GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Methanobacterium lacus AL-21

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

Query= reanno::pseudo6_N2E2:Pf6N2E2_2050
         (263 letters)



>NCBI__GCF_000191585.1:WP_013645374.1
          Length = 223

 Score =  126 bits (317), Expect = 3e-34
 Identities = 83/232 (35%), Positives = 134/232 (57%), Gaps = 15/232 (6%)

Query: 9   NTQPLLDIRGLRKQY--GPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQ 66
           N   ++ I+ L+K+Y  G +  L  VDL ++RG  V++IG SGSGK+TLL  +  L++  
Sbjct: 2   NDNTIIKIKNLKKEYEDGSIIALNNVDLEIERGESVSIIGPSGSGKSTLLNMIGGLDKAN 61

Query: 67  GGQIMLDGESIGYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLK 126
            GQI + G ++  D+ D    R  E          G  FQ  NL P+LT L+NV + LL 
Sbjct: 62  EGQISVAGVNL-MDNSDLSNFRSNE---------IGFVFQLHNLIPNLTVLENVQIPLLG 111

Query: 127 VKKLPKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVT 186
              +   +    A K L+ V L  + D  P +LSGG++QRVAIARA+  +PS++L DE T
Sbjct: 112 TD-IDDKKMEERALKLLKSVNLENKVDQKPTKLSGGERQRVAIARALVNHPSIILADEPT 170

Query: 187 SALDPELVGEVLNVIKGL-AEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIE 237
            ALD E    +L ++  +  ++ +T+++VTHE  +  + +D+ +++  G+I+
Sbjct: 171 GALDSETQEVILKLLLDIHKKENVTLIMVTHE-PYVAKQADRSIYVLDGKIK 221


Lambda     K      H
   0.320    0.138    0.392 

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: 150
Number of extensions: 14
Number of successful extensions: 3
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