GapMind for catabolism of small carbon sources

 

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

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein

Query= TCDB::Q52666
         (263 letters)



>NCBI__GCF_000191585.1:WP_013645374.1
          Length = 223

 Score =  149 bits (375), Expect = 6e-41
 Identities = 89/224 (39%), Positives = 138/224 (61%), Gaps = 9/224 (4%)

Query: 17  VSDEIAIQISQMNKWY--GQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEH 74
           ++D   I+I  + K Y  G    L +++L + RGE + I GPSGSGKST++  I  L++ 
Sbjct: 1   MNDNTIIKIKNLKKEYEDGSIIALNNVDLEIERGESVSIIGPSGSGKSTLLNMIGGLDKA 60

Query: 75  QSGKIIVDGIEL--TSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKR 132
             G+I V G+ L   SDL N     +E+G VFQ  NL P+LT+LEN+ + P+    +  +
Sbjct: 61  NEGQISVAGVNLMDNSDLSNFRS--NEIGFVFQLHNLIPNLTVLENVQI-PLLGTDIDDK 117

Query: 133 EAEETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEM 192
           + EE A+  L+ V +  +  + P +LSGG++QRVAIAR+L   P I+L DEPT ALD E 
Sbjct: 118 KMEERALKLLKSVNLENKVDQKPTKLSGGERQRVAIARALVNHPSIILADEPTGALDSET 177

Query: 193 IKEVLDTMIQL-AEEGMTMLCVTHEMGFAQAVANRVIFMADGQI 235
            + +L  ++ +  +E +T++ VTHE   A+  A+R I++ DG+I
Sbjct: 178 QEVILKLLLDIHKKENVTLIMVTHEPYVAKQ-ADRSIYVLDGKI 220


Lambda     K      H
   0.320    0.134    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: 145
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: 263
Length of database: 223
Length adjustment: 23
Effective length of query: 240
Effective length of database: 200
Effective search space:    48000
Effective search space used:    48000
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: 46 (22.3 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