Aligments for a candidate for CAT1 in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Aligments for a candidate for CAT1 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources