GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Lentibacillus jeotgali Grbi

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_010532044.1 ON01_RS16145 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>NCBI__GCF_000224785.1:WP_010532044.1
          Length = 480

 Score =  337 bits (865), Expect = 4e-97
 Identities = 181/469 (38%), Positives = 286/469 (60%), Gaps = 5/469 (1%)

Query: 9   MYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIER 68
           M I+GQ+V    D  ++VVNPA    +  +P+G  ++A +A++AA  A   W  L A +R
Sbjct: 10  MSINGQWVGSDLDT-LNVVNPANGETVGTVPNGGEKEAEQAVNAAYDAFESWSNLTAHDR 68

Query: 69  ASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQ 128
           A +L+K++  + E   E++ ++  E GK    +  EV + A +I++ AE  +R +G +I 
Sbjct: 69  AVYLKKLNQLMLENQEELAQMMTIEMGKPINESRGEVKYAASFIEWFAEEGKRIDGAVIP 128

Query: 129 SDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAF 188
           +   G+ + ++K+ +GV   I PWNFP  ++ RKM PAL +G T ++KPS  +P  A+  
Sbjct: 129 THAAGKRLQVWKKPVGVAAAITPWNFPAAMLTRKMGPALASGCTFIMKPSSESPLTAVKL 188

Query: 189 AKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248
            ++ ++ G P+GV NLV G    + + +  N KV  V+ TGS   G+ ++  +A  + K+
Sbjct: 189 MELCEQAGFPKGVVNLVTGSSSKIAKVVMENSKVRKVTFTGSTEVGKTLIRQSADQVKKL 248

Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEA 308
            LELGG AP +V+DDAD++LAVK  V S+  N+GQ C CA R+YVQ+G+YD++V +L +A
Sbjct: 249 SLELGGHAPLVVLDDADVDLAVKGTVASKFRNAGQTCICANRIYVQEGVYDEYVEKLTKA 308

Query: 309 MQAVQFGNPA-ERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAV-EGKGYYYP 366
           ++ ++ G+   E NDI  GPLIN   L++V++ V  A  +GA +  GGKAV +  G +Y 
Sbjct: 309 VEELKAGDGTDESNDI--GPLINQDGLDKVKRHVDDATSKGASITTGGKAVTDNGGLFYQ 366

Query: 367 PTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKA 426
           PT+L DV Q M IM EETFGPV PV    + E+A+ ++ND+ YGL + ++T N+    + 
Sbjct: 367 PTVLKDVDQSMVIMEEETFGPVTPVEKISSDEEAVKLSNDTPYGLAAYVFTSNVARGYQL 426

Query: 427 IKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475
           I+ L FG    N     A Q    G ++SGIG   G  G+ E++++Q V
Sbjct: 427 IEKLDFGIVGWNEGGPSAAQVPFGGMKESGIGREGGHEGIEEFVESQYV 475


Lambda     K      H
   0.318    0.135    0.392 

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: 555
Number of extensions: 20
Number of successful extensions: 3
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: 479
Length of database: 480
Length adjustment: 34
Effective length of query: 445
Effective length of database: 446
Effective search space:   198470
Effective search space used:   198470
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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