GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Dechlorosoma suillum PS

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Dsui_0437 Dsui_0437 succinate-semialdehyde dehydrogenase

Query= BRENDA::Q8BH00
         (487 letters)



>FitnessBrowser__PS:Dsui_0437
          Length = 483

 Score =  310 bits (794), Expect = 7e-89
 Identities = 172/479 (35%), Positives = 260/479 (54%), Gaps = 5/479 (1%)

Query: 7   LLMLENFIGGKFLPCNSYIDSYDPSTGEVYCKVPNSGKEEIEAAVEAAREAFPAWSSRSP 66
           LL  + ++ G+++   S    ++P++G    +VP  G  E  AA+ AA  A+PAW SR+ 
Sbjct: 8   LLRQQCYLNGQWVGGESDFPVHNPASGAELARVPRFGAAETRAAIAAADAAWPAWRSRTA 67

Query: 67  QERSLVLNRLADVLEQSLEELAQAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLHHVS 126
           +ER+ VL R  +++ Q  ++LA   + +QGK L  AR  ++  +     +FA        
Sbjct: 68  KERTGVLRRWFELMNQHADDLALLMTSEQGKPLAEARG-EVAYAASFVEWFAEEAKRAYG 126

Query: 127 ECTQMSHLGCMHYTVRTPVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVT 186
           E             ++ P+G+   I+PWN P  ++T K+APA+AAG TV+ KP+E T +T
Sbjct: 127 ETIPAVAADKRMLVIKQPIGVCAAITPWNFPAAMITRKVAPALAAGCTVVVKPAEQTPLT 186

Query: 187 AWMFCKLLDKAGVPPGVINIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPH 246
           A    +L  +AG P GV N++ G    +G  L S+P V  +SFTGS      +    AP 
Sbjct: 187 ALALAELAHRAGFPAGVFNVITGDPVAIGGELTSNPTVRKLSFTGSTEVGRLLMGQCAPS 246

Query: 247 CKKLSLELGGKNPAIIFEDANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFLKR 306
            KKLSLELGG  P I+F+DA+L+  +   + S + N G+ C+C +R+ VQ  IY  F  R
Sbjct: 247 IKKLSLELGGNAPFIVFDDADLDAAVEGAMISKYRNTGQTCVCANRLLVQDGIYEAFAAR 306

Query: 307 FVEATRKWKVGVPSDPSANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLPLR 366
                   KVG  ++     G LI    L KV +++  A   GAR+L G    +      
Sbjct: 307 LAAKVATLKVGEGTEAGVTQGPLIDADALAKVEAHIADAVAHGARVLAGGRRHE----RY 362

Query: 367 NQAGYFMLPTVITDIKDESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVWSK 426
            + G F  PTV+ D+  + R   EE FGPV  +  F +EEE I  AN+  +GLA+  +S+
Sbjct: 363 REGGAFFQPTVLADVTPQMRVAREETFGPVAPLFRFQTEEEAIALANATEFGLASYFYSR 422

Query: 427 DVGRIHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITI 485
           D+GRI RV + L+ G+V  N  LI     PFGG+K SG+GREG+K   + + E+K + +
Sbjct: 423 DIGRIFRVGEALEYGMVGVNTGLISNEVAPFGGIKQSGLGREGSKYGLEEYLEVKYLCL 481


Lambda     K      H
   0.319    0.134    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: 520
Number of extensions: 23
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: 487
Length of database: 483
Length adjustment: 34
Effective length of query: 453
Effective length of database: 449
Effective search space:   203397
Effective search space used:   203397
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: 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