Aligments for a candidate for adh in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources