GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5405 in Dechlorosoma suillum PS

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  155 bits (391), Expect = 1e-42
 Identities = 86/243 (35%), Positives = 146/243 (60%), Gaps = 10/243 (4%)

Query: 15  IQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVVD 74
           I+++ + K +G F  L D++L++  GE + L GPSG GK+T +R +  +E   +G+++ +
Sbjct: 3   IEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFE 62

Query: 75  GVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAE----EIA 130
           G E T+    + A  R+VG VFQH+ LF H+ + +N     + V+   +R  E    +  
Sbjct: 63  GSEATH----LHARERQVGFVFQHYALFRHMNVFENVAFG-LRVKPRKERPCESEIRKRV 117

Query: 131 MHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLD 190
           M  L  V++   A +YP QLSGGQ+QR+A+ARAL ++PK++L DEP  ALD ++ KE+  
Sbjct: 118 MDLLSLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRR 177

Query: 191 TMIGLAED-GMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFL 249
            +  L ++  ++ + VTH+   A  VA+RV+ M+KG I +  +P++ + NP +     FL
Sbjct: 178 WLRRLHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFL 237

Query: 250 SQI 252
             +
Sbjct: 238 GNV 240


Lambda     K      H
   0.322    0.137    0.407 

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: 228
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: 254
Length of database: 360
Length adjustment: 27
Effective length of query: 227
Effective length of database: 333
Effective search space:    75591
Effective search space used:    75591
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 Apr 09 2024. 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