GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Sulfurivirga caldicuralii DSM 17737

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD

Query= reanno::psRCH2:GFF857
         (371 letters)



>NCBI__GCF_900141795.1:WP_074200832.1
          Length = 227

 Score =  116 bits (290), Expect = 7e-31
 Identities = 75/216 (34%), Positives = 116/216 (53%), Gaps = 11/216 (5%)

Query: 7   RDICKSY-DG---TPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLI 62
           R++ K+Y DG   TP+ + + L +   E V  VG SG GKSTLL L+ GL+  T G++L+
Sbjct: 9   RNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGEVLL 68

Query: 63  DNQRVNDLPP------KDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEA 116
             Q  + L        ++R +G V+Q + L P +T  EN+   L +    +   + +  A
Sbjct: 69  LGQPFSKLGEAARGRLRNRHMGFVYQFHHLLPELTAEENVMMPLLIRRESEATARDKALA 128

Query: 117 VAEILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEI 176
           + + + L +    KP +LSGG+RQRVA+ R +V EP   L DEP  NLD+    Q+   +
Sbjct: 129 LLDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVLSLM 188

Query: 177 ARLHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEI 212
             L+QR  + ++ VTHD V      D+ + L  G I
Sbjct: 189 DDLNQRFGTALLVVTHD-VNIAARMDRTLTLRDGMI 223


Lambda     K      H
   0.322    0.139    0.405 

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: 11
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: 371
Length of database: 227
Length adjustment: 26
Effective length of query: 345
Effective length of database: 201
Effective search space:    69345
Effective search space used:    69345
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