GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Desulfoscipio geothermicus DSM 3669

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein

Query= TCDB::P73650
         (240 letters)



>NCBI__GCF_900115975.1:WP_092484009.1
          Length = 344

 Score =  112 bits (280), Expect = 1e-29
 Identities = 71/210 (33%), Positives = 114/210 (54%), Gaps = 6/210 (2%)

Query: 21  LQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQIVRR 80
           L  IN  +  GE   ++GP G GK+ + +TI G+  P +G I FK  N+  L  +Q   R
Sbjct: 16  LLDINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLATLAPEQ---R 72

Query: 81  GMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFPKLA--QRRNQRAGTLS 138
            + +V Q   +F  LTV EN+  GA + + P + +K ++  +   L      N+   TLS
Sbjct: 73  KVGFVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLNRHPSTLS 132

Query: 139 GGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATGKAIIL-VEQNAK 197
           GGE+Q  A+ RAL++ P++LLLDEP +AL P   ++   ++K I+ T K   L V  +  
Sbjct: 133 GGEQQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTLHVTHDFN 192

Query: 198 QALMMADRGYVLENGRDKLEGSGQSLLNDP 227
           +A+ +AD+  V+  G+    G+ Q +   P
Sbjct: 193 EAMYLADKIGVMHQGQIIQVGTPQEIFYKP 222


Lambda     K      H
   0.320    0.139    0.393 

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: 183
Number of extensions: 10
Number of successful extensions: 3
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: 344
Length adjustment: 26
Effective length of query: 214
Effective length of database: 318
Effective search space:    68052
Effective search space used:    68052
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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