GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Dechlorosoma suillum PS

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate Dsui_0437 Dsui_0437 succinate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>FitnessBrowser__PS:Dsui_0437
          Length = 483

 Score =  314 bits (805), Expect = 4e-90
 Identities = 181/459 (39%), Positives = 263/459 (57%), Gaps = 9/459 (1%)

Query: 32  NPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERIAVLRKVGDLILERKEEL 91
           NPA+  +L  V   GAAE   A+ AA  A    W+  TA ER  VLR+  +L+ +  ++L
Sbjct: 30  NPASGAELARVPRFGAAETRAAIAAADAAWPA-WRSRTAKERTGVLRRWFELMNQHADDL 88

Query: 92  SVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNE---ATQMDDVALNYAIRRPV 148
           ++L + + GKP       ++  AA    +F++  +    E   A   D   L   I++P+
Sbjct: 89  ALLMTSEQGKPL-AEARGEVAYAASFVEWFAEEAKRAYGETIPAVAADKRML--VIKQPI 145

Query: 149 GVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVLAEICRDAGVPDGVVN 208
           GV   I PWN P  ++T K+APALAAG TVV+KPAE TP+TA  LAE+   AG P GV N
Sbjct: 146 GVCAAITPWNFPAAMITRKVAPALAAGCTVVVKPAEQTPLTALALAELAHRAGFPAGVFN 205

Query: 209 LVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKRLSYELGGKNPNVIFA 268
           ++ G  P + G  LT +P V  +SFTG T  G+++M   A ++K+LS ELGG  P ++F 
Sbjct: 206 VITG-DPVAIGGELTSNPTVRKLSFTGSTEVGRLLMGQCAPSIKKLSLELGGNAPFIVFD 264

Query: 269 DSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVAKTKELVVGDPFDAKT 328
           D++LD  +E  M S + N G+ C+C +R+ V+   YEAF  +  AK   L VG+  +A  
Sbjct: 265 DADLDAAVEGAMISKYRNTGQTCVCANRLLVQDGIYEAFAARLAAKVATLKVGEGTEAGV 324

Query: 329 KVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGL-EKGYFLEPTIITGLTRDCRVV 387
             G LI  +   +V  +I  AV  G  +L GG+R E   E G F +PT++  +T   RV 
Sbjct: 325 TQGPLIDADALAKVEAHIADAVAHGARVLAGGRRHERYREGGAFFQPTVLADVTPQMRVA 384

Query: 388 KEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHRVAGQIEAGIVWVNTW 447
           +EE FGPV  +  F TEEE +   N T +GL++  ++ D+ R  RV   +E G+V VNT 
Sbjct: 385 REETFGPVAPLFRFQTEEEAIALANATEFGLASYFYSRDIGRIFRVGEALEYGMVGVNTG 444

Query: 448 FLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486
            + +   PFGG+KQSG+GREG  +  E Y E+  +C+ L
Sbjct: 445 LISNEVAPFGGIKQSGLGREGSKYGLEEYLEVKYLCLGL 483


Lambda     K      H
   0.318    0.136    0.404 

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: 554
Number of extensions: 22
Number of successful extensions: 5
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: 486
Length of database: 483
Length adjustment: 34
Effective length of query: 452
Effective length of database: 449
Effective search space:   202948
Effective search space used:   202948
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: 52 (24.6 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