GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5405 in Bacteroides thetaiotaomicron VPI-5482

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



>FitnessBrowser__Btheta:350819
          Length = 463

 Score =  144 bits (363), Expect = 3e-39
 Identities = 82/241 (34%), Positives = 139/241 (57%), Gaps = 6/241 (2%)

Query: 12  EGIIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRI 71
           + II++  V+K++G    L D+ LNVK+GE + + GPSG GK+T +R +   +   +G I
Sbjct: 7   KSIIEVSHVSKFFGDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEI 66

Query: 72  VVDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAM 131
            + G E+T    Q    +R V  VFQ + LFPHL +  N     + ++K PK+   +   
Sbjct: 67  RISGKEIT----QTPPHKRPVNTVFQKYALFPHLNVYDNIAFG-LKLKKTPKQTIGKKVK 121

Query: 132 HYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDT 191
             L+ V + +  ++    LSGGQQQRVAIARA+  +P+++L DEP +ALD +M K++   
Sbjct: 122 AALKMVGMTDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQME 181

Query: 192 MIGLAED-GMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLS 250
           +  + +  G+T + VTH+   A T+++ ++ M +G+I +   P D ++ P N     F+ 
Sbjct: 182 LKEMHKSLGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIG 241

Query: 251 Q 251
           +
Sbjct: 242 E 242


Lambda     K      H
   0.322    0.137    0.407 

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: 286
Number of extensions: 14
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: 254
Length of database: 463
Length adjustment: 29
Effective length of query: 225
Effective length of database: 434
Effective search space:    97650
Effective search space used:    97650
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: 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