Alignments for a candidate for H281DRAFT_01113 in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Pseudomonas fluorescens FW300-N2C3

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_23205
          Length = 517

 Score =  327 bits (837), Expect = 8e-94
 Identities = 187/494 (37%), Positives = 290/494 (58%), Gaps = 9/494 (1%)

Query: 11  LSQPFL-EVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDE 69
           L +P+L EVV V K F GV AL  V L  + G +  L+GENG GKSTL+KII+G   PD 
Sbjct: 21  LDEPYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDA 80

Query: 70  GQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFD 129
           G+L + G P    + L AL AGI  ++Q+L+L+P+MS+AEN+ +  E            D
Sbjct: 81  GELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNG----LHMVD 136

Query: 130 RRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTS 189
              +    AR LE + +  + E Q   +  L +A RQ+V IA+A++ ++  +IMDEPT++
Sbjct: 137 HGEMHRCTARLLERLRIKLDPEEQ---VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSA 193

Query: 190 LTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKA 249
           +T+ EV +L +++A+L++QG  +++++HK++E +AI  EV V RDG  +           
Sbjct: 194 ITETEVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGD 253

Query: 250 QISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSG 309
            +  +M GR LS           ++VL VR  +  G F  VSF LH GEILG+ GL+ SG
Sbjct: 254 SLISMMVGRELSQLFPVREQPIGELVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSG 313

Query: 310 RNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDN 369
           R  +A A+ GV P+  G++ LDGQ + +  P  A       + EDR   GLF    + +N
Sbjct: 314 RTNVAEAIFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLEN 373

Query: 370 VITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWL 429
           +  A++       G I +   +AL E   K+L++ TP +++ + +LSGGNQQ+ L+ RWL
Sbjct: 374 MEMAVLPHYVGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWL 432

Query: 430 AIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKK 489
             +PR+LIL  PT G+DVG+K  IYR++  L+  G+ +I+IS +LPE+L   DR+++M +
Sbjct: 433 MTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHE 492

Query: 490 GHVSAEYRADELSE 503
           G +       E ++
Sbjct: 493 GDLMGTLDRSEATQ 506



 Score = 68.2 bits (165), Expect = 7e-16
 Identities = 60/261 (22%), Positives = 116/261 (44%), Gaps = 19/261 (7%)

Query: 1   MNQQEVSSAPLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKI 60
           + +Q +    LS   L + G+ K         GVS     G+I  + G  G G++ + + 
Sbjct: 270 VREQPIGELVLSVRDLSLDGIFK---------GVSFDLHAGEILGIAGLMGSGRTNVAEA 320

Query: 61  ISGAQPPDEGQLVIEGVPHARLSALEALAAGIETVYQDLSL---LPNMSVAENVALTSEL 117
           I G  P   G++ ++G P        A+  G   + +D  L    P +SV EN+    E+
Sbjct: 321 IFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENM----EM 376

Query: 118 ATHEGRLARTF-DRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIAS 176
           A     +   F  ++ L A      + + +   S  Q   I+ L    +Q   +AR + +
Sbjct: 377 AVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQC--IDTLSGGNQQKALLARWLMT 434

Query: 177 EAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQ 236
             + +I+DEPT  +       +  +++ L ++G+ V+ +S +L E   +   V+V+ +G 
Sbjct: 435 NPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGD 494

Query: 237 KMAQGPIAEFTKAQISELMTG 257
            M     +E T+ ++ +L +G
Sbjct: 495 LMGTLDRSEATQERVMQLASG 515


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: 587
Number of extensions: 39
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: 517
Length adjustment: 35
Effective length of query: 480
Effective length of database: 482
Effective search space:   231360
Effective search space used:   231360
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.

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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 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