GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Herbaspirillum seropedicae SmR1

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate HSERO_RS07235 HSERO_RS07235 aldehyde dehydrogenase

Query= reanno::pseudo1_N1B4:Pf1N1B4_1229
         (505 letters)



>FitnessBrowser__HerbieS:HSERO_RS07235
          Length = 477

 Score =  243 bits (619), Expect = 1e-68
 Identities = 147/476 (30%), Positives = 243/476 (51%), Gaps = 9/476 (1%)

Query: 12  VKLLIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAFQTWKLTPIG 71
           V+L I+GEW  S +    D++NPAT++V+ K+  A  A++D A+ AA + F+TW+     
Sbjct: 5   VQLFINGEWTASASGRTIDVINPATEEVIGKIAHADRADLDRALEAASKGFETWRNMSAF 64

Query: 72  ARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHACSIGSLQMGEF 131
            R +IM +   L+RE ++ +A +++ EQGK +A+A+ +     + ++          G  
Sbjct: 65  ERSKIMRRAADLLRERAEEVARLMTMEQGKPLAEAKMETLGAADTIDWFAEEARRTYGRL 124

Query: 132 AENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTM 191
                 G     +++P+G  A  TP+NFP    +     A+A G + ++K  E+ P S  
Sbjct: 125 VPARVPGAYQMVIKEPVGPVAAFTPWNFPLNQVVRKLSAALAAGCSIIVKAPEETPASPA 184

Query: 192 LLVELAIEAGIPPGVLNVVHG-GKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGK 250
            L+    +AG+P GV+N+V+G   ++ + L  H  IK +SF GST VG  +  LAG+H K
Sbjct: 185 ELIRAYADAGVPAGVINLVYGVPAEISEYLIPHPVIKKISFTGSTPVGKQLAALAGQHMK 244

Query: 251 RVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMA-TSVVVLVGAAKQWLPDLK 309
           R    +G    A+V  DA+ + A   L  A F  AGQ C++ T  +V  G    ++    
Sbjct: 245 RATMELGGHAPAMVFDDADVDVAAKMLATAKFRNAGQVCVSPTRFLVQKGVFNAFVDKFV 304

Query: 310 ALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDISVPGYEKGN 369
             A++LKV  G E G  +GPV +KR    +  LI+  + +GA+L   G+ I      KG 
Sbjct: 305 TYAEQLKVGNGLEAGITMGPVANKRRIPALEALIDDAVSQGAQLRTGGKRIG----NKGY 360

Query: 370 FVGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAAA 429
           F  PT+ + +  + +   +E FGP+ ++   +TLD+ I   N  P+G     F +S    
Sbjct: 361 FFQPTVLTNLPLQARAMNEEPFGPLALINSFETLDEVITEANRLPYGLAAYAFAKSAHTK 420

Query: 430 RKFQTEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVT 485
                 ++ G + IN  + + +P   F G + S  G  G  G + ++ Y  TK VT
Sbjct: 421 HALAARVESGMLTIN-HLGLALPELPFGGIKDSGYGSEG--GTEAIEAYINTKLVT 473


Lambda     K      H
   0.319    0.135    0.397 

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: 521
Number of extensions: 25
Number of successful extensions: 4
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: 505
Length of database: 477
Length adjustment: 34
Effective length of query: 471
Effective length of database: 443
Effective search space:   208653
Effective search space used:   208653
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 (21.7 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