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_013402619.1 CALHY_RS03455 ABC transporter permease

Query= uniprot:A0KWY7
         (320 letters)



>NCBI__GCF_000166355.1:WP_013402619.1
          Length = 328

 Score =  149 bits (377), Expect = 7e-41
 Identities = 103/310 (33%), Positives = 166/310 (53%), Gaps = 12/310 (3%)

Query: 16  LLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSGV 75
           L  +F+  +     F +   + +++       + ALG+T VII+ GIDLS+G V+ LS V
Sbjct: 24  LFLLFVFFSLASPNFCTFENIISIILATCVNGMLALGVTFVIITSGIDLSIGTVMTLSAV 83

Query: 76  VTSLLITEYQWHPLLAFVVILPLGT--LFGALMGTIIHVYKLQPFIVTLAGMFLARGLAT 133
           ++ + IT   WH  +   V+  +GT  L G + G +I   KL PFI TL  M +A+GLA 
Sbjct: 84  MSGVFIT--YWHLPVWLGVLGGIGTGMLCGFVNGIVISKMKLPPFIATLGMMMIAKGLAL 141

Query: 134 TLSEES--IAIDHPFYDAVAEMSIA---LPGNGALDLSSLIFILFFVIIAVVMHYTRFGT 188
            +S  +     D P +  +A  SI    +PG   +  + LIFILF +I  +++  T  G 
Sbjct: 142 VISGATPIYYTDAPSFSDIAMGSIIGKIIPG-ADIPNAILIFILFAIIANIILTKTAIGR 200

Query: 189 NVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDA 248
             +AIG N+ +A L G+++ +  I IY +  F   + GI+      S       G ELDA
Sbjct: 201 YDFAIGSNEEAARLSGLNVDRWKIIIYMLCGFFVGIGGILMASRLNSAQPALGQGYELDA 260

Query: 249 IAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFILL 308
           IAAVVIGGT L+GG G ++GTV+G ++M  +   +    S+   W  ++ G+++   + L
Sbjct: 261 IAAVVIGGTSLSGGEGSIIGTVIGALIMSTLTNGLRI-LSVPQEWQIVISGIIVIGAVYL 319

Query: 309 QKLLNGRKTQ 318
             ++  R+T+
Sbjct: 320 D-IIRRRRTK 328


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: 352
Number of extensions: 23
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: 320
Length of database: 328
Length adjustment: 28
Effective length of query: 292
Effective length of database: 300
Effective search space:    87600
Effective search space used:    87600
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