GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Synechococcus elongatus PCC 7942

Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Synpcc7942_0842 Synpcc7942_0842 glutathione reductase

Query= reanno::Smeli:SMc03204
         (464 letters)



>FitnessBrowser__SynE:Synpcc7942_0842
          Length = 446

 Score =  214 bits (546), Expect = 4e-60
 Identities = 146/449 (32%), Positives = 222/449 (49%), Gaps = 19/449 (4%)

Query: 8   LLVLGAGPGGYVAAIRAGQLGVNTVIVEKAKAGGTCLNVGCIPSKALIHA---ADEYHRL 64
           LLV+GAG GG  A+ RA   G    I E    GGTC+  GC+P K +++A   A +YH  
Sbjct: 7   LLVIGAGSGGLAASKRAASYGAKVAIAETDLVGGTCVIRGCVPKKLMVYASSFASQYHYA 66

Query: 65  RAAASGKGPLGLSLSAPAIDLRRTIAWKDGIVGRLNGGVTGLLKKAGVKAVIGEGRFVDG 124
            A        G S   P     + IA  D  V RL+     LL+KAGV  ++G  +FVD 
Sbjct: 67  EA-------YGWSAVQPQFSWPKLIAAIDAEVNRLSRLHISLLEKAGVDLILGHAQFVDE 119

Query: 125 KTVDVETETGLQRIRAEAIVIATGSAPVELPDLPFGGSVISSTQALALTDVPQTLAVIGG 184
             + V    G +++ A  I+IA G  P++LP +P G   I+S +   L + PQ  AVIGG
Sbjct: 120 HRLQV----GDRQVTAAKILIAAGGRPIKLP-IPGGELAITSREMFHLPEQPQRFAVIGG 174

Query: 185 GYIGLELGTAFAKLGSKVTVLEALDRILPQYDADLSKPVMKRLGELGVEVFTRTAAKRLS 244
           GYIG E       LGS+VT +   DRIL  +D +L + V   + + GV+  T    +R+ 
Sbjct: 175 GYIGCEFAGILRSLGSEVTQIIRRDRILQGFDQELREAVQTGMSQHGVQFRTGVTVERID 234

Query: 245 ADRRGLLAEENGRAFEVPAEKVLVTVGRRPVTDGWGLEEIDLDHSGRFIRIDDQCRTSMR 304
               GL    +  + ++  ++VL+  GR P  +G  L+   +   GR I +D   RT+  
Sbjct: 235 QTETGLQLSYSDGSQQI-VDQVLMATGREPWLEGLNLDAAGVAIEGRRIAVDAWSRTNQP 293

Query: 305 GVYAIGDVTGEPMLAHRAMAQGEMVAEIVAGHK-RSWDKRCIPAVCFTDPEIVGAGLSPE 363
            ++A+GD T    L   A+A+G   A+   G K R      I +  F+ PE    GLS E
Sbjct: 294 HIFAVGDCTDRVNLTPVAIAEGRAFADTEFGQKPRQISYENIASAVFSQPEACSVGLSEE 353

Query: 364 EARAAGID--VKIGQFPFQANGRAMTTLSEDGFVRVIARADNHLVLGIQAVGHGVSELSA 421
            A+A   +  +++ +  F+     +    E   ++++   ++  VLG   VG   +E+  
Sbjct: 354 AAKAEYGEERIRVYRSRFRPMFYTLPQAEERVLMKLVVETESDRVLGAHMVGKDAAEIIQ 413

Query: 422 TFALAIEMGARLEDIAGTIHAHPTQSEAF 450
           + A+A+ MGA   D   T+  HPT +E F
Sbjct: 414 SVAIAVTMGATKADFDATMALHPTSAEEF 442


Lambda     K      H
   0.319    0.137    0.396 

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: 464
Number of extensions: 28
Number of successful extensions: 8
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: 464
Length of database: 446
Length adjustment: 33
Effective length of query: 431
Effective length of database: 413
Effective search space:   178003
Effective search space used:   178003
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: 51 (24.3 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