GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araZsh in Caldicellulosiruptor hydrothermalis 108

Align Inner-membrane translocator (characterized, see rationale)
to candidate WP_013402606.1 CALHY_RS03375 ABC transporter permease

Query= uniprot:A0KWY7
         (320 letters)



>NCBI__GCF_000166355.1:WP_013402606.1
          Length = 332

 Score =  151 bits (382), Expect = 2e-41
 Identities = 90/289 (31%), Positives = 171/289 (59%), Gaps = 12/289 (4%)

Query: 36  VTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSGVVTSLLITEYQ-WHPLLAFVV 94
           +++LL + A L I  +GM LVI++ GIDLSVG+V+AL+G++++L++++YQ   P++A ++
Sbjct: 44  ISDLLTNTAILAILTVGMMLVIVTRGIDLSVGSVLALAGMISALIVSKYQNVSPIVAILI 103

Query: 95  ILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLATTLSEES--IAIDHPF-YDAVA 151
            + +G + G + G +I    + P I TL  M + RG+   +S+     A + P  +  +A
Sbjct: 104 GIFVGAICGVINGFLISKTNILPIIATLGTMNIYRGITYMISKGQWVSADEMPLSFKRIA 163

Query: 152 EMSIALPGNGALDLSSLIFILFFVIIAVVMHYTRFGTNVYAIGGNQHSAELMGISIAKTT 211
             SI L  N  + ++ + +I+F+  +     +TR G  +YAIG N  +A + GI+++K  
Sbjct: 164 TGSI-LGINNLIVVAIITYIVFYYFV----QHTRTGRQIYAIGSNPEAARISGINVSKLI 218

Query: 212 ISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDAIAAVVIGGTLLTGGSGFVLGTVL 271
           +++Y +   L+ LAG+++     S  +  A G E++ IAA V+GG  + GGSG + G +L
Sbjct: 219 LTVYFLMGVLSGLAGVLWVSKFASAQSDTATGYEMNVIAAAVLGGVSIAGGSGRISGIIL 278

Query: 272 GVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFILLQKL--LNGRKTQ 318
           G +L+G++   +    ++S +W + + G ++   +++  L  +N  K Q
Sbjct: 279 GTLLLGILNNALPL-VNVSPFWQQAIQGFIILIAVIVNVLVRMNMEKAQ 326


Lambda     K      H
   0.330    0.145    0.424 

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: 349
Number of extensions: 19
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: 320
Length of database: 332
Length adjustment: 28
Effective length of query: 292
Effective length of database: 304
Effective search space:    88768
Effective search space used:    88768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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