Alignments for a candidate for H281DRAFT_01113 in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Moritella dasanensis ArB 0140

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_017221119.1 A923_RS0107850 ribose ABC transporter ATP-binding protein RbsA

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



>NCBI__GCF_000276805.1:WP_017221119.1
          Length = 501

 Score =  308 bits (789), Expect = 3e-88
 Identities = 174/496 (35%), Positives = 287/496 (57%), Gaps = 9/496 (1%)

Query: 11  LSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEG 70
           ++Q  L++ G+ K F GV AL    L+   G++  LLGENG GKSTL+K+++G    D+G
Sbjct: 1   MTQAILKLSGIEKSFPGVKALDNACLNVYPGKVMALLGENGAGKSTLMKVLTGIYHMDKG 60

Query: 71  QLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDR 130
            +  +G          +   GI  ++Q+L+L+P +++AEN+ L  E     G +  T   
Sbjct: 61  SINYQGSDVTFDGPRHSQEVGISIIHQELNLIPELTIAENIYLGRETTNAFGGIKWT--- 117

Query: 131 RVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSL 190
             + A A   L+ + +  +S     L+ +L L  +Q+V IA+A++ +++ ++MDEPT +L
Sbjct: 118 -QMFADADALLQRLNVKHSSR---QLLGELSLGEQQMVEIAKALSFKSQVIVMDEPTDAL 173

Query: 191 TQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQ 250
           T+ E  +L  V+  LR +G  ++++SH+L E + I  ++ VLRDG+ +A+  + +  +  
Sbjct: 174 TESETKSLFKVINELRNEGCGIVYISHRLKEIFEICDDITVLRDGKFIAEIAVTDIDEDG 233

Query: 251 ISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGR 310
           + E M GR L     R  A    + L+V      G   DVSF L  GEILG++GL+ +GR
Sbjct: 234 LIEKMVGRRLDEIYPRIDAKHGTLCLEVENIVAPG-VRDVSFTLDHGEILGISGLMGAGR 292

Query: 311 NELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNV 370
            EL +A+ G  P QSGDV+LD + ++  TP D   + I Y+ EDR  +GL L   +++N+
Sbjct: 293 TELMKAIYGALPRQSGDVILDDKVVSPITPRDGLANGIAYISEDRKGDGLILGLSVKENM 352

Query: 371 ITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLA 430
               + +L     Q+D  +     E  +++  + TP  D+ + +LSGGNQQ+V I + L 
Sbjct: 353 SLCALDALSKGL-QLDHAKEATAVEDFMRQFNVKTPSRDQIIGNLSGGNQQKVAIAKGLM 411

Query: 431 IDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKG 490
             P+VLIL  PT GVDVG+K  IY+++ +    G+ IIL+S ++PE+L   DRIL+M +G
Sbjct: 412 TRPKVLILDEPTRGVDVGAKKEIYQLINQFKAEGMSIILVSSEMPEVLGMSDRILVMHEG 471

Query: 491 HVSAEYRADELSEADL 506
            +S E+ A + ++  L
Sbjct: 472 RISGEFMAADANQEKL 487



 Score = 76.6 bits (187), Expect = 2e-18
 Identities = 56/236 (23%), Positives = 116/236 (49%), Gaps = 12/236 (5%)

Query: 31  LRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALAA 90
           +R VS +   G+I  + G  G G++ L+K I GA P   G ++++    + ++  + LA 
Sbjct: 269 VRDVSFTLDHGEILGISGLMGAGRTELMKAIYGALPRQSGDVILDDKVVSPITPRDGLAN 328

Query: 91  GIETVYQDLS---LLPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARALEAVGLP 147
           GI  + +D     L+  +SV EN++L +  A  +G        ++  A  A A+E     
Sbjct: 329 GIAYISEDRKGDGLILGLSVKENMSLCALDALSKGL-------QLDHAKEATAVEDFMRQ 381

Query: 148 GNSEFQST--LIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANL 205
            N +  S   +I  L    +Q VAIA+ + +  K +I+DEPT  +       +  ++   
Sbjct: 382 FNVKTPSRDQIIGNLSGGNQQKVAIAKGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQF 441

Query: 206 RAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTGRHLS 261
           +A+G++++ VS ++ E   +   ++V+ +G+   +   A+  + ++     G+ ++
Sbjct: 442 KAEGMSIILVSSEMPEVLGMSDRILVMHEGRISGEFMAADANQEKLMACAVGKKIN 497



 Score = 67.8 bits (164), Expect = 9e-16
 Identities = 50/233 (21%), Positives = 105/233 (45%), Gaps = 6/233 (2%)

Query: 279 RGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALR 338
           + F       +    ++ G+++ + G   +G++ L + L G+     G +   G  +   
Sbjct: 13  KSFPGVKALDNACLNVYPGKVMALLGENGAGKSTLMKVLTGIYHMDKGSINYQGSDVTFD 72

Query: 339 TPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTV 398
            P  ++   I  + ++ LN  L  +  I +N+     ++  + FG I  T+  A A+  +
Sbjct: 73  GPRHSQEVGISIIHQE-LN--LIPELTIAENIYLGRETT--NAFGGIKWTQMFADADALL 127

Query: 399 KELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQ 458
           + L +      + +  LS G QQ V I + L+   +V+++  PT  +       +++++ 
Sbjct: 128 QRLNVKHSS-RQLLGELSLGEQQMVEIAKALSFKSQVIVMDEPTDALTESETKSLFKVIN 186

Query: 459 RLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYHALL 511
            L   G GI+ IS  L E+ + CD I +++ G   AE    ++ E  L   ++
Sbjct: 187 ELRNEGCGIVYISHRLKEIFEICDDITVLRDGKFIAEIAVTDIDEDGLIEKMV 239


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: 559
Number of extensions: 36
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 515
Length of database: 501
Length adjustment: 34
Effective length of query: 481
Effective length of database: 467
Effective search space:   224627
Effective search space used:   224627
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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