GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Shewanella oneidensis MR-1

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate 200449 SO1271 polyamine ABC transporter, ATP-binding protein (NCBI ptt file)

Query= reanno::Smeli:SMc02121
         (258 letters)



>FitnessBrowser__MR1:200449
          Length = 378

 Score =  155 bits (393), Expect = 9e-43
 Identities = 88/259 (33%), Positives = 144/259 (55%), Gaps = 8/259 (3%)

Query: 1   MANTATAPKLAVSTTD--VAIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKS 58
           MA+T+       + T   V ++I  ++K + D   + D++L + +GE   + G SGSGKS
Sbjct: 1   MASTSGVTNKPTTKTQEKVLLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKS 60

Query: 59  TMIRCINRLEEHQKGKIVVDGIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLA 118
           T++R +   E    G+I +DG ++T+    +    R + M+FQ + LFPH+T+ +N    
Sbjct: 61  TLLRMLAGFERPTSGRIYLDGEDITD----LPPYERPINMMFQSYALFPHMTVAQNIAFG 116

Query: 119 PIWVRKMPKKEAEQVAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFD 178
            +   K+PK E EQ     L+ V + +   + P QLSGGQ+QRVA+ARSL  RPK+LL D
Sbjct: 117 -LKQDKLPKAEIEQRVQEMLKLVHMEQYGKRKPHQLSGGQRQRVALARSLAKRPKLLLLD 175

Query: 179 EPTSALDPEMVKEV-LDTMVGLAEEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSP 237
           EP  ALD ++  ++ L+ +  L   G+T + VTH+   A  +A R+  M  G I +  SP
Sbjct: 176 EPMGALDKKLRTQMQLEVVEILERVGVTCVMVTHDQEEAMTMAGRISIMSDGWIAQTGSP 235

Query: 238 AEFFDNPQHERTKLFLSQI 256
            + +++P       F+  +
Sbjct: 236 MDIYESPNSRMIAEFIGSV 254


Lambda     K      H
   0.322    0.136    0.397 

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: 230
Number of extensions: 15
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: 258
Length of database: 378
Length adjustment: 27
Effective length of query: 231
Effective length of database: 351
Effective search space:    81081
Effective search space used:    81081
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 (21.9 bits)
S2: 48 (23.1 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