GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Echinicola vietnamensis KMM 6221, DSM 17526

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components

Query= reanno::Phaeo:GFF2754
         (331 letters)



>FitnessBrowser__Cola:Echvi_2123
          Length = 318

 Score =  162 bits (411), Expect = 8e-45
 Identities = 105/331 (31%), Positives = 178/331 (53%), Gaps = 20/331 (6%)

Query: 1   MTALQLTNVCKSFGPVEV-LKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGE 59
           M+ L+++ V K +    + L+D +L V+ G  V  VG SG GKS+LLR+I+GLE  +AG 
Sbjct: 1   MSYLKVSEVSKRYDAGSLALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGV 60

Query: 60  ISIGGQTVTTTP----PAKRGIAMVFQSYALYPHLSVRENMA--LALKQERQPKEEIAAR 113
           + +G Q +        P    I ++ Q Y LYP+ +V EN+A  L L  +   KE    R
Sbjct: 61  VHLGDQKILNPAQKLVPGYDEIQLIHQEYKLYPNSTVEENIARPLLLYDKAYQKE----R 116

Query: 114 VAEASRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTR 173
            AE   +LSL  + D++P +LSGGQ+Q+VAIGRA+  EP++ L DEP S+LDA  + +  
Sbjct: 117 TAEILELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLI 176

Query: 174 LEIARLHRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEF 233
            E+  +   L  ++I+VTHD  +A+ +++++++++ G++ Q G   E++  PA+ +VA  
Sbjct: 177 EELKEIFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARL 236

Query: 234 IGAPAMNFVPAQRLGGNPGQFIGIRPEYARISPVGPLAGEVIHVEKLGGDTNILVDMGED 293
            G   +N +P         +   +RP   +I+    +  EV+  + L     + V + + 
Sbjct: 237 FG--YLNLIPG-------AEEAYVRPSEVKITSKTSIKAEVVKQQFLIHYNLLTVKLEDS 287

Query: 294 LTFTARLFGQHDTNVGETLQFDFDPANCLSF 324
             F          NVG+ +  D+     + F
Sbjct: 288 ELFWKVDDPSRSVNVGDEVFLDYQKEQLIQF 318


Lambda     K      H
   0.320    0.137    0.391 

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: 239
Number of extensions: 13
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: 331
Length of database: 318
Length adjustment: 28
Effective length of query: 303
Effective length of database: 290
Effective search space:    87870
Effective search space used:    87870
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 (21.8 bits)
S2: 48 (23.1 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