GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Arenitalea lutea P7-3-5

Align Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate WP_035106002.1 P735_RS0102575 ATP-binding cassette domain-containing protein

Query= TCDB::Q9HU32
         (257 letters)



>NCBI__GCF_000283015.1:WP_035106002.1
          Length = 244

 Score =  150 bits (378), Expect = 3e-41
 Identities = 89/251 (35%), Positives = 141/251 (56%), Gaps = 16/251 (6%)

Query: 6   PALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQIL 65
           P LEI++L K +G+  VL G +L   +G+ + I+G SGSGKS  ++C+  L     G I 
Sbjct: 4   PILEIKDLRKSFGNNHVLNGFNLQLFEGENLVIMGKSGSGKSVMIKCLVGLMQADSGSIK 63

Query: 66  VSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNV---IEAPRRV 122
           V G           D+   +   +N LR+E+GF+FQ   L+  M++ +N+   +   +  
Sbjct: 64  VMGN----------DINTLNEHDLNELRTEIGFLFQGSALYDSMTVRENLEFPLRRHKHK 113

Query: 123 LGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTS 182
            G  K +   + E L   VG+ D     PA+LSGG Q+R A+ARTL ++PK+IL+DEPTS
Sbjct: 114 FGIVKEKTPLVIEAL-ESVGLVDAIDLMPAELSGGMQRRVALARTLILKPKIILYDEPTS 172

Query: 183 ALDPEMVQEVLNVIRALAEEGRT-MLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVF 241
            LDP   +E++ ++R +  E +T  L++TH++  AR VS  +V L  G+   +GT  +  
Sbjct: 173 GLDPITAKEIIELMRRIQREYKTSSLIITHDVDCARVVSERMVLLVDGINYAEGT-FETL 231

Query: 242 ENPQSARCKQF 252
           +N    + K F
Sbjct: 232 KNSNDEKVKAF 242


Lambda     K      H
   0.317    0.133    0.367 

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: 113
Number of extensions: 5
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: 257
Length of database: 244
Length adjustment: 24
Effective length of query: 233
Effective length of database: 220
Effective search space:    51260
Effective search space used:    51260
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. 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