GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24005 in Desulfoscipio geothermicus DSM 3669

Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease

Query= uniprot:B2TBJ7
         (240 letters)



>NCBI__GCF_900115975.1:WP_092487756.1
          Length = 234

 Score =  137 bits (346), Expect = 1e-37
 Identities = 75/218 (34%), Positives = 126/218 (57%), Gaps = 9/218 (4%)

Query: 17  VLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELLVIYL 76
           ++   A +T+ +T+ ++A+G + G +   ++LSR + LR +   Y   FRG P L+ I++
Sbjct: 11  LIFQGAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFI 70

Query: 77  FYFG--------GSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLA 128
            YFG         S +V S G    A+ F  +P F+   +A  + SGAY AE++R+ V +
Sbjct: 71  VYFGIPKLLMDLQSFMVDSYGMTPVADSFA-LPRFLAAVIACSLNSGAYVAEIFRAGVQS 129

Query: 129 VSRGELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLR 188
           + RG++EAARS+GM      R +++PQ  +  +P +GN +   LKD++L+SV G AEL R
Sbjct: 130 IERGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAELTR 189

Query: 189 TSQVAAGSTHQYFTFFVVGGALYLIMTSISNRVFNRAE 226
             Q+    T++ F  ++  G +YLIMT   +R+ +  E
Sbjct: 190 NGQLIIARTYESFAIWLTVGFIYLIMTFTLSRIVDYLE 227


Lambda     K      H
   0.327    0.141    0.403 

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: 104
Number of extensions: 3
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: 240
Length of database: 234
Length adjustment: 23
Effective length of query: 217
Effective length of database: 211
Effective search space:    45787
Effective search space used:    45787
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 (21.7 bits)
S2: 46 (22.3 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