GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Dyella japonica UNC79MFTsu3.2

Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773
         (244 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1085
          Length = 336

 Score =  167 bits (422), Expect = 3e-46
 Identities = 101/249 (40%), Positives = 147/249 (59%), Gaps = 10/249 (4%)

Query: 1   MISIKSINKWYG----DFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKG 56
           MI    ++K Y     D   L   S ++  GEV  + G SG+GKSTLI+ +N LE    G
Sbjct: 1   MIRFVDVHKSYRVDGKDIPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGG 60

Query: 57  DIVVDGTSI-ADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATK 115
            I++DGT + A     L   R R+GM+FQHF L    T+ +N+    +++ G +     K
Sbjct: 61  SILIDGTEMTALGDAALRAQRRRIGMIFQHFNLLSSQTVADNIAFP-LRLAGETDAGKIK 119

Query: 116 KGL-QLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNE 174
             + +LL RVGL AHA K+P QLSGGQ+QRV IARALA  P ++L DE TSALDP+    
Sbjct: 120 ARVDELLRRVGLEAHASKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTAS 179

Query: 175 VLDVMVQLAHE-GMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARAER 233
           VL+++ ++  E  +T++ +THEM   R+V DRV  +D G+I+E     + F  ++ R   
Sbjct: 180 VLELLAEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVF--LHPRHPT 237

Query: 234 TQHFLNKIL 242
           T+ F+N+ L
Sbjct: 238 TRRFVNEAL 246


Lambda     K      H
   0.321    0.136    0.394 

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: 209
Number of extensions: 7
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: 244
Length of database: 336
Length adjustment: 26
Effective length of query: 218
Effective length of database: 310
Effective search space:    67580
Effective search space used:    67580
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: 47 (22.7 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