GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Cupriavidus basilensis 4G11

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate RR42_RS00210 RR42_RS00210 ABC transporter ATP-binding protein

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__Cup4G11:RR42_RS00210
          Length = 241

 Score =  190 bits (482), Expect = 2e-53
 Identities = 98/234 (41%), Positives = 152/234 (64%), Gaps = 5/234 (2%)

Query: 5   LVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIF 64
           L VK +  GY   V +L  ++  +APG++  ++G NGAGKSTL + I GL  P QG++++
Sbjct: 10  LSVKGLTTGY-DKVNVLHDVSIDVAPGKITCILGANGAGKSTLIRAILGLTPPRQGQVLW 68

Query: 65  KGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDR---IYT 121
            G+++ G  +  I+  G+  +P+   +F  +TVAENL +GA+L     + ++DR   +Y 
Sbjct: 69  DGKDLAGEKTHNIIATGIACIPEGRKIFPRMTVAENLALGAYLETDAAR-VRDRLAKVYD 127

Query: 122 MFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKA 181
           +FP+L +R  Q AGT+SGGE+ M+++GR LM +P LL++DEPS  LSP+ VK+ F  IK 
Sbjct: 128 IFPRLKERATQLAGTMSGGEQAMVSIGRGLMAEPKLLVIDEPSLGLSPLYVKENFKVIKQ 187

Query: 182 INATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235
           INA G  ++LVEQNA+Q L ++  GYVL  GR   +G+ ++L ++  V   Y G
Sbjct: 188 INALGITVLLVEQNARQTLAISHYGYVLSQGRVVAQGTAEALASNDEVRSAYFG 241


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: 163
Number of extensions: 9
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: 241
Length adjustment: 23
Effective length of query: 217
Effective length of database: 218
Effective search space:    47306
Effective search space used:    47306
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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