GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natE in Magnetospirillum magneticum AMB-1

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_011384207.1 AMB_RS09120 ABC transporter ATP-binding protein

Query= TCDB::P73650
         (240 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384207.1 AMB_RS09120 ABC
           transporter ATP-binding protein
          Length = 237

 Score =  187 bits (475), Expect = 2e-52
 Identities = 103/238 (43%), Positives = 150/238 (63%), Gaps = 5/238 (2%)

Query: 4   LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEII 63
           +L ++ + +GY   +  L G++ ++A GE+V ++G NGAGK+TL  TI G    + G + 
Sbjct: 1   MLRIESLHSGY-GRIQALHGVDINVAEGEIVALVGANGAGKTTLLMTICGNPRATAGTVR 59

Query: 64  FKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKD--RIYT 121
             GE+ITGL +  I+RRG+ + P+   +F  ++V ENL MGA     P    +D  R+  
Sbjct: 60  LAGEDITGLATHHIMRRGLAHSPEGRRIFARMSVLENLQMGA-ARGNPAHFAQDLERVLG 118

Query: 122 MFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKA 181
           +FP+L +R  QR GTLSGGE+QMLA+GRALM  P +LLLDEPS  L+P++V+ +F  +  
Sbjct: 119 LFPRLEERLAQRGGTLSGGEQQMLAIGRALMSRPKILLLDEPSLGLAPLVVRQIFEIVAT 178

Query: 182 IN-ATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLGAAY 238
           IN   G  + LVEQNA  AL +A RGYV+ NG+  L G+G  LL +  +   YLG  +
Sbjct: 179 INREQGVTVFLVEQNAHHALRLAHRGYVMVNGKVTLSGTGAELLANEEIRAHYLGGGH 236


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: 151
Number of extensions: 7
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: 237
Length adjustment: 23
Effective length of query: 217
Effective length of database: 214
Effective search space:    46438
Effective search space used:    46438
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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