GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Phaeobacter inhibens BS107

Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate GFF3227 PGA1_c32800 aldehyde dehydrogenase

Query= reanno::BFirm:BPHYT_RS25810
         (796 letters)



>lcl|FitnessBrowser__Phaeo:GFF3227 PGA1_c32800 aldehyde
           dehydrogenase
          Length = 802

 Score =  943 bits (2437), Expect = 0.0
 Identities = 484/799 (60%), Positives = 582/799 (72%), Gaps = 24/799 (3%)

Query: 1   MSVAEYFSSMEYGPAPEDDQPARAWLAQHEDGFGHFIGGAWHAPAAGERFASNAPATGEQ 60
           ++V E F +M+YGPAPE    A AWL      FGHFI G + AP  G+ F S  PATGE 
Sbjct: 25  LTVKEIFETMDYGPAPESAADALAWLVDQGARFGHFINGEFTAP--GDGFDSKNPATGEV 82

Query: 61  LAQVAQGDAADIDAAVAAARAAQPGWLALGGAGRARHLYALARMVQRHSRLFAVLEALDN 120
           LA ++Q   +D+D+AV AAR AQ  W A GGA RAR+LYA+AR++Q+H+RLFAVLE LDN
Sbjct: 83  LATLSQATQSDVDSAVDAARKAQTKWSAAGGAARARYLYAIARLMQKHARLFAVLETLDN 142

Query: 121 GKPIRETRDIDVPLVARHFLHHAGWAQLQESEFADYAPLGVVGQIVPWNFPLLMLAWKIA 180
           GKPIRE+RDIDVPL  RHF +HAG AQL ESE  D   LGV GQI+PWNFPLLMLAWK+A
Sbjct: 143 GKPIRESRDIDVPLAQRHFYYHAGMAQLMESELPDREALGVCGQIIPWNFPLLMLAWKVA 202

Query: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHRAGLPAGVLNVVTGDGRTGAALVEHPQVDKI 240
           PAIA GN VVLKPAEYT LTALLFA++  +AGLP GV+N+VTGDG  G  +V    VDKI
Sbjct: 203 PAIAMGNTVVLKPAEYTSLTALLFADICRQAGLPKGVVNIVTGDGAVGEMIV-GADVDKI 261

Query: 241 AFTGSTEVGRLIRSATAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300
           AFTGST VGR IR ATAGSGK+LTLELGGKSP+IVFDDAD+D A+EG+VDAIWFNQGQVC
Sbjct: 262 AFTGSTAVGRRIREATAGSGKALTLELGGKSPYIVFDDADIDSAIEGLVDAIWFNQGQVC 321

Query: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGTSLDKSIDLGAIVDPVQLERIQSLV---ET 357
           CAGSRLLVQEGI  RF  KL+ RM+ LR+G  LDKSID+GAIVDPVQL  I  +V     
Sbjct: 322 CAGSRLLVQEGIAERFHTKLRVRMDKLRIGNPLDKSIDVGAIVDPVQLTTISEMVAANTA 381

Query: 358 GRREGCSVWQSPDTTIPSGGCFFPPTLVTGVAPASTLAQEEIFGPVLVTMSFRTPDEAIA 417
           GR     V       +P  GCF+PPTL+ G+AP+  L QEEIFGPVLV+ +FRTP EA+ 
Sbjct: 382 GRMHQAQV------AVPERGCFYPPTLIEGLAPSDALMQEEIFGPVLVSTTFRTPSEAVE 435

Query: 418 LANNSRYGLAASVWSETIGRALDVAPRLASGVVWINATNLFDAAVGFGGYRESGYGREGG 477
           LANN+RYGLAA++W+E +  ALD+AP+L +GVVW+NATNLFDAA GFGG RESG+GREGG
Sbjct: 436 LANNTRYGLAATLWTENVNLALDIAPKLVAGVVWVNATNLFDAAAGFGGTRESGFGREGG 495

Query: 478 REGIYEYLKPRAWLKLAERRAAQDVVRDAAALDPLSNVTSIDRTAKLFIGGKQARPDSGY 537
            EG+  Y KP+   K  E+        D A +D      ++DRTAK ++GGKQ RPD GY
Sbjct: 496 WEGLSAYTKPKGKTKALEK--VTGFSGDGAPVD------AVDRTAKFYVGGKQTRPDGGY 547

Query: 538 SLPVLAPDGTPVGEVAAGNRKDIRNAVEAARAAQKWSQASTHNRAQVLFYLAENLAVRAD 597
           S  + +  G  +G V  GNRKD+RNAVEAA  A  WS+ + H RAQ+L+Y+ ENL+ R  
Sbjct: 548 SKAIHSKSGGLLGHVGLGNRKDVRNAVEAAAGANAWSKTTGHLRAQILYYIGENLSARVG 607

Query: 598 EFVRQLVVRNGATEAAARAEVDASVQRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGV 657
           EF  ++    G ++ A   EV+AS+QRLFT AAWADK+DG  H  P+RGVALAM EP+GV
Sbjct: 608 EFADRIDRMTGKSQGA--QEVEASIQRLFTAAAWADKYDGQAHGVPIRGVALAMKEPVGV 665

Query: 658 IGIACPDEAPLLGFVSLAAPALAMGNRVVVLPSEASPLTVTDFYQVAETSDVPGGVLNIV 717
           IG  C DEAPLLG VS+ APA+AMGNRVV+  SEA PL+ TDFYQV ETSD+PGGV+NI+
Sbjct: 666 IGALCADEAPLLGLVSVMAPAIAMGNRVVLAASEAYPLSATDFYQVLETSDLPGGVVNIL 725

Query: 718 TGERGALLPALVKHDDVDAVWCFGSAADSTLVERESVGNLKRTFVDYGRQFDWFDRASEG 777
           TG    +   L  H +VDAVW F S+  S ++E  S GNLKRT+V+ G   DW   A   
Sbjct: 726 TGRHAEMASPLASHLNVDAVWSFSSSDLSAMIEEASAGNLKRTWVNNGLAMDW--SADHS 783

Query: 778 RPFLRQAVQVKNIWIPYGD 796
           R FL  A +VKNIWIPYG+
Sbjct: 784 RRFLEAATEVKNIWIPYGE 802


Lambda     K      H
   0.319    0.135    0.408 

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: 1702
Number of extensions: 67
Number of successful extensions: 9
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: 796
Length of database: 802
Length adjustment: 41
Effective length of query: 755
Effective length of database: 761
Effective search space:   574555
Effective search space used:   574555
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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