GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntB in Desulfoscipio geothermicus DSM 3669

Align TRAP-type large permease component (characterized, see rationale)
to candidate WP_092483295.1 BM299_RS09255 TRAP transporter large permease

Query= uniprot:Q930R2
         (425 letters)



>NCBI__GCF_900115975.1:WP_092483295.1
          Length = 429

 Score =  325 bits (834), Expect = 1e-93
 Identities = 169/413 (40%), Positives = 252/413 (61%)

Query: 4   VVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIPFFI 63
           ++ ++ LL  + +G P+AFSL    V  +   G     ++ Q +    D+F LLA+PFF+
Sbjct: 5   LILLLVLLLLLLVGFPIAFSLAMAAVAALLSKGTIPLTVVPQRLFTATDSFILLAVPFFV 64

Query: 64  LAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAAILI 123
           LAGELM  GG+SRR+++FA   +G I GGL +V+I +A   A+ISGS+AA TAA+  ++ 
Sbjct: 65  LAGELMQHGGISRRLVNFASDLLGWISGGLALVSIASAAFFAAISGSSAATTAAIGGVMY 124

Query: 124 PMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLIMGI 183
           P M + GY    +A + A GG +  VIPPS+  I++GV    SI  LF+AGI+PGL+   
Sbjct: 125 PEMRQRGYKPDFTAVVQAVGGTLGVVIPPSIPLIIYGVITGASIGDLFLAGIIPGLLGAA 184

Query: 184 ALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEAAVV 243
             +A    +  K   + + R+ +K+   +   A W L MPVIILGGI  GV TPTEAAVV
Sbjct: 185 VYMAVAWKMAGKLGYKTMQRSSLKKTWHSFREASWGLLMPVIILGGIYGGVFTPTEAAVV 244

Query: 244 AAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSEITG 303
           A VYAL VG  IY+EL  ++   +++++  T+A+IM L+  A + +W++T  NIP  ITG
Sbjct: 245 AVVYALLVGFFIYKELNWKNFYSMLVKSGLTSAMIMLLIATASLFTWIMTIENIPQAITG 304

Query: 304 FISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVLFIM 363
            I  + +   + + ++ +V L+ G  LD    IL+L P+  PI  Q G+DPV+FGV+ + 
Sbjct: 305 AILSMTESKLVFLLLVNMVFLIAGMFLDTVAIILLLIPIFFPIALQLGVDPVHFGVIAVF 364

Query: 364 NTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDI 416
           N  +G +TPP GV L V SGV  V L K+   V P+L+A  +++ LL   P +
Sbjct: 365 NLAVGQMTPPFGVCLFVSSGVSGVSLEKLFKAVLPYLLAAFILILLLTYVPSL 417


Lambda     K      H
   0.331    0.145    0.430 

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: 471
Number of extensions: 17
Number of successful extensions: 1
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: 425
Length of database: 429
Length adjustment: 32
Effective length of query: 393
Effective length of database: 397
Effective search space:   156021
Effective search space used:   156021
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 51 (24.3 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