Alignments for a candidate for H281DRAFT_01113 in Tistlia consotensis USBA 355

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Tistlia consotensis USBA 355

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_085120648.1 B9O00_RS01470 sugar ABC transporter ATP-binding protein

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



>NCBI__GCF_900177295.1:WP_085120648.1
          Length = 634

 Score =  302 bits (774), Expect = 2e-86
 Identities = 186/504 (36%), Positives = 279/504 (55%), Gaps = 23/504 (4%)

Query: 13  QPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQL 72
           +  L   G+ K F    AL G  L  + G+++ LLG NG GKSTL K+ISG    D G+L
Sbjct: 12  EAILVASGIEKTFDRTRALAGADLELRAGEVHGLLGANGAGKSTLSKVISGHVQRDAGRL 71

Query: 73  VIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRV 132
           V +G P A  S  EAL AGI  V Q+ SL P++SV EN+ L                R  
Sbjct: 72  VYKGRPLALRSTREALEAGIAIVMQETSLAPDLSVLENIFLPE------------LGRPG 119

Query: 133 LAATAARALEAVGLPGNSEFQSTL-----IEQLPLATRQLVAIARAIASEAKFVIMDEPT 187
           L +  +    AVGL  N   +  L     + +L  A RQLV IA+A+A +A  +I DEPT
Sbjct: 120 LLSYGSMRRRAVGLLANLGHEHVLPLDREVARLSAAQRQLVEIAKALALDADLIIFDEPT 179

Query: 188 TSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQG-PIAEF 246
            SL+  EV+ L  ++A LR  G  ++FVSH+L+E +AI   V ++R+G  +A   P A  
Sbjct: 180 ASLSPSEVERLFDIMAKLRDDGRALIFVSHRLEEVFAITDRVTIMREGATVAASQPTASL 239

Query: 247 TKAQISELMTGRHL----SNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGV 302
           T+A++   M GR +    +    +E       V  V          +VSF +  GEILG+
Sbjct: 240 TQAEVIRHMVGRDIGALYATPGLQEEDERAPAVFSVENLAAPPAVRNVSFFVRRGEILGL 299

Query: 303 TGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFL 362
            GL+ +GR+E A A+ G+ P  +G + L+G++IA R P+DA R  IG+V EDR  + +  
Sbjct: 300 GGLVGAGRSETAEAIFGLRPRSAGTIRLEGREIAPRKPADAVRAGIGFVAEDRRVQNIVP 359

Query: 363 DKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQR 422
           D  +++N++ A + + R  FG   R R Q + E        A   +D  + + SGG QQ+
Sbjct: 360 DLSVKENLLLAHLGAHRG-FGLGYRRRRQKVEELMAALGLPAERLLDANMLNFSGGMQQK 418

Query: 423 VLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCD 482
           ++I RWL ++P+VLIL  PT GVD+G++  IY I++R++  G+ +++IS D  ELL  C+
Sbjct: 419 IIIARWLLLEPKVLILDEPTKGVDIGTRQAIYGILRRIADEGVAVVVISSDFEELLGVCE 478

Query: 483 RILMMKKGHVSAEYRADELSEADL 506
           R+++M  G+  A+  +  L E  L
Sbjct: 479 RVVVMSDGNAIADLPSALLDEEKL 502



 Score = 84.7 bits (208), Expect = 9e-21
 Identities = 66/232 (28%), Positives = 111/232 (47%), Gaps = 8/232 (3%)

Query: 30  ALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALA 89
           A+R VS   +RG+I  L G  G G+S   + I G +P   G + +EG   A     +A+ 
Sbjct: 283 AVRNVSFFVRRGEILGLGGLVGAGRSETAEAIFGLRPRSAGTIRLEGREIAPRKPADAVR 342

Query: 90  AGIETVYQDL---SLLPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARALEAVGL 146
           AGI  V +D    +++P++SV EN+ L + L  H G     + RR         + A+GL
Sbjct: 343 AGIGFVAEDRRVQNIVPDLSVKENLLL-AHLGAHRG-FGLGYRRR--RQKVEELMAALGL 398

Query: 147 PGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLR 206
           P      + ++       +Q + IAR +  E K +I+DEPT  +       +  +L  + 
Sbjct: 399 PAERLLDANMLN-FSGGMQQKIIIARWLLLEPKVLILDEPTKGVDIGTRQAIYGILRRIA 457

Query: 207 AQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTGR 258
            +GV V+ +S   +E   +   V+V+ DG  +A  P A   + +++ L   R
Sbjct: 458 DEGVAVVVISSDFEELLGVCERVVVMSDGNAIADLPSALLDEEKLTLLAAPR 509


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: 672
Number of extensions: 33
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 515
Length of database: 634
Length adjustment: 36
Effective length of query: 479
Effective length of database: 598
Effective search space:   286442
Effective search space used:   286442
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: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources