GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtD in Methanobacterium arcticum M2

Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_048081634.1 EI99_RS08980 ABC transporter ATP-binding protein

Query= TCDB::Q97VF5
         (362 letters)



>NCBI__GCF_000746075.1:WP_048081634.1
          Length = 229

 Score =  115 bits (288), Expect = 1e-30
 Identities = 88/240 (36%), Positives = 139/240 (57%), Gaps = 18/240 (7%)

Query: 45  ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104
           I+E+  L   YD+G    IKA+N +   + KGE + IIG SGSGK+TL++ I  A+   G
Sbjct: 6   IIEIKGLKKSYDKGK---IKALNGIDLEIRKGEFVSIIGPSGSGKSTLLNMI-GALDTAG 61

Query: 105 KIISGKVIFNGMDIF-SMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHG 163
           +   G V   G+D+  +  + +FR    ++I +V Q     L P L + E      I   
Sbjct: 62  E---GSVEVAGIDLTKTKDLSKFRS---QEIGFVFQLHN--LIPNLTVLENVQIPMIGTS 113

Query: 164 EADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223
            + K  + +RA +LLK V L+    +   P +LSGG +QRV IA +L+ NP +IL DEPT
Sbjct: 114 ISGKD-MEKRALKLLKSVDLEDR--IDQRPTKLSGGERQRVAIARALVNNPSIILADEPT 170

Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283
            ALD    +++L L+K+++++  VT+V VTH+   +A +A+R++ +  G ++EE KT  I
Sbjct: 171 GALDSKTGDIILDLLKDLHKKENVTLVMVTHEPY-VANMADRIITVRDGKILEE-KTNNI 228


Lambda     K      H
   0.319    0.138    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: 192
Number of extensions: 7
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: 362
Length of database: 229
Length adjustment: 26
Effective length of query: 336
Effective length of database: 203
Effective search space:    68208
Effective search space used:    68208
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 Sep 24 2021. 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