GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5405 in Pseudomonas litoralis 2SM5

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_090275879.1 BLU11_RS18455 methionine ABC transporter ATP-binding protein

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



>NCBI__GCF_900105005.1:WP_090275879.1
          Length = 334

 Score =  162 bits (410), Expect = 8e-45
 Identities = 97/242 (40%), Positives = 137/242 (56%), Gaps = 6/242 (2%)

Query: 14  IIQMQGVNKWYG----QFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQG 69
           +I+ Q VNK Y         L   +L ++ G+   + G SG+GKST +R +NRLEE   G
Sbjct: 1   MIEFQQVNKAYRVGGRDIPALHATDLTIEAGQVYGIIGHSGAGKSTLLRLINRLEEPSNG 60

Query: 70  RIVVDGVELTN-DLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEE 128
           RI+V G + T  + + +   R+ VGM+FQHFNL    T+  N  L         +++   
Sbjct: 61  RIMVAGEDTTALNAEGLRRFRQRVGMIFQHFNLLSSATVADNVALPLRLAGSANRQQIAA 120

Query: 129 IAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEV 188
                L+RV + + A KYP QLSGGQ+QRV IARAL  +P I+L DE TSALDP    +V
Sbjct: 121 RVASLLDRVGLSDHASKYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPHTTGQV 180

Query: 189 LDTMIGL-AEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKL 247
           L  +  +  E  +T++ +THEM   R V ++V  MD G IVEQ    D F +PQ+  T+ 
Sbjct: 181 LQLLSEINRELNLTIVLITHEMDVIRRVCDQVAVMDGGRIVEQGTVADVFLHPQHPTTRS 240

Query: 248 FL 249
           F+
Sbjct: 241 FV 242


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: 203
Number of extensions: 7
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: 334
Length adjustment: 26
Effective length of query: 228
Effective length of database: 308
Effective search space:    70224
Effective search space used:    70224
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 24 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