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_1096 Echvi_1096 nitrate transport ATP-binding subunits C and D

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



>FitnessBrowser__Cola:Echvi_1096
          Length = 294

 Score =  151 bits (382), Expect = 2e-41
 Identities = 91/216 (42%), Positives = 133/216 (61%), Gaps = 9/216 (4%)

Query: 1   MTALQLTNVCKSFGP----VEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDAT 56
           M  ++L NV KSFG     V+VL DINL V +GEFV  VG SG GK+TL+ +++GL    
Sbjct: 1   MAIIELNNVSKSFGMGASRVDVLSDINLQVAEGEFVAIVGFSGSGKTTLINLLNGLAFPD 60

Query: 57  AGEISIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQ--ERQPKEEIAARV 114
            GE+ + GQ VT   P  RG+  +FQ+Y+L P LSV  N+ LA+ +   +   +E A+ +
Sbjct: 61  QGEVLLHGQPVTGPGP-DRGV--IFQNYSLLPWLSVYNNVKLAVDEVFPQLSSKEKASHI 117

Query: 115 AEASRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRL 174
            +   M++L   +D+ P ELSGG RQRV++ RA+   P++ L DEPLS LDA  R + + 
Sbjct: 118 KKYIGMVNLTPAMDKLPKELSGGMRQRVSVARALAMNPEILLMDEPLSALDALTRGSLQE 177

Query: 175 EIARLHRQLSASMIYVTHDQIEAMTLADKIVVLRDG 210
           EI R+  Q   + I +T+D  E + +AD+I+ L  G
Sbjct: 178 EIIRIWSQDKKTAILITNDVDEGILMADRIIPLTPG 213


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: 205
Number of extensions: 9
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: 294
Length adjustment: 27
Effective length of query: 304
Effective length of database: 267
Effective search space:    81168
Effective search space used:    81168
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