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; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex (uncharacterized)
to candidate Synpcc7942_1118 Synpcc7942_1118 mercuric reductase

Query= curated2:O84561
         (465 letters)



>FitnessBrowser__SynE:Synpcc7942_1118
          Length = 516

 Score =  241 bits (615), Expect = 4e-68
 Identities = 151/460 (32%), Positives = 241/460 (52%), Gaps = 27/460 (5%)

Query: 3   EAFDCVVIGAGPGGYVAAI--TAAQAGLKTALIEKREAGGTCLNRGCIPSKALLAGAEVV 60
           + +D VVIGAG  G V A   T    GLK ALIEK+  GG CLN GC+PSKAL+  + V+
Sbjct: 36  DCYDLVVIGAGTTGLVVAAGATGLGLGLKVALIEKQLMGGDCLNFGCVPSKALIRSSRVI 95

Query: 61  TQIRHADQFGIHV--EGFSINYPAMVQRKDSVVRSIRDGLNGLIRSNK-----ITVFSGR 113
            +++ A+  GI V  E  ++++ A+++R    +R +R G++    + +     + VF G+
Sbjct: 96  GELQRANTLGIQVAPEAIAVDFAAVMER----LRKVRAGMSVHDSAQRFQALGVDVFLGQ 151

Query: 114 GSLISSTEVKILGENPSVIKAHSIILATGSEPRAFPGIPFSAESPRILCSTGVLNLKEIP 173
                   +++ GE  + +K    ++ATG+    +P I    E+   L +  V +L   P
Sbjct: 152 ACFCDRNTIQV-GE--ATLKFRKAVIATGARA-TYPNIE-GLEASGFLTNETVFSLSNCP 206

Query: 174 QKMAIIGGGVIGCEFASLFHTLGSEVSVIEASSQILALNNPDISKTMFDKFTRQGLRFVL 233
           +++A+IGGG IGCE A  F  LGS+V++ +  SQ+L   + + ++ + ++    G++  L
Sbjct: 207 RRLAVIGGGPIGCELAQAFQRLGSQVTLFQRRSQLLPKEDFEAAEVIQNQLRADGVQVCL 266

Query: 234 EASVSNIEDIGDRVRLTING----NVEEYDYVLVSIGRRLNTENIGLDKAGVICDERGVI 289
            A ++ IE       +T       +V E D +LV  GR  N +++ L+  GV  D    +
Sbjct: 267 SAEITRIERTASGKLITFRQEGRESVLEVDEILVGTGRSPNVQDLNLEAVGVDYDSVHGV 326

Query: 290 PTDATMRTNVPNIYAIGDITGKWQLAHVASHQGIIAARNIAGH-----KEEIDYSAVPSV 344
             +  ++T  P IYA GD+   W+  H A     I  +N         K ++    +P V
Sbjct: 327 KVNDYLQTTNPKIYAAGDVCSPWKFTHAADAAARIVIKNALFSPFGLGKSKVSDLIIPRV 386

Query: 345 IFTFPEVASVGLSPTAAQQQKIPVKVTKFPFRAIGKAVAMGEADGFAAIISHETTQQILG 404
            FT PEVA VGLS TAA+ Q I +     P   + + V  GE  GF  I     + +ILG
Sbjct: 387 TFTDPEVAHVGLSETAARHQGIAIATITIPLDQVDRTVLDGETAGFIRIHHQPNSDKILG 446

Query: 405 AYVIGPHASSLISEITLAVRNELTLPCIYETIHAHPTLAE 444
           A ++ PHA  +ISE+T A+ N+L +  +   IH +PT AE
Sbjct: 447 ATIVAPHAGEMISEVTTAIANQLGMSALSSVIHPYPTQAE 486


Lambda     K      H
   0.319    0.135    0.388 

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: 509
Number of extensions: 22
Number of successful extensions: 6
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: 465
Length of database: 516
Length adjustment: 34
Effective length of query: 431
Effective length of database: 482
Effective search space:   207742
Effective search space used:   207742
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: 52 (24.6 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