GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Methanobacterium lacus AL-21

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein

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



>NCBI__GCF_000191585.1:WP_013645374.1
          Length = 223

 Score =  126 bits (316), Expect = 6e-34
 Identities = 74/213 (34%), Positives = 122/213 (57%), Gaps = 10/213 (4%)

Query: 4   VTLRDICKSY-DGTPIT-RHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL- 60
           + ++++ K Y DG+ I   ++DL+IE GE V  +GPSG GKSTLL +I GL+    G + 
Sbjct: 7   IKIKNLKKEYEDGSIIALNNVDLEIERGESVSIIGPSGSGKSTLLNMIGGLDKANEGQIS 66

Query: 61  -----LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVE 115
                L+DN  +++   +   +G VFQ + L P++TV EN+   L    +D ++++ R  
Sbjct: 67  VAGVNLMDNSDLSNF--RSNEIGFVFQLHNLIPNLTVLENVQIPLLGTDIDDKKMEERAL 124

Query: 116 AVAEILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIE 175
            + + + L+  +++KP  LSGG+RQRVAI R +V  P + L DEP   LD+  +  +   
Sbjct: 125 KLLKSVNLENKVDQKPTKLSGGERQRVAIARALVNHPSIILADEPTGALDSETQEVILKL 184

Query: 176 IARLHQRIRSTMIYVTHDQVEAMTLADKIVVLN 208
           +  +H++   T+I VTH+   A      I VL+
Sbjct: 185 LLDIHKKENVTLIMVTHEPYVAKQADRSIYVLD 217


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: 173
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: 223
Length adjustment: 26
Effective length of query: 345
Effective length of database: 197
Effective search space:    67965
Effective search space used:    67965
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: 47 (22.7 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