GapMind for catabolism of small carbon sources

 

Aligments for a candidate for L-LDH in Dyella japonica UNC79MFTsu3.2

Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate N515DRAFT_1250 N515DRAFT_1250 L-lactate dehydrogenase (cytochrome)

Query= reanno::acidovorax_3H11:Ac3H11_1623
         (390 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1250 N515DRAFT_1250
           L-lactate dehydrogenase (cytochrome)
          Length = 379

 Score =  444 bits (1142), Expect = e-129
 Identities = 222/377 (58%), Positives = 278/377 (73%), Gaps = 4/377 (1%)

Query: 7   ITCIEDLRAIAQRRVPRMFYDYADSGSYTEGTYRANESDFQRIKLRQRVAVNMEGRSTRT 66
           IT + DLR +A+RRVPR F++YAD G+Y E T R N +  + IK RQRV +N++ RS  T
Sbjct: 5   ITNVLDLRELARRRVPRAFFEYADRGAYDEVTLRGNRAALESIKFRQRVMMNVDQRSLAT 64

Query: 67  TMVGQDVAMPVAIAPTGLTGMQHADGEILGAKAAKAFGIPFTLSTMSICSIEDIAEHTGR 126
           ++VGQ ++MP+AIAPTGLTG+QH  GEILGA+AA   GIPF LST+SICSIE + +   +
Sbjct: 65  SVVGQPISMPLAIAPTGLTGLQHGAGEILGARAATKAGIPFCLSTVSICSIEQVRDAV-Q 123

Query: 127 HPFWFQVYVMRDRDFIERLIDRAKAANCSALQLTLDLQILGQRHKDIKNGLSAPPKPTIA 186
            PFWFQ+YVMRDR F   LI RA  A CSAL LT DL + GQRH++IKNGLS PPK T+ 
Sbjct: 124 APFWFQLYVMRDRGFARDLIRRASDAGCSALMLTADLTVQGQRHREIKNGLSVPPKITLR 183

Query: 187 NLINLATKPRWCLGMLGTKRRSFGNIVGHAKGVGDLSSLSSWTAEQFDPQLNWGDVEWIK 246
           NL ++ +KPRW   ML    RSFGN+ G  +G   L++L+ W A QFDP LNW D+EWI+
Sbjct: 184 NLFDVMSKPRWAWSMLRAPSRSFGNLAGRIQGTDSLTTLAQWIANQFDPTLNWQDLEWIR 243

Query: 247 KRWGGKLILKGIMDAEDARLAVNSGADALIVSNHGGRQLDGAPSSIAALPGIADAVAQMG 306
           + W GKLILKGIMD EDARLA   G DA++VSNHGGRQLDGAP+SI  LP IADAV   G
Sbjct: 244 ELWPGKLILKGIMDEEDARLAAAHGVDAIVVSNHGGRQLDGAPASIEVLPRIADAV---G 300

Query: 307 GGIEVWMDGGIRSGQDVLKARALGAQGTLIGRSFLYGLGAYGEAGVTRALQIIQKELDIT 366
             ++V  DGGI SGQDVLKA ALGA+  LIG++FLYGLGA GE GV R ++II++EL ++
Sbjct: 301 DKLDVLFDGGILSGQDVLKALALGARAGLIGKAFLYGLGALGEDGVARTIEIIRRELSVS 360

Query: 367 MAFCGHTNINTVDRSIL 383
           MA  G T++  + R +L
Sbjct: 361 MALTGQTDVRRIGRDVL 377


Lambda     K      H
   0.320    0.137    0.412 

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: 424
Number of extensions: 15
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: 390
Length of database: 379
Length adjustment: 30
Effective length of query: 360
Effective length of database: 349
Effective search space:   125640
Effective search space used:   125640
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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