GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctC in Herbaspirillum seropedicae SmR1

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate HSERO_RS14225 HSERO_RS14225 protein fixB

Query= BRENDA::H6LBB1
         (418 letters)



>FitnessBrowser__HerbieS:HSERO_RS14225
          Length = 364

 Score =  228 bits (582), Expect = 2e-64
 Identities = 132/347 (38%), Positives = 201/347 (57%), Gaps = 14/347 (4%)

Query: 49  KKGPEGVLILEEDEKVAIDKSLYRGITVYVDHIEGQIHPVTFELIGKARELAAVIGHPVY 108
           +KG +G   L+E  K       Y+G+ V+++H  G++HPV++EL+G+ R+LA  +G  + 
Sbjct: 10  RKGGKGKYELDERLKA------YQGVWVFIEHERGEVHPVSWELLGEGRKLADQLGVSLS 63

Query: 109 ALLMGTN---ITEKADELLKYGVDKVFVYDKPELKHFVIEPYANVLEDFIEKVKPSSILV 165
            +++G       +  ++   +G D  ++   P L  +  +P+   L D + + +P  +L+
Sbjct: 64  GVVLGAPDLATRQFCEQAFHHGADSCYLMADPTLSAYRNQPFTKGLTDLVNRYQPEILLL 123

Query: 166 GATNVGRSLAPRVAARYRTGLTADCTILEMK-ENTDLVQIRPAFGGNIMAQIVTENTRPQ 224
           GAT  GR LA  VA   +TGLTADCT L +  EN  +   RP FGG+++  I+T N RPQ
Sbjct: 124 GATAQGRDLAGSVATTLKTGLTADCTGLTIDMENRSMAASRPTFGGSLLCTILTLNYRPQ 183

Query: 225 FCTVRYKVFTAPERVNEPWGDV---EMMDIEKAKLVSAIEVMEVIKKEKGIDLSEAETIV 281
             TVR +V   PE      G +    +  +E   +   +E +   +++K   L  A+ IV
Sbjct: 184 MATVRPRVMAMPEPDRSRSGQIIEHPLCLVESDIITKVLEYIPDNQQDKP-QLPFADIIV 242

Query: 282 AVGRGVKCEKDLDMIHEFAEKIGATVACTRPGIEAGWFDARLQIGLSGRTVKPKLIIALG 341
           A GRG+K  ++  +I + A  +GA V  TRP ++A W  A  Q+G SG+TV+PKL IA G
Sbjct: 243 AGGRGMKRAENFQLIWDLAMVLGAEVGATRPVVQANWVQAERQVGQSGKTVRPKLYIAAG 302

Query: 342 ISGAVQFAAGMQNSEYIIAINSDPKAPIFNIAHCGMVGDLYEILPEL 388
           ISGA+Q   GM +S+ IIAINSDP APIF+ A  G+VG+   ILP L
Sbjct: 303 ISGAIQHRVGMADSDVIIAINSDPNAPIFDFASYGIVGNAMTILPAL 349


Lambda     K      H
   0.319    0.137    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: 395
Number of extensions: 14
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: 418
Length of database: 364
Length adjustment: 31
Effective length of query: 387
Effective length of database: 333
Effective search space:   128871
Effective search space used:   128871
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: 50 (23.9 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