GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Lentibacillus jeotgali Grbi

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_010532194.1 ON01_RS16870 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-11560
         (497 letters)



>NCBI__GCF_000224785.1:WP_010532194.1
          Length = 474

 Score =  287 bits (735), Expect = 5e-82
 Identities = 179/471 (38%), Positives = 263/471 (55%), Gaps = 11/471 (2%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           +INGE+ ++   ET E ++P     +  ++     D +RAV  AR  F S  +SQ +   
Sbjct: 8   YINGEWVESTGSETMEVINPATEEVMGHISLGTQEDLDRAVRAARDAFPS--FSQTSKEY 65

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           R   L + AD   K  ++L  + T ++G P+  S  +            AE +       
Sbjct: 66  RIELLEKIADEYEKRKDDLIKVITEELGAPLNLSEKVHYMMGYSHFKQAAEELR----HF 121

Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202
           + T       + +E +GV G I PWNFP      K+  A A G++V+LKP+E +P  A+ 
Sbjct: 122 SFTEKRDKSTIVKEAIGVSGLITPWNFPTNQTSTKIASAFAAGSTVILKPAEITPYAAMI 181

Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262
           +A +   AG+P GV N++ G G  VG A++ H D+D + +TGS    +++M  A + ++K
Sbjct: 182 LADIFEAAGLPKGVFNLVNGTGEGVGNAISSHPDIDFVSYTGSGVAGRKVMENAAK-DIK 240

Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMV 322
           ++ LE GGKSP IV  DA D+Q AA+ A + I+ N G+VCTA +R+LV ++IK +F   V
Sbjct: 241 KVALELGGKSPMIVLEDA-DVQKAAKIAVANISNNTGQVCTAATRVLVPKTIKPQFEEEV 299

Query: 323 VEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE-TGGT 381
             A++    G+P +    VG LV  +Q + V  YI+ G  +GAK+L GG    E    G 
Sbjct: 300 KAAVEKLTVGDP-EQDNKVGPLVAEKQWDRVQGYIQTGMDEGAKVLIGGVGKPEGLKQGY 358

Query: 382 YVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKA 441
           +  PT+F  V+N M IAQEEIFGPV ++I +DT +EA+ IANDT YGLA  +   D    
Sbjct: 359 FAMPTVFTDVSNDMTIAQEEIFGPVTTIIPYDTLDEAIEIANDTIYGLAGYVVGEDPDTL 418

Query: 442 HKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKA 492
            K A  +RAG + VN     D +APFGGFKQSG GR+     +E+Y E KA
Sbjct: 419 QKAASGIRAGQIRVNSAP-TDFSAPFGGFKQSGIGREWGDFGIEEYLEPKA 468


Lambda     K      H
   0.316    0.132    0.390 

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: 506
Number of extensions: 26
Number of successful extensions: 7
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: 497
Length of database: 474
Length adjustment: 34
Effective length of query: 463
Effective length of database: 440
Effective search space:   203720
Effective search space used:   203720
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 (21.6 bits)
S2: 52 (24.6 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