GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__SB2B:6936480 Sama_0668 iron(III) ABC
           transporter, ATP-binding protein (RefSeq)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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