GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Shewanella amazonensis SB2B

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)

Query= reanno::Smeli:SMc03065
         (362 letters)



>FitnessBrowser__SB2B:6936480
          Length = 341

 Score =  184 bits (467), Expect = 3e-51
 Identities = 114/299 (38%), Positives = 170/299 (56%), Gaps = 16/299 (5%)

Query: 1   MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60
           M+ L ++ +   Y    V+ G++L + +GE    +GPSGCGK+TLLR IAGL++I+ G +
Sbjct: 1   MSTLSIQGLHSDYRGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSI 60

Query: 61  FIDGERVND----VPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRG 116
            I+G+ V+     V P KR I M+FQ YAL+PH+TV DN+ FG+R  +  K+    R+  
Sbjct: 61  AINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGVR--QLDKQSRSVRLEE 118

Query: 117 AADMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEI 176
              +++L     R P  LSGGQ+QRV+I RA+   P + L DEP SN+DA +R A  +EI
Sbjct: 119 MLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEI 178

Query: 177 AKLSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIG 236
             +  +  + + ++VTH + EA   AD + +  AG I Q G P  LY+ P   +VA F+G
Sbjct: 179 RAIL-KARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLG 237

Query: 237 SPAMNVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADD 295
             A N +   + A GQ   +S  G   +  D    ASE G+   + +RPE L +    D
Sbjct: 238 --ASNYLDVRLEA-GQ--LISTLGAFPLPQDFKA-ASETGR---WLLRPEQLLIEARAD 287


Lambda     K      H
   0.320    0.137    0.387 

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: 276
Number of extensions: 11
Number of successful extensions: 4
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: 362
Length of database: 341
Length adjustment: 29
Effective length of query: 333
Effective length of database: 312
Effective search space:   103896
Effective search space used:   103896
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 (21.8 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