GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Dechlorosoma suillum PS

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

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



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  159 bits (403), Expect = 6e-44
 Identities = 92/247 (37%), Positives = 147/247 (59%), Gaps = 14/247 (5%)

Query: 17  VAIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIV 76
           ++IEI N+ K +G+F  L D++L +  GE + + GPSG GK+T++R I  +E   +G+++
Sbjct: 1   MSIEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVM 60

Query: 77  VDGIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKEA------ 130
            +G E T+    +    R+VG VFQH+ LF H+ + EN       +R  P+KE       
Sbjct: 61  FEGSEATH----LHARERQVGFVFQHYALFRHMNVFENVAFG---LRVKPRKERPCESEI 113

Query: 131 EQVAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVK 190
            +  M  L  V++   A +YP QLSGGQ+QR+A+AR+L + PK+LL DEP  ALD ++ K
Sbjct: 114 RKRVMDLLSLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRK 173

Query: 191 EVLDTMVGLAEE-GMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHERT 249
           E+   +  L +E  ++ + VTH+   A +VA+RV+ M++G+I +  SP E + NP     
Sbjct: 174 ELRRWLRRLHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFV 233

Query: 250 KLFLSQI 256
             FL  +
Sbjct: 234 YQFLGNV 240


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: 13
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: 360
Length adjustment: 27
Effective length of query: 231
Effective length of database: 333
Effective search space:    76923
Effective search space used:    76923
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.

Links

Downloads

Related tools

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