GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21720 in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate WP_068168721.1 HTA01S_RS07505 ABC transporter permease subunit

Query= reanno::pseudo5_N2C3_1:AO356_00470
         (220 letters)



>NCBI__GCF_001592305.1:WP_068168721.1
          Length = 226

 Score =  122 bits (305), Expect = 7e-33
 Identities = 72/216 (33%), Positives = 118/216 (54%), Gaps = 7/216 (3%)

Query: 8   LHELWVARDTLWAGFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLIRG 67
           + +LW+    L  G   +VQ +L ++V+G  +GLV       GRT +R   R    L+RG
Sbjct: 1   MDDLWLYAGQLLQGAWVTVQLALSSLVVGLALGLVLAAGSLSGRTLLRRAVRLCTGLLRG 60

Query: 68  TPVFVLVLACFYMAPAL-------GWQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRG 120
            P F++VL C++    L         +I  F AGV  L++   ++ +E+ RG+  A+PRG
Sbjct: 61  IPEFLIVLVCYFGLSNLINNHLDGAVEISPFAAGVFALSIVFAAYASEVFRGSFAAIPRG 120

Query: 121 QMEASQAIGLTFYQSLGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQ 180
           Q+EA+QA GLT  Q+   V LPQA R  LP+  N    ++K ++L+SV+G+ +LL  +  
Sbjct: 121 QIEAAQAFGLTATQTFFAVRLPQAWRIALPSLGNLWQSLLKDTSLVSVVGLEDLLKKSNM 180

Query: 181 IIARTFMTLEFYLFAGFLFFIINYAIELLGRHIEKR 216
               T     F+L A  ++F+  +A + +   +E+R
Sbjct: 181 AAQATHQPFLFFLAAATVYFVFLHASQPVFAWLERR 216


Lambda     K      H
   0.330    0.142    0.443 

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: 166
Number of extensions: 7
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: 226
Length adjustment: 22
Effective length of query: 198
Effective length of database: 204
Effective search space:    40392
Effective search space used:    40392
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: 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