GapMind for catabolism of small carbon sources

 

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

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

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



>FitnessBrowser__Dyella79:N515DRAFT_1085
          Length = 336

 Score =  163 bits (413), Expect = 4e-45
 Identities = 93/230 (40%), Positives = 133/230 (57%), Gaps = 2/230 (0%)

Query: 30  DFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIVVDGIELTN-DLKK 88
           D   L+  +L +  GE   + G SG+GKST+IR IN LE    G I++DG E+T      
Sbjct: 17  DIPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGSILIDGTEMTALGDAA 76

Query: 89  IDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKEAEQVAMHFLERVKIPEQAL 148
           +   RR +GM+FQHFNL    T+ +N         +    + +      L RV +   A 
Sbjct: 77  LRAQRRRIGMIFQHFNLLSSQTVADNIAFPLRLAGETDAGKIKARVDELLRRVGLEAHAS 136

Query: 149 KYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVKEVLDTMVGLAEE-GMTMI 207
           KYP QLSGGQ+QRV IAR+L  RP ILL DE TSALDP+    VL+ +  +  E  +T++
Sbjct: 137 KYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASVLELLAEINRELKLTIV 196

Query: 208 CVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHERTKLFLSQIL 257
            +THEM   R+V +RV  +D G+IVE  + A+ F +P+H  T+ F+++ L
Sbjct: 197 LITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTRRFVNEAL 246


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: 202
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: 258
Length of database: 336
Length adjustment: 26
Effective length of query: 232
Effective length of database: 310
Effective search space:    71920
Effective search space used:    71920
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