GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Sinorhizobium meliloti 1021

Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate SM_b21301 SM_b21301 ly membrane-anchored aldehyde dehydrogenase

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



>FitnessBrowser__Smeli:SM_b21301
          Length = 794

 Score = 1087 bits (2812), Expect = 0.0
 Identities = 549/797 (68%), Positives = 630/797 (79%), Gaps = 4/797 (0%)

Query: 1   MSVAEYFSSMEYGPAPEDDQPARAWLAQHEDGFGHFIGGAWHAPAAGERFASNAPATGEQ 60
           MSVA +F  M YGPAPE D  ARAWL +HE   GHFI GA+   A+G+ F +  PATG+ 
Sbjct: 1   MSVATFFDEMSYGPAPEADTEARAWLTRHEGKLGHFINGAFVGSASGKSFDTFEPATGKL 60

Query: 61  LAQVAQGDAADIDAAVAAARAAQPGWLALGGAGRARHLYALARMVQRHSRLFAVLEALDN 120
           LA++A G   D++AAVAAAR AQ  W  L G  RARHLYALAR++QRH+RL AV+EALDN
Sbjct: 61  LAKIAHGGRDDVNAAVAAARKAQGPWAKLSGHARARHLYALARLIQRHARLIAVVEALDN 120

Query: 121 GKPIRETRDIDVPLVARHFLHHAGWAQLQESEFADYAPLGVVGQIVPWNFPLLMLAWKIA 180
           GKPIRETRDID+PL ARHF HHAGWAQLQE+EFAD  P+GVVGQ++PWNFP LMLAWK+A
Sbjct: 121 GKPIRETRDIDIPLAARHFYHHAGWAQLQETEFADQVPVGVVGQVIPWNFPFLMLAWKVA 180

Query: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHRAGLPAGVLNVVTGDGRTGAALVEHPQVDKI 240
           PA+A GN V+LKPAE+TPLTALLFAELA  AGLP GVLNVVTG+G TGA +VEH  +DKI
Sbjct: 181 PALALGNSVILKPAEFTPLTALLFAELAAAAGLPPGVLNVVTGEGETGALIVEHEDIDKI 240

Query: 241 AFTGSTEVGRLIRSATAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300
           AFTGSTEVGRLIR  TAGSGKSLTLELGGKSPFIVFDDAD+D AVEGVVDAIWFNQGQVC
Sbjct: 241 AFTGSTEVGRLIREKTAGSGKSLTLELGGKSPFIVFDDADIDAAVEGVVDAIWFNQGQVC 300

Query: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGTSLDKSIDLGAIVDPVQLERIQSLVETGRR 360
           CAGSRLLVQEG+   F  +LKRRMETLRVG  LDK+ID+ AIV PVQL+RI+ LV  G  
Sbjct: 301 CAGSRLLVQEGVAPVFHDRLKRRMETLRVGHPLDKAIDMAAIVAPVQLQRIEELVAKGVA 360

Query: 361 EGCSVWQSPDTTIPSGGCFFPPTLVTGVAPASTLAQEEIFGPVLVTMSFRTPDEAIALAN 420
           EG S+ Q P   +P GG FF PTL+TGV P S +A EEIFGPV V+M+FRTP+EAI LAN
Sbjct: 361 EGASMHQ-PKIELPKGGSFFRPTLLTGVQPTSVVATEEIFGPVAVSMTFRTPEEAIQLAN 419

Query: 421 NSRYGLAASVWSETIGRALDVAPRLASGVVWINATNLFDAAVGFGGYRESGYGREGGREG 480
           +SRYGLAASVWSETIG AL VA +LA+GVVW+NATNLFDA+ GFGG RESG+GREGGREG
Sbjct: 420 HSRYGLAASVWSETIGLALHVAAKLAAGVVWVNATNLFDASSGFGGKRESGFGREGGREG 479

Query: 481 IYEYLKPRAWLKLAERRAAQDVVRDAAALDPLSNVTSIDRTAKLFIGGKQARPDSGYSLP 540
            YEYLKP+AW+    R          AA D    V ++DRTAKLF+GGKQARPD  YS P
Sbjct: 480 CYEYLKPKAWMGRKLRPEHGLPAPKQAAGD--FAVPALDRTAKLFVGGKQARPDGNYSRP 537

Query: 541 VLAPDGTPVGEVAAGNRKDIRNAVEAARAAQKWSQASTHNRAQVLFYLAENLAVRADEFV 600
           VL+P G  +GEV  GNRKDIRNAV AAR A  WS A+ HNRAQ+L+Y+AENL+ R  EF 
Sbjct: 538 VLSPKGKVIGEVGEGNRKDIRNAVVAARGASGWSSATAHNRAQILYYIAENLSSRGAEFA 597

Query: 601 RQLVVRNGATEAAARAEVDASVQRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVIGI 660
            ++    GA+ A ARAEV+AS+ RLF+Y AWADK++G VH PPLRGVALAM EP GV+G+
Sbjct: 598 GRIAAMTGASAANARAEVEASIARLFSYGAWADKYEGTVHQPPLRGVALAMPEPQGVVGV 657

Query: 661 ACPDEAPLLGFVSLAAPALAMGNRVVVLPSEASPLTVTDFYQVAETSDVPGGVLNIVTGE 720
            CP EAPLLG VSL AP +A+GNRVV +PSEA PL  TDFY V ETSDVP GV+NIVTG 
Sbjct: 658 ICPPEAPLLGLVSLVAPLIAVGNRVVAVPSEAHPLAATDFYSVLETSDVPPGVINIVTGS 717

Query: 721 RGALLPALVKHDDVDAVWCFGSAADSTLVERESVGNLKRTFVDYGRQFDWFDR-ASEGRP 779
              L  AL  H+DVDA+W FGS   STLVE+ SVGNLKRTFVDYG+  DW DR A+EG+ 
Sbjct: 718 AIELAKALAAHNDVDALWAFGSPELSTLVEKLSVGNLKRTFVDYGKAIDWTDRSAAEGQA 777

Query: 780 FLRQAVQVKNIWIPYGD 796
           FLR+AV VKNIWIPYG+
Sbjct: 778 FLRRAVDVKNIWIPYGE 794


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: 1827
Number of extensions: 71
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: 794
Length adjustment: 41
Effective length of query: 755
Effective length of database: 753
Effective search space:   568515
Effective search space used:   568515
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