GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctC in Dyella japonica UNC79MFTsu3.2

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate N515DRAFT_4319 N515DRAFT_4319 electron transfer flavoprotein alpha subunit apoprotein

Query= BRENDA::H6LBB1
         (418 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4319
          Length = 314

 Score =  140 bits (353), Expect = 5e-38
 Identities = 98/318 (30%), Positives = 160/318 (50%), Gaps = 15/318 (4%)

Query: 74  ITVYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTNITEKADELLKY-GVDKVF 132
           I V  +H+ G+++  T   +  A   AAV G  +  L++  ++   A E  K  GV KV 
Sbjct: 4   ILVVAEHLNGKLNSSTARAVSAA---AAVKGDSIDVLVLADSVDAIAAEAAKIDGVGKVL 60

Query: 133 VYDKPELKHFVIEPYANVLEDFIEKVKP--SSILVGATNVGRSLAPRVAARYRTGLTADC 190
              + E  H    P A VL   + K     S +   +T  G+ +APRVAA       +D 
Sbjct: 61  TIARAENAH----PLAAVLAPQVAKAAAGYSHVFFPSTTFGKDVAPRVAALLGVSQVSDV 116

Query: 191 TILEMKENTDLVQIRPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGDVEMMD 250
             +E   +      RP + GN +  +          T+R   + A     +    VE + 
Sbjct: 117 MSVEGAHSFK----RPIYAGNAIVTVEANPAHAVVATIRTASWPAAGSRGDS-AAVEALA 171

Query: 251 IEKAKLVSAIEVMEVIKKEKGIDLSEAETIVAVGRGVKCEKDLDMIHEFAEKIGATVACT 310
           ++ A       V     K    DL  A  +V+ GRGV  +++ ++I++ A+KIGA V  +
Sbjct: 172 VDAALPAHTRFVELQQGKSDRPDLQGAGKVVSGGRGVGSKENFEVIYKLADKIGAAVGAS 231

Query: 311 RPGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSDPKAPIF 370
           R  ++AG+    LQ+G +G+ + P+L +A GISGA+Q   G++++  I+AIN D +APIF
Sbjct: 232 RAAVDAGYVPNELQVGQTGKIIAPELYMAFGISGAIQHLTGIKDAGTIVAINKDGEAPIF 291

Query: 371 NIAHCGMVGDLYEILPEL 388
            IA  G+VGDL++++PE+
Sbjct: 292 EIADIGLVGDLFKLIPEI 309


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: 266
Number of extensions: 10
Number of successful extensions: 2
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: 314
Length adjustment: 29
Effective length of query: 389
Effective length of database: 285
Effective search space:   110865
Effective search space used:   110865
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: 49 (23.5 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