GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Dechlorosoma suillum PS

Align ATPase (characterized, see rationale)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  158 bits (399), Expect = 2e-43
 Identities = 95/243 (39%), Positives = 145/243 (59%), Gaps = 9/243 (3%)

Query: 22  IYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWI 81
           I    + K +GN F AL  VSL++  GE+V ++GPSG GK+T LR +  +E+   G++  
Sbjct: 3   IEIRNIAKRFGN-FVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMF 61

Query: 82  EGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLA-PVQVRRWPVAQAEATAR- 139
           EG   +H    +    ++VG VFQ + LF H+ V +N+     V+ R+    ++E   R 
Sbjct: 62  EGSEATH----LHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRV 117

Query: 140 -QLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLD 198
             LL  V++   AD+YP QLSGGQ+QR+A+ARALA++P++LL DEP  ALD ++ +E+  
Sbjct: 118 MDLLSLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRR 177

Query: 199 VMRDLASE-GMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFL 257
            +R L  E  ++ +  TH+   A EVADRVV+M  G+I +   PD  ++ P S    QFL
Sbjct: 178 WLRRLHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFL 237

Query: 258 AQI 260
             +
Sbjct: 238 GNV 240


Lambda     K      H
   0.321    0.134    0.387 

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: 237
Number of extensions: 16
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: 261
Length of database: 360
Length adjustment: 27
Effective length of query: 234
Effective length of database: 333
Effective search space:    77922
Effective search space used:    77922
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