GapMind for catabolism of small carbon sources

 

Alignments for a candidate for L-LDH in Azospirillum thiophilum BV-S

Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate WP_082109398.1 AL072_RS27445 alpha-hydroxy-acid oxidizing protein

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



>NCBI__GCF_001305595.1:WP_082109398.1
          Length = 415

 Score =  556 bits (1432), Expect = e-163
 Identities = 267/380 (70%), Positives = 320/380 (84%), Gaps = 4/380 (1%)

Query: 7   ITCIEDLRAIAQRRVPRMFYDYADSGSYTEGTYRANESDFQRIKLRQRVAVNMEGRSTRT 66
           ITCIEDLR +A+RRVPRMFYDY D GS+TE TYRAN +D   ++ RQR+ +++ GR+T +
Sbjct: 8   ITCIEDLRILARRRVPRMFYDYVDCGSWTESTYRANTADLAALQFRQRIGMSIAGRTTES 67

Query: 67  TMVGQDVAMPVAIAPTGLTGMQHADGEILGAKAAKAFGIPFTLSTMSICSIEDIAEHTGR 126
            ++G+ VAMPVA+APTGLTGMQHADGEIL A+AA+ FG+PFTLST+SICSIED+A +TG+
Sbjct: 68  RILGESVAMPVALAPTGLTGMQHADGEILAARAAERFGVPFTLSTVSICSIEDVAANTGK 127

Query: 127 HPFWFQVYVMRDRDFIERLIDRAKAANCSALQLTLDLQILGQRHKDIKNGLSAPPKPTIA 186
            PFWFQ+YVMRDR F+ERLI RAKAANCSAL LTLDLQI GQRHKD+KNGLS PPKPT+ 
Sbjct: 128 -PFWFQLYVMRDRAFVERLIARAKAANCSALVLTLDLQIQGQRHKDLKNGLSTPPKPTLR 186

Query: 187 NLINLATKPRWCLGMLGTKRRSFGNIVGHAKGVGDLSSLSSWTAEQFDPQLNWGDVEWIK 246
           NL++LATKP WCLGML TKRR+FGNIVGH  GV D+SSL++W ++QFDP L W DV WIK
Sbjct: 187 NLVDLATKPGWCLGMLRTKRRTFGNIVGHVSGVSDVSSLAAWVSQQFDPTLTWEDVRWIK 246

Query: 247 KRWGGKLILKGIMDAEDARLAVNSGADALIVSNHGGRQLDGAPSSIAALPGIADAVAQMG 306
           K WGGKLI+KG++D EDARLAV +GADA++VSNHGGRQLDGAPSSIA LP IA+AV Q  
Sbjct: 247 KLWGGKLIVKGVLDVEDARLAVENGADAIVVSNHGGRQLDGAPSSIAMLPAIAEAVGQQ- 305

Query: 307 GGIEVWMDGGIRSGQDVLKARALGAQGTLIGRSFLYGLGAYGEAGVTRALQIIQKELDIT 366
              EV  D GIRSGQD+LKA ALGA+G ++GR+FLYGLGA GEAGVTR L+I+Q+ELD+T
Sbjct: 306 --TEVLFDSGIRSGQDILKAAALGAKGVMVGRAFLYGLGAMGEAGVTRCLEILQRELDLT 363

Query: 367 MAFCGHTNINTVDRSILLPG 386
           M  CG T+I   D SIL+ G
Sbjct: 364 MGLCGLTDIGAADPSILING 383


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: 560
Number of extensions: 24
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: 415
Length adjustment: 31
Effective length of query: 359
Effective length of database: 384
Effective search space:   137856
Effective search space used:   137856
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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