GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Synechococcus elongatus PCC 7942

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase

Query= uniprot:A0A165KQ08
         (355 letters)



>FitnessBrowser__SynE:Synpcc7942_0947
          Length = 355

 Score =  292 bits (748), Expect = 8e-84
 Identities = 164/358 (45%), Positives = 224/358 (62%), Gaps = 8/358 (2%)

Query: 1   MAS-SLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDE 59
           MAS +L++  + K +     SV  +  + + + PGEFL L+GPSGCGKST L +IAGLD+
Sbjct: 1   MASFALELRQLRKAYSP---SVVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQ 57

Query: 60  PTEGEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRI 119
           PT G I +G + +  +PP DRD+AMVFQSYALYP L+V  N+   L++R+    E ++R+
Sbjct: 58  PTSGSIWLGDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRL 117

Query: 120 DEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRA 179
            +VA  L++ HLLDRRP+QLSGGQRQRVA+GRAL RQP +FL DEPLSNLDA LR ++RA
Sbjct: 118 QQVAHNLELDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRA 177

Query: 180 EIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFI 239
           ++K L        VYVTHDQ EA++L  RIA++ GG +QQL +PD IY  PAN +VA FI
Sbjct: 178 QMKALFSQQASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFI 237

Query: 240 GSPTMNLLRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQETAPWRG---RV 296
           GSP MNLL   +  GQ  +   AL +    ++ ++VL G+RPEHL +      R    ++
Sbjct: 238 GSPRMNLLPLPIHSGQAWLGSRALPIPSHLAARSQVLWGLRPEHLKLATPEVERAIPVQL 297

Query: 297 SVVEPTGPDTYVMVDTAAG-SVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSEERL 353
            + E  G    + V  AA   V LR    +       + +   P   HWF   + +RL
Sbjct: 298 HLTENLGMQRLLTVAIAANPEVRLRLLMPSDQPIPTDLQVTFEPESQHWFCPSTGDRL 355


Lambda     K      H
   0.318    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: 352
Number of extensions: 16
Number of successful extensions: 1
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: 355
Length of database: 355
Length adjustment: 29
Effective length of query: 326
Effective length of database: 326
Effective search space:   106276
Effective search space used:   106276
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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