GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Synechococcus elongatus PCC 7942

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__SynE:Synpcc7942_0960
          Length = 417

 Score =  284 bits (726), Expect = 4e-81
 Identities = 169/407 (41%), Positives = 238/407 (58%), Gaps = 58/407 (14%)

Query: 7   DNIYKRYPNAKHYS-------VENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITE 59
           + I KR+P             +   NL+I D EF+V VGPSGCGKST LR++AGLE  + 
Sbjct: 29  EEIEKRFPEQARSPQKGEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSR 88

Query: 60  GNLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLR-------------- 105
           G + + D+ ++    K RDIAMVFQ+YALYPH+SVY+N+AFGL+ +              
Sbjct: 89  GLIKVGDRRVDRLPAKARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALAT 148

Query: 106 -------KYKKDD---INKRVHEAAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAK 155
                  +Y+ +    I +RV E A +L L   L+R+P  LSGGQ+QRVA+GRAI R+ +
Sbjct: 149 RSLPKSLQYEPEQEARIKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRAIARNPQ 208

Query: 156 VFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNP 215
           VFLMDEPLSNLDAKLR   RA+I  + R++G TT+YVTHDQTEAMT+ DRI +++     
Sbjct: 209 VFLMDEPLSNLDAKLRAETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVLNR---- 264

Query: 216 DKTGSIGRIEQIGTPQELYNEPANKFVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQ 275
                 G ++Q+ +P E+Y+ PAN+FVA FIGSP MN   VTV     +  +     LP+
Sbjct: 265 ------GHLQQVASPLEIYDRPANRFVAQFIGSPPMNLIPVTVRAPLQLTTENFRCTLPE 318

Query: 276 GQEKILEEKGYLGKKVTLGIRPEDISSDQIVHETFPNASVTADILVS----ELLGSESML 331
             E +L  + Y G+ V LGIRPE +            A+ + ++L++    E LGS++ +
Sbjct: 319 AWEPVL--RLYDGQTVELGIRPEHLE---------VGAAASKNLLITVTGVEALGSDTFI 367

Query: 332 --YVKFGSTEFTARVNARDSHSPGEKVQLTFNIAKGHFFDLETEKRI 376
              +K       AR+  +     G+++ LTF   + H FDLET K I
Sbjct: 368 AGELKESGIAVQARLAPQQCWQMGDRLWLTFKPDQIHLFDLETGKAI 414


Lambda     K      H
   0.318    0.135    0.379 

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: 375
Number of extensions: 13
Number of successful extensions: 5
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: 377
Length of database: 417
Length adjustment: 31
Effective length of query: 346
Effective length of database: 386
Effective search space:   133556
Effective search space used:   133556
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: 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