GapMind for catabolism of small carbon sources

 

Alignments for a candidate for L-LDH in Pseudomonas simiae WCS417

Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate GFF3053 PS417_15625 lactate dehydrogenase

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



>FitnessBrowser__WCS417:GFF3053
          Length = 386

 Score =  582 bits (1501), Expect = e-171
 Identities = 286/383 (74%), Positives = 332/383 (86%), Gaps = 4/383 (1%)

Query: 7   ITCIEDLRAIAQRRVPRMFYDYADSGSYTEGTYRANESDFQRIKLRQRVAVNMEGRSTRT 66
           IT IEDLR +AQ+RVPRMFYDYADSGS+TE TYRANESDF  IK RQRVA N++ RS R 
Sbjct: 4   ITTIEDLRKLAQKRVPRMFYDYADSGSWTESTYRANESDFASIKFRQRVARNIDERSIRA 63

Query: 67  TMVGQDVAMPVAIAPTGLTGMQHADGEILGAKAAKAFGIPFTLSTMSICSIEDIAEHTGR 126
           TM+GQ++AMPVA+APTGL GMQHADGEIL A+AA AFG+ +TLSTMSICS+EDIAEH G+
Sbjct: 64  TMIGQEMAMPVALAPTGLAGMQHADGEILTARAAAAFGLRYTLSTMSICSLEDIAEHVGQ 123

Query: 127 HPFWFQVYVMRDRDFIERLIDRAKAANCSALQLTLDLQILGQRHKDIKNGLSAPPKPTIA 186
            PFWFQ+YVMRDR FIE+LI+RAKAA   AL LTLDLQILGQRHKD+ NGLSAPPK T+ 
Sbjct: 124 -PFWFQLYVMRDRAFIEQLIERAKAAGVDALVLTLDLQILGQRHKDLINGLSAPPKLTLP 182

Query: 187 NLINLATKPRWCLGMLGTKRRSFGNIVGHAKGVGDLSSLSSWTAEQFDPQLNWGDVEWIK 246
           N++N+ATKPRW +GMLGT+RR FGNIVGH KGV D+SSLSSWTA+QFDP+L+W DVEWIK
Sbjct: 183 NILNMATKPRWVMGMLGTQRRGFGNIVGHVKGVADMSSLSSWTAQQFDPRLSWDDVEWIK 242

Query: 247 KRWGGKLILKGIMDAEDARLAVNSGADALIVSNHGGRQLDGAPSSIAALPGIADAVAQMG 306
           K WGGKLI+KGI+D EDA LA N+GADAL+VSNHGGRQLDGAPSSI+ LP I +AV   G
Sbjct: 243 KCWGGKLIIKGILDVEDAHLAANAGADALVVSNHGGRQLDGAPSSISQLPAIVEAV---G 299

Query: 307 GGIEVWMDGGIRSGQDVLKARALGAQGTLIGRSFLYGLGAYGEAGVTRALQIIQKELDIT 366
             IEVW+DGGIRSGQDVLKA ALGA+GT+IGR  LYGLGA GEAGVT+AL+II +ELD++
Sbjct: 300 ERIEVWLDGGIRSGQDVLKAMALGAKGTMIGRPHLYGLGAMGEAGVTKALEIIARELDVS 359

Query: 367 MAFCGHTNINTVDRSILLPGTYP 389
           MA CG+ +I  V+R ILLPGT+P
Sbjct: 360 MALCGYNDIRDVNREILLPGTFP 382


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: 519
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: 386
Length adjustment: 30
Effective length of query: 360
Effective length of database: 356
Effective search space:   128160
Effective search space used:   128160
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.

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