GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21720 in Desulfoscipio geothermicus DSM 3669

Align ABC transporter for D-glucosamine, permease component 2 (characterized)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_21720
         (220 letters)



>NCBI__GCF_900115975.1:WP_092487756.1
          Length = 234

 Score =  128 bits (321), Expect = 1e-34
 Identities = 69/218 (31%), Positives = 124/218 (56%), Gaps = 19/218 (8%)

Query: 18  LWSGFLTSVQCSVLAIMLGTLIGIVAGLVLTYGTLWMRAPFRFYVDLIRGTPVFVLVLAC 77
           ++ G   ++Q +++++ +G L+G++ GL        +R     YVD  RGTP+ V +   
Sbjct: 12  IFQGAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFIV 71

Query: 78  FYMAPALGWQIDAFQ-------------------AGVLGLTLFCGSHVAEIVRGALQALP 118
           ++  P L   + +F                    A V+  +L  G++VAEI R  +Q++ 
Sbjct: 72  YFGIPKLLMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFRAGVQSIE 131

Query: 119 RGQMEASKAIGLTFYQALAYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLST 178
           RGQMEA++++G+T  QA+ YV+LPQA ++++P   N    ++K ++LLSVIG AEL  + 
Sbjct: 132 RGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAELTRNG 191

Query: 179 QQIIARTFMTLEFYLFAGFLFFIINYAIELLGRHIEKR 216
           Q IIART+ +   +L  GF++ I+ + +  +  ++E+R
Sbjct: 192 QLIIARTYESFAIWLTVGFIYLIMTFTLSRIVDYLERR 229


Lambda     K      H
   0.330    0.142    0.440 

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: 143
Number of extensions: 8
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: 220
Length of database: 234
Length adjustment: 22
Effective length of query: 198
Effective length of database: 212
Effective search space:    41976
Effective search space used:    41976
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 (21.9 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