GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF3227
          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 (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