GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3609634
          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 (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