GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Dechlorosoma suillum PS

Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

Query= CharProtDB::CH_024626
         (378 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  249 bits (637), Expect = 6e-71
 Identities = 134/305 (43%), Positives = 191/305 (62%), Gaps = 18/305 (5%)

Query: 18  VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77
           +++  I K F     +  + L+I  GE + LLGPSGCGKTT+LR+IAG+ET D G++M +
Sbjct: 3   IEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFE 62

Query: 78  NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRM----QKTPAAEITPRVMEALR 133
             + TH+ A  R V  VFQ YALF HM VFENVAFGLR+    ++   +EI  RVM+ L 
Sbjct: 63  GSEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLS 122

Query: 134 MVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKAL 193
           +VQL+  A R P QLSGGQ+QR+A+ARA+  +P++LLLDE   ALD K+RK+++  L+ L
Sbjct: 123 LVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRRL 182

Query: 194 QRKLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINM 253
             ++ I+ VFVTHDQEEAL ++DR+VVM  GRIEQ G+P E+Y  P + FV  F+G +N+
Sbjct: 183 HDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGNVNV 242

Query: 254 FNATVIERLDEQRVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRVEEINDDNHAEGL 313
           F+             + V G    +     V  GQ+    +RP D+ ++ +      E  
Sbjct: 243 FH-------------SRVHGAWAEV-ARDDVPAGQEAVAFIRPHDIDIDTVATPESLEAK 288

Query: 314 IGYVR 318
           + YV+
Sbjct: 289 VSYVQ 293


Lambda     K      H
   0.319    0.136    0.385 

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: 335
Number of extensions: 12
Number of successful extensions: 3
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: 378
Length of database: 360
Length adjustment: 30
Effective length of query: 348
Effective length of database: 330
Effective search space:   114840
Effective search space used:   114840
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 (21.7 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