GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01113 in Bradyrhizobium sp. BTAi1

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>NCBI__GCF_000015165.1:WP_012042345.1
          Length = 516

 Score =  301 bits (772), Expect = 3e-86
 Identities = 177/515 (34%), Positives = 293/515 (56%), Gaps = 18/515 (3%)

Query: 7   SSAPLSQP-FLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQ 65
           S+ P ++P  LE+ G+ K F  + AL+ V  +   G+I+ LLGENG GKSTLIK+++G  
Sbjct: 5   SAPPAARPSLLEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVF 64

Query: 66  PPDEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLA 125
             D G + + G   A  SA +A+ AGI TVYQ+++LLPN+SVA+N+ L  +         
Sbjct: 65  ARDAGTVRLAGDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQPTRFGVVRQ 124

Query: 126 RTFDRRVLAATAARALEA-VGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMD 184
               RR  A      L+  VG P         +    +A + + AIARA+   A+ +I+D
Sbjct: 125 AEMRRRAHALLLDYGLDIDVGAP---------LASYSVAVQHITAIARAVDLSARVLILD 175

Query: 185 EPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIA 244
           EPT SL + EV+ L  V+  L A G+ ++FVSH LD+ Y I   V VLR+G+ +    I 
Sbjct: 176 EPTASLDRHEVEILFRVMRKLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTRDIT 235

Query: 245 EFTKAQISELMTGRHLSNERYRESAH----AQDIVLDVRGFTRAGQFSDVSFKLHGGEIL 300
           +  +  +  +M GR L+   +  +A     A+++ +  +GF + G  +    +L  GE++
Sbjct: 236 DLPRLDLIRMMLGRELAETTHERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVV 295

Query: 301 GVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGL 360
           G+ GLL SGR E AR + G   A SG+  + G+ + L +P DA     GY PE+R  EG+
Sbjct: 296 GLAGLLGSGRTETARLVFGAERADSGEASVAGKAVRLNSPRDAAGLGFGYCPEERKTEGI 355

Query: 361 FLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQ 420
             D  +R+N++ A + + R     + R     +A + ++ L I  P  ++P+  LSGGNQ
Sbjct: 356 VADLTVRENIVLA-LQARRGLHRPLSRREQDEIAMRYIRMLDIRPPDPERPIGLLSGGNQ 414

Query: 421 QRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQN 480
           Q+ L+ RWLA  P++L+L  PT G+DVG+   I R+++ L ++G+ +++IS +L E++  
Sbjct: 415 QKALLARWLATSPKLLVLDEPTRGIDVGAHAEIIRLVRDLCEQGLALLVISSELDEIVTY 474

Query: 481 CDRILMMK-KGHVSAEYRADELSEADLYHALLSEA 514
            +R+++++ + HV  E + D +  + +  A+ ++A
Sbjct: 475 SNRVVVLRDRAHVE-ELKGDAVEVSSILAAIAADA 508


Lambda     K      H
   0.319    0.135    0.376 

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: 585
Number of extensions: 23
Number of successful extensions: 7
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: 515
Length of database: 516
Length adjustment: 35
Effective length of query: 480
Effective length of database: 481
Effective search space:   230880
Effective search space used:   230880
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 (21.7 bits)
S2: 52 (24.6 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