GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b20002
         (358 letters)



>NCBI__GCF_000191585.1:WP_013645374.1
          Length = 223

 Score =  132 bits (331), Expect = 1e-35
 Identities = 77/216 (35%), Positives = 124/216 (57%), Gaps = 7/216 (3%)

Query: 4   LQLSDVRKSY--GGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLT 61
           +++ +++K Y  G +  +  VDL+I+ GE V  +GPSG GKSTLL MI GL++ + G ++
Sbjct: 7   IKIKNLKKEYEDGSIIALNNVDLEIERGESVSIIGPSGSGKSTLLNMIGGLDKANEGQIS 66

Query: 62  IDDVRMNDVDP----SKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEA 117
           +  V + D           I  VFQ + L P++TV EN+   L    +   ++E+R  + 
Sbjct: 67  VAGVNLMDNSDLSNFRSNEIGFVFQLHNLIPNLTVLENVQIPLLGTDIDDKKMEERALKL 126

Query: 118 AHILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIA 177
              + L   +D+KP +LSGG+RQRVAI RA+V HP I L DEP   LD+E +  +   + 
Sbjct: 127 LKSVNLENKVDQKPTKLSGGERQRVAIARALVNHPSIILADEPTGALDSETQEVILKLLL 186

Query: 178 RLHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVE 213
            +HK+   T++ VTH+   A   AD+ + +  G ++
Sbjct: 187 DIHKKENVTLIMVTHEPYVAKQ-ADRSIYVLDGKIK 221


Lambda     K      H
   0.321    0.139    0.396 

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: 179
Number of extensions: 10
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: 358
Length of database: 223
Length adjustment: 26
Effective length of query: 332
Effective length of database: 197
Effective search space:    65404
Effective search space used:    65404
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 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