GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286
          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:

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:

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:

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:

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