Aligments for a candidate for BPHYT_RS34245 in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Aligments for a candidate for BPHYT_RS34245 in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate Pf1N1B4_4286 Inositol transport system ATP-binding protein

Query= uniprot:B2T9V9
         (510 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286 Inositol transport
           system ATP-binding protein
          Length = 526

 Score =  274 bits (701), Expect = 5e-78
 Identities = 164/472 (34%), Positives = 258/472 (54%), Gaps = 6/472 (1%)

Query: 14  VVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRF 73
           ++E + V+K F    AL+DV +RV PG   AL+G NGAGKSTL+ I+ G+ +PD GE+R 
Sbjct: 32  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 91

Query: 74  SGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRG-GVIDWQAMRRDAR 132
            G          A +  +A ++Q   ++  +S+AEN++I R+ L G  +ID + M R   
Sbjct: 92  RGKPVVFETPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMIDHREMHRCTA 151

Query: 133 ALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRR 192
            LL+  +I++  +   G+LS+  RQ+VEIA+A+SY +  +I+DEPT+ +   E+  LF  
Sbjct: 152 KLLERLRINLDPEELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 211

Query: 193 ISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGG 252
           I++L+R+G   ++I+H + EV+ I   V V RD  +I      ++  + LI  M G    
Sbjct: 212 IADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 271

Query: 253 LAVADAAARGALPADTAVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEAI 312
                   R     D  +++   +L G  ++ VSF +  GE++G+ G   SGRT+VAEAI
Sbjct: 272 QLF---PVREKPIGDLLLSVRDLKLDGI-FKDVSFDLHAGEILGIAGLMGSGRTNVAEAI 327

Query: 313 AGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARV 372
            G+  +  G I +DG ++   D   ++  G   + +DR   GL    SV EN  M +   
Sbjct: 328 FGITPSDGGEIRLDGEVVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPH 387

Query: 373 LGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVL 432
               G        A  + M   L +     E  +  LSGGNQQK ++AR L TNP +L+L
Sbjct: 388 YVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILIL 447

Query: 433 IDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRG 483
            +PT G+DV +K  +  ++  +  EG AV+++S EL + L   DRV+VM  G
Sbjct: 448 DEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEG 499



 Score = 64.3 bits (155), Expect = 1e-14
 Identities = 60/242 (24%), Positives = 104/242 (42%), Gaps = 6/242 (2%)

Query: 13  PVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVR 72
           P+ + L   +         DVS  +  GE   + G  G+G++ +   + G+   D GE+R
Sbjct: 280 PIGDLLLSVRDLKLDGIFKDVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEIR 339

Query: 73  FSGAAAPSIADRDAWRERVACVYQH---STIIRDLSVAENLFINRQP--LRGGVIDWQAM 127
             G          A  +  A + +    S +   LSV EN+ +   P  +  G I  +A+
Sbjct: 340 LDGEVVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGFIQQKAL 399

Query: 128 RRDARALLDHWKIDVREDARAGD-LSVEARQLVEIARALSYGARFIILDEPTAQLDGDEI 186
           R     +    ++      +  D LS   +Q   +AR L    R +ILDEPT  +D    
Sbjct: 400 RALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAK 459

Query: 187 KRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAM 246
             ++R IS L  EG+  + IS  L EV  +   V V+ +   + +   S   +E++++  
Sbjct: 460 AEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLA 519

Query: 247 TG 248
           +G
Sbjct: 520 SG 521


Lambda     K      H
   0.318    0.134    0.377 

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: 536
Number of extensions: 24
Number of successful extensions: 7
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: 510
Length of database: 526
Length adjustment: 35
Effective length of query: 475
Effective length of database: 491
Effective search space:   233225
Effective search space used:   233225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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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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, or view the source code.

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