GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Dinoroseobacter shibae DFL-12

Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)

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



>lcl|FitnessBrowser__Dino:3609634 Dshi_3017 aldehyde dehydrogenase
           (RefSeq)
          Length = 780

 Score =  967 bits (2499), Expect = 0.0
 Identities = 495/795 (62%), Positives = 588/795 (73%), Gaps = 16/795 (2%)

Query: 1   MSVAEYFSSMEYGPAPEDDQPARAWLAQHEDGFGHFIGGAWHAPAAGERFASNAPATGEQ 60
           M+V E F +MEYGPAPEDD PA+AWL +H   FG FIGG + AP  G+ FA+  PA G +
Sbjct: 1   MTVKEIFETMEYGPAPEDDGPAQAWLDRHGRRFGVFIGGTFQAP--GKTFATRNPARGTE 58

Query: 61  LAQVAQGDAADIDAAVAAARAAQPGWLALGGAGRARHLYALARMVQRHSRLFAVLEALDN 120
           LAQV QG  ADI+AAV AAR AQP W  LGG G AR LYA+AR++Q+HSRLFAVLE LDN
Sbjct: 59  LAQVTQGTEADIEAAVTAARRAQPAWARLGGQGWARVLYAIARLLQKHSRLFAVLETLDN 118

Query: 121 GKPIRETRDIDVPLVARHFLHHAGWAQLQESEFADYAPLGVVGQIVPWNFPLLMLAWKIA 180
           GKPIRE+RDID+PL  RHF +HAG A L E E  D  P+GV GQIVPWNFPLLMLAWKIA
Sbjct: 119 GKPIRESRDIDIPLAQRHFYYHAGMAALMEDELPDRVPVGVCGQIVPWNFPLLMLAWKIA 178

Query: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHRAGLPAGVLNVVTGDGRTGAALVEHPQVDKI 240
           PA+A GN VVLKPAE+TPLTALLFAE+   AG+P GV+N+VTGDG TGAALV HP VDKI
Sbjct: 179 PALAMGNTVVLKPAEWTPLTALLFAEICGEAGVPPGVVNIVTGDGATGAALVSHPGVDKI 238

Query: 241 AFTGSTEVGRLIRSATAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300
           AFTGST+VGR IR ATAG+GK+LTLELGGKSP++VF+DADLD AVEG+VDAIWFNQGQVC
Sbjct: 239 AFTGSTDVGREIRRATAGTGKALTLELGGKSPYVVFEDADLDSAVEGLVDAIWFNQGQVC 298

Query: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGTSLDKSIDLGAIVDPVQLERIQSLVETGRR 360
           CAGSRLLVQEGI   F AKL+ RM TLR+G  LDK ID+GA+VDP    ++  +V     
Sbjct: 299 CAGSRLLVQEGIAEAFYAKLRARMATLRIGDPLDKCIDVGAMVDPAHCAKVAEMVAGSNG 358

Query: 361 EGCSVWQSPDTTIPSGGCFFPPTLVTGVAPASTLAQEEIFGPVLVTMSFRTPDEAIALAN 420
           E          T+P+ G F+PPTL+TG+ PA  L ++EIFGPVLV  +FRTP EA+ +AN
Sbjct: 359 E-----VHQPGTVPAEGAFYPPTLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVAN 413

Query: 421 NSRYGLAASVWSETIGRALDVAPRLASGVVWINATNLFDAAVGFGGYRESGYGREGGREG 480
            +RYGLAA++WSE I RALD+AP+LA+GVVW+NATNLFDAA GFGG RESG+GREGG EG
Sbjct: 414 ATRYGLAATLWSENINRALDIAPKLAAGVVWVNATNLFDAAAGFGGVRESGFGREGGWEG 473

Query: 481 IYEYLKPRAWLKLAERRAAQDVVRDAAALDPLSNVTSIDRTAKLFIGGKQARPDSGYSLP 540
           +  Y K  A  K     AA   +   AA  P      +DRTAK++IGGKQARPDSGYS P
Sbjct: 474 LRAYTKQAAPPKALVPVAA---IPAPAAPKP----GGLDRTAKMYIGGKQARPDSGYSRP 526

Query: 541 VLAPDGTPVGEVAAGNRKDIRNAVEAARAAQKWSQASTHNRAQVLFYLAENLAVRADEFV 600
           V +P G  +G    G+RKDIRNAVEAA  A  W + + H RAQ+L+Y+AENL+ R +EF 
Sbjct: 527 VWSPKGVLLGHAPEGSRKDIRNAVEAATGAASWGRTTGHLRAQILYYVAENLSARTEEFA 586

Query: 601 RQLVVRNGATEAAARAEVDASVQRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVIGI 660
            ++    G+    A AEV A++ RLFTYAAWADK+DGAV   P+RGVALAM EP+GVIG 
Sbjct: 587 TRIAEMTGSRVPRAEAEVSAAIDRLFTYAAWADKYDGAVKPVPIRGVALAMPEPVGVIGA 646

Query: 661 ACPDEAPLLGFVSLAAPALAMGNRVVVLPSEASPLTVTDFYQVAETSDVPGGVLNIVTGE 720
             PD+APLLG VS+   ALAMGNR+V++PSE  PL  TD YQV +TSDVP GV+NIVTG 
Sbjct: 647 FAPDDAPLLGAVSILGAALAMGNRLVLVPSEPFPLAATDLYQVLDTSDVPAGVVNIVTGA 706

Query: 721 RGALLPALVKHDDVDAVWCFGSAADSTLVERESVGNLKRTFVDYGRQFDWFDRASEGRPF 780
             AL   L  H  VDAVW F  A  ST +E E+ GNLKRT+V++GR  DW     + R F
Sbjct: 707 HEALAKPLASHLGVDAVWSFSGADISTTIEAEAAGNLKRTWVNHGRARDWMQ--VDARSF 764

Query: 781 LRQAVQVKNIWIPYG 795
           L QA + K IW+PYG
Sbjct: 765 LAQATETKTIWVPYG 779


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: 1793
Number of extensions: 81
Number of successful extensions: 8
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: 780
Length adjustment: 41
Effective length of query: 755
Effective length of database: 739
Effective search space:   557945
Effective search space used:   557945
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, 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