Alignments for a candidate for H281DRAFT_01113 in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Pseudomonas fluorescens FW300-N2E3

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein

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



>FitnessBrowser__pseudo3_N2E3:AO353_21385
          Length = 521

 Score =  330 bits (847), Expect = 6e-95
 Identities = 184/498 (36%), Positives = 293/498 (58%), Gaps = 9/498 (1%)

Query: 7   SSAPLSQPFL-EVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQ 65
           ++ P+ +P+L E++ V K F GV AL  V L  + G +  L+GENG GKSTL+KII+G  
Sbjct: 18  NAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIY 77

Query: 66  PPDEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLA 125
            PD G+L + G P    + L AL AGI  ++Q+L+L+P+MS+AEN+ +  E         
Sbjct: 78  QPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNG----F 133

Query: 126 RTFDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDE 185
              D R +    A+ LE + +  + E Q   +  L +A RQ+V IA+A++ ++  +IMDE
Sbjct: 134 HMIDHREMHRCTAQLLERLRINLDPEEQ---VGNLSIAERQMVEIAKAVSYDSDILIMDE 190

Query: 186 PTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAE 245
           PT+++T KEV +L +++A+L+AQG  +++++HK++E ++I  EV V RDG  +       
Sbjct: 191 PTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADS 250

Query: 246 FTKAQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGL 305
                +  +M GR LS           D+++ VR     G F  VSF LH GEILG+ GL
Sbjct: 251 MDGDSLISMMVGRELSQLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGL 310

Query: 306 LDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKP 365
           + SGR  +A A+ G+ P+  G++ LDGQ + +  P  A       + EDR   GLF    
Sbjct: 311 MGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLS 370

Query: 366 IRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLI 425
           + +N+  A++       G I +   +AL E   K+L++ TP +++ + +LSGGNQQ+ L+
Sbjct: 371 VLENMEMAVLPHYAGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALL 429

Query: 426 GRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRIL 485
            RWL  +PR+LIL  PT G+DVG+K  IYR++  L+  G+ +I+IS +LPE+L   DR++
Sbjct: 430 ARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVM 489

Query: 486 MMKKGHVSAEYRADELSE 503
           +M +G +       E ++
Sbjct: 490 VMHEGDLMGTLDRSEATQ 507



 Score = 70.5 bits (171), Expect = 1e-16
 Identities = 57/237 (24%), Positives = 110/237 (46%), Gaps = 10/237 (4%)

Query: 24  RFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLS 83
           R  GV   +GVS     G+I  + G  G G++ + + I G  P D G++ ++G P     
Sbjct: 287 RLDGV--FKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISD 344

Query: 84  ALEALAAGIETVYQDLSL---LPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARA 140
              A+  G   + +D  L    P +SV EN+ + + L  + G       ++ L A     
Sbjct: 345 PHMAIEKGFALLTEDRKLSGLFPCLSVLENMEM-AVLPHYAGN--GFIQQKALRALCEDM 401

Query: 141 LEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIA 200
            + + +   S  Q   I+ L    +Q   +AR + +  + +I+DEPT  +       +  
Sbjct: 402 CKKLRVKTPSLEQC--IDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYR 459

Query: 201 VLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTG 257
           +++ L ++G+ V+ +S +L E   +   V+V+ +G  M     +E T+ ++ +L +G
Sbjct: 460 LISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 516


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: 596
Number of extensions: 41
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: 521
Length adjustment: 35
Effective length of query: 480
Effective length of database: 486
Effective search space:   233280
Effective search space used:   233280
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 17 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 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