSLKSILSPKNVEPSKFSGLIVNISAGLLAALIITVCIVAVLGREAL 514
           S S+ G LP      + S +  K   P K S +I+ +  GL AA +     + V+G E  
Sbjct: 345 SISKDGLLP-----KMFSDVHAKFKTPYK-SNIILCVFIGLFAAFVP----MNVVG-EMT 393

Query: 515 AEGTLWAVFVMTGSVLLCMLVTGIIWRQPESKTKLSFKVPFVPVLPVLSIFVNIYLMMQL 574
           + GTL A  ++   +L        I R+   + K  FKVPFVP++P+L I   I +M+ L
Sbjct: 394 SIGTLLAFLMVCVGIL--------ILRKTNPEAKRPFKVPFVPLIPILGILTCIAMMVFL 445

Query: 575 DQGTWVRFAVWMLIGFTIYFGYG 597
              TW+R AVW++IG  IYF YG
Sbjct: 446 PWETWLRLAVWLIIGLAIYFWYG 468


Lambda     K      H
   0.324    0.138    0.417 

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: 769
Number of extensions: 35
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 622
Length of database: 483
Length adjustment: 36
Effective length of query: 586
Effective length of database: 447
Effective search space:   261942
Effective search space used:   261942
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 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