GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc7a1 in Dyella japonica UNC79MFTsu3.2

Align high affinity cationic amino acid transporter 1 (characterized)
to candidate N515DRAFT_2924 N515DRAFT_2924 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)

Query= CharProtDB::CH_091324
         (622 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2924
          Length = 492

 Score =  258 bits (659), Expect = 4e-73
 Identities = 151/423 (35%), Positives = 232/423 (54%), Gaps = 33/423 (7%)

Query: 25  ESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLCY 84
           E+ L R L    LV LG+G+ +GAG++V+ G  A E+AGPAIV+SF+ A +A  LA LCY
Sbjct: 26  EATLKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALCY 85

Query: 85  GEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELIGKPI 144
            EF A +P +GSAY YSY T+GE  A+  GW+L+L Y+   ++VA  WS  F++L+    
Sbjct: 86  AEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALIS 145

Query: 145 GEFSRQHMALNAPGVLAQTP---------------DIFAVIIIIILTGLLTLGVKESAMV 189
           G        ++ P  LA  P               ++ AV II  +TGL  +G+ +SA V
Sbjct: 146 GWIGHD---VSLPQTLAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFV 202

Query: 190 NKIFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVL 249
           N I   I V V+   +                K  + +N    +   EG    +G++GV 
Sbjct: 203 NSIIVAIKVTVILLFIA------------FATKYINPDNWHPFIPASEGA-SKYGWAGVG 249

Query: 250 SGAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYFC 309
             AA  F++++GFD ++T   E KNPQ+ +P+GI+ SL++C I Y  V+  LT +  +  
Sbjct: 250 RAAAIVFFSYIGFDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADFRL 309

Query: 310 LDIDSPLPGAF-KHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFL 368
           L    P+  A   +      +  V IG++  LS+ +L  +   PR+ Y+MA DGL+    
Sbjct: 310 LGTPEPVSTALDNYPSLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVF 369

Query: 369 AKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLRY-QP 427
            +I+ + +TP + TV  G +AA +  LF +  L +++++GTLLA++ V   VLVLRY +P
Sbjct: 370 GRIHQKFRTPHVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRP 429

Query: 428 EQP 430
           E P
Sbjct: 430 ELP 432



 Score = 40.4 bits (93), Expect = 2e-07
 Identities = 36/118 (30%), Positives = 55/118 (46%), Gaps = 9/118 (7%)

Query: 491 ISAGLLAALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCMLVTGIIWRQPESKTKLS 550
           +  G+LAA +  +  + VLG E +A GTL A         +C+ V  + + +PE     +
Sbjct: 384 VVVGVLAAALGGLFNIGVLG-EMVAMGTLLAF------ATVCIGVLVLRYTRPELPR--A 434

Query: 551 FKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGIWHSEEASLAA 608
           F+VP   ++  L     + L +Q     W     W+ IG  IYF YG  HS+    AA
Sbjct: 435 FRVPVPWIVCPLGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSKLRKPAA 492



 Score = 25.0 bits (53), Expect = 0.008
 Identities = 29/134 (21%), Positives = 52/134 (38%), Gaps = 27/134 (20%)

Query: 485 SGLIVNISAGLLAALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCMLVTGIIWRQPE 544
           +G+ +N+ A  + A I  +C V +  + A     + A+ V   +V+L  +     +  P+
Sbjct: 173 TGMFINLPAVAIIAAITGLCYVGIT-QSAFVNSIIVAIKV---TVILLFIAFATKYINPD 228

Query: 545 SKTKLSFKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGIWHSEEA 604
           +        PF+P     S +             W        I F  Y G+     +  
Sbjct: 229 NWH------PFIPASEGASKY------------GWAGVGRAAAIVFFSYIGF-----DAV 265

Query: 605 SLAAGQAKTPDSNL 618
           S AAG+AK P  ++
Sbjct: 266 STAAGEAKNPQRDM 279


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: 773
Number of extensions: 49
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 622
Length of database: 492
Length adjustment: 36
Effective length of query: 586
Effective length of database: 456
Effective search space:   267216
Effective search space used:   267216
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