GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Dechlorosoma suillum PS

Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Dsui_0437 Dsui_0437 succinate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-16246
         (477 letters)



>FitnessBrowser__PS:Dsui_0437
          Length = 483

 Score =  324 bits (831), Expect = 4e-93
 Identities = 189/461 (40%), Positives = 262/461 (56%), Gaps = 5/461 (1%)

Query: 11  YIDGAFVESAAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAGH 70
           Y++G +V   +   V NPA+GA L+RVP   A E   A+AAA AA   W  + A ER G 
Sbjct: 14  YLNGQWVGGESDFPVHNPASGAELARVPRFGAAETRAAIAAADAAWPAWRSRTAKERTGV 73

Query: 71  LRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEIIASDR 130
           LRR    +   A  +A  +T EQGK  + A  EV + A ++++ AE A+R  GE I +  
Sbjct: 74  LRRWFELMNQHADDLALLMTSEQGKPLAEARGEVAYAASFVEWFAEEAKRAYGETIPAVA 133

Query: 131 PGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFARL 190
             + + + ++P+GV A I PWNFP  +I RK+APAL  G T+VVKP+E+TP      A L
Sbjct: 134 ADKRMLVIKQPIGVCAAITPWNFPAAMITRKVAPALAAGCTVVVKPAEQTPLTALALAEL 193

Query: 191 VAETDLPRGVFNVVCG-AGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNLE 249
                 P GVFNV+ G    +GG L+S+P V  +SFTGS E G  +M   AP++ KL+LE
Sbjct: 194 AHRAGFPAGVFNVITGDPVAIGGELTSNPTVRKLSFTGSTEVGRLLMGQCAPSIKKLSLE 253

Query: 250 LGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMAA 309
           LGG AP IV  DADL+ AV+    S+  N+GQ C CA R+ VQ  + E F  R+AA +A 
Sbjct: 254 LGGNAPFIVFDDADLDAAVEGAMISKYRNTGQTCVCANRLLVQDGIYEAFAARLAAKVAT 313

Query: 310 TRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAER---PGHHYQPT 366
            + G+   E  V  GPLI+   L K++A +  A+A GA ++ GG   ER    G  +QPT
Sbjct: 314 LKVGEG-TEAGVTQGPLIDADALAKVEAHIADAVAHGARVLAGGRRHERYREGGAFFQPT 372

Query: 367 VLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALR 426
           VL       R+ REE FGPV P+      +EAIALAN  E+GL S  ++RD+ +      
Sbjct: 373 VLADVTPQMRVAREETFGPVAPLFRFQTEEEAIALANATEFGLASYFYSRDIGRIFRVGE 432

Query: 427 ELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEY 467
            L++G   +N            G+++SG+G    K+GL EY
Sbjct: 433 ALEYGMVGVNTGLISNEVAPFGGIKQSGLGREGSKYGLEEY 473


Lambda     K      H
   0.320    0.136    0.395 

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: 527
Number of extensions: 21
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: 477
Length of database: 483
Length adjustment: 34
Effective length of query: 443
Effective length of database: 449
Effective search space:   198907
Effective search space used:   198907
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: 51 (24.3 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