GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA2 in Methanobacterium arcticum M2

Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_048082401.1 EI99_RS13040 ATP-binding cassette domain-containing protein

Query= uniprot:P70970
         (276 letters)



>NCBI__GCF_000746075.1:WP_048082401.1
          Length = 279

 Score =  201 bits (512), Expect = 1e-56
 Identities = 111/259 (42%), Positives = 164/259 (63%), Gaps = 5/259 (1%)

Query: 9   ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68
           AL +IN S   G  +A++G  G+GKSTL  H NG+L+PT G + + +  +    K +DL 
Sbjct: 19  ALENINFSAPTGKIIALLGPNGAGKSTLFLHFNGILQPTSGSVMVDNACLNY--KKEDLM 76

Query: 69  KLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEELLDR 128
            LR+KVGIVFQ P+ QLF  TV++D++FGP+N G+ KE+ +++  E L+ V + E    +
Sbjct: 77  NLRQKVGIVFQNPDDQLFAPTVVEDVAFGPVNLGLSKEEVKKRVDESLRRVEMIE-FKHK 135

Query: 129 SPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTTIL 188
           +P  LSGGQ +RVAIAG+LAM P+++VLDEPT+GLDPRG  +IM + YEL++ G +T I+
Sbjct: 136 APHHLSGGQKKRVAIAGILAMHPKIMVLDEPTSGLDPRGASKIMKLLYELNREG-ITIII 194

Query: 189 VTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEEMAGWGLDLPETIKFQRHLEAAL 248
            TH ++    YA  + ++ KG I   GSP+++F   E +    L LP        L+   
Sbjct: 195 STHDVDLVPLYAHSVYIISKGNIIKKGSPQEVFEDAETIRKANLRLPRIAHLVEILQKED 254

Query: 249 GVRFNEPM-LTIEDAAAEI 266
            V F++P  LTI +A   I
Sbjct: 255 KVPFDKPYPLTIGEARKRI 273


Lambda     K      H
   0.318    0.136    0.380 

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: 222
Number of extensions: 9
Number of successful extensions: 4
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: 276
Length of database: 279
Length adjustment: 25
Effective length of query: 251
Effective length of database: 254
Effective search space:    63754
Effective search space used:    63754
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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