GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Desulfovibrio vulgaris Miyazaki F

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 8499890 DvMF_0655 ABC transporter related (RefSeq)

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__Miya:8499890
          Length = 350

 Score =  261 bits (667), Expect = 2e-74
 Identities = 154/375 (41%), Positives = 224/375 (59%), Gaps = 30/375 (8%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M+ ++L N+ + + + +  +V++ + ++     +V +GPSGCGKSTTLR+IAGLE +T G
Sbjct: 1   MSAIQLLNVSRHWGDVR--AVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSG 58

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            + I ++ +    P  R +AMVFQ+YAL+PH++V EN+ FGL +RK  + +  KR+  A 
Sbjct: 59  RIMIGERDVTHLPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRLTRAV 118

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
           +ILGL+  L+RKP +LSGGQ+QRVA+GRA+V +A V LMDEPLSNLDAKLR  MR EI  
Sbjct: 119 DILGLSALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMRREIRA 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           + + +G T +YVTHDQTEAM++ADRI++M            GRI Q  TP ELY+ PA  
Sbjct: 179 LQQTLGMTMVYVTHDQTEAMSMADRIILMQG----------GRIVQNATPSELYSRPATT 228

Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDI 300
           F   FIG+P MN   +   +  +      S     G   +++   Y+     LGIRPE I
Sbjct: 229 FAGNFIGTPPMNLVRLDDARGSVCVAGSRS-----GTVSVVDSADYV-----LGIRPEHI 278

Query: 301 SSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQLTF 360
              +IV E +      A +   E LGS S+L  + G  E +  V+   + + G ++ L  
Sbjct: 279 ---RIVPEGW-----RAVVESVEYLGSGSVLGCRVGGEELSVVVDGVPTIAVGAEIYLHC 330

Query: 361 NIAKGHFFDLETEKR 375
                H FD +T +R
Sbjct: 331 PDEHIHIFDAKTGER 345


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: 316
Number of extensions: 9
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: 377
Length of database: 350
Length adjustment: 29
Effective length of query: 348
Effective length of database: 321
Effective search space:   111708
Effective search space used:   111708
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.

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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