GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Desulfoscipio geothermicus DSM 3669

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_092482139.1 BM299_RS03860 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_900115975.1:WP_092482139.1
          Length = 390

 Score =  158 bits (400), Expect = 2e-43
 Identities = 95/299 (31%), Positives = 163/299 (54%), Gaps = 25/299 (8%)

Query: 4   IRVENLSKIF-----------KKGKTEVKAVD---------NVSITIDSGMAFGVLGPSG 43
           + V+NL+KIF           K+G ++ K ++         N S  ++ G  F ++G SG
Sbjct: 5   VEVKNLTKIFGRNPKAILEKVKQGMSKEKILEDTGHTVGIRNASFQVEEGEVFVIMGLSG 64

Query: 44  HGKTTFLRLIAGLEEPTSGYIYFDNEAVSS-PRRVMMSPEKRGIAMVFQNWALYPNMTVF 102
            GK+T +R +  L +PT+G IY D + +    ++ +    +  +AMVFQ++ L  + TV 
Sbjct: 65  SGKSTLIRCLNLLNKPTAGEIYVDGDNILEYDKKQLKKFRQEKVAMVFQHFGLLSHRTVI 124

Query: 103 DNIAFPLKLAKVPKDKIENKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPK 162
            N+ + L++ K+PK++     K+     GL+G  N+ P ELSGG  QR  +ARAL  DP 
Sbjct: 125 GNVEYGLEVKKIPKNERCEIAKKAIANAGLAGWENKMPNELSGGMQQRVGLARALANDPD 184

Query: 163 VLLLDEPFSNLDAQIRESARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFA 222
           +LL+DEPFS LD  IR   +  + ++Q   K T + ++HD  + F I ++  V+ +G   
Sbjct: 185 ILLMDEPFSALDPLIRRDMQYELMELQSRLKKTIIFITHDINEAFKIGDRVAVMKDGVIE 244

Query: 223 QIGTPTEIYEYPATDLIARLTGEIN---LIQAK-IIENNAIIANLKVPLNNMELKGQSN 277
           QIGTP E+   P ++ I     +I+   ++QAK ++    ++ ++K  L    ++ +SN
Sbjct: 245 QIGTPEELLASPESEYIENFVKDIDRSKVLQAKHVMFKPTVLVSIKEGLKAAMMEMKSN 303


Lambda     K      H
   0.317    0.136    0.374 

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: 321
Number of extensions: 15
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: 371
Length of database: 390
Length adjustment: 30
Effective length of query: 341
Effective length of database: 360
Effective search space:   122760
Effective search space used:   122760
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 (21.6 bits)
S2: 50 (23.9 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