GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Flavobacterium sp. LM5

Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate WP_024981057.1 BXU11_RS07070 ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_25895
         (367 letters)



>NCBI__GCF_002017945.1:WP_024981057.1
          Length = 220

 Score =  122 bits (306), Expect = 9e-33
 Identities = 69/215 (32%), Positives = 115/215 (53%), Gaps = 10/215 (4%)

Query: 7   KNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAG---TIELD 63
           KN+ K ++   ++KG+DL +   E V  VG SG GK+TLL+++  L+  T+    ++ ++
Sbjct: 5   KNIHKFYDQLEVLKGVDLHITKGEIVSIVGASGAGKTTLLQILGTLDRPTSNENSSLLIN 64

Query: 64  GRDITEVSPA------KRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEA 117
           G D+ +++          +L  +FQ + L P  +  +N+     +AG NK E E +  + 
Sbjct: 65  GEDVLKMNDKALSRFRNLNLGFIFQFHQLLPEFTALENVCIPAFIAGKNKLETEIEAKKL 124

Query: 118 ARILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELA 177
              L L      KP +LSGG++QRVA+ RA++  P I   DEP  NLD      +     
Sbjct: 125 LDYLGLSHRHHHKPNELSGGEQQRVAVARALINKPDILFADEPSGNLDTTSAENLHQLFF 184

Query: 178 RLHKELQATMIYVTHDQVEAMTLADKVVVLNGGRI 212
           +L  EL  T + VTH++ E   +AD+ +V+  G+I
Sbjct: 185 KLRDELGQTFVIVTHNE-ELANMADRKLVMVDGQI 218


Lambda     K      H
   0.321    0.137    0.390 

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: 156
Number of extensions: 6
Number of successful extensions: 2
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: 367
Length of database: 220
Length adjustment: 26
Effective length of query: 341
Effective length of database: 194
Effective search space:    66154
Effective search space used:    66154
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: 47 (22.7 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