Alignments for a candidate for HSERO_RS05250 in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Pseudomonas fluorescens FW300-N1B4

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf1N1B4_4286 Inositol transport system ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286
          Length = 526

 Score =  462 bits (1190), Expect = e-134
 Identities = 255/511 (49%), Positives = 342/511 (66%), Gaps = 9/511 (1%)

Query: 8   STTGVAASSSSSVPV-----IALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKS 62
           S+T +     ++ PV     + + NV K FPGV+AL + Q  +  G V ALMGENGAGKS
Sbjct: 13  SSTPLMGVQPTATPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKS 72

Query: 63  TLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGR 122
           TLMKI++G+YQ D+G++ L GKPV    P  A   GI +IHQELNLM H+S A+NI+IGR
Sbjct: 73  TLMKIIAGIYQPDAGELRLRGKPVVFETPLAALQAGIAMIHQELNLMPHMSIAENIWIGR 132

Query: 123 EPRKAMGLFIDEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVL 182
           E    + + ID  E++R  A +  R+R+++DP   VG L++A +QMVEIAKA+S+DS +L
Sbjct: 133 EQLNGLHM-IDHREMHRCTAKLLERLRINLDPEELVGNLSIAERQMVEIAKAVSYDSDIL 191

Query: 183 IMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATV 242
           IMDEPT+A+ + E+A LF II DL+ QG GI+YI+HKM+E+  IAD V+V RDG YI   
Sbjct: 192 IMDEPTSAITDKEVAHLFSIIADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQ 251

Query: 243 PMQETSMDTIISMMVGRALDGEQRIPP-DTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEI 301
                  D++ISMMVGR L   Q  P  +    D++L VR L      +DVSF L  GEI
Sbjct: 252 RADSMDGDSLISMMVGRELS--QLFPVREKPIGDLLLSVRDLKLDGIFKDVSFDLHAGEI 309

Query: 302 LGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFG 361
           LG AGLMG+GRT VA AIFG  P + GEI + G    I  P  A+  G   L+EDRK  G
Sbjct: 310 LGIAGLMGSGRTNVAEAIFGITPSDGGEIRLDGEVVRISDPHMAIEKGFALLTEDRKLSG 369

Query: 362 LAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQ 421
           L   + V  N+ ++ +  +   GF+ Q+A+R   +   ++L +KTPS+EQ    LSGGNQ
Sbjct: 370 LFPCLSVLENMEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQ 429

Query: 422 QKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRM 481
           QK ++A+WL+ +  IL  DEPTRGIDVGAK+EIY+L+  LA +G A++MISSELPEVL M
Sbjct: 430 QKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGM 489

Query: 482 SHRVLVMCEGRITGELARADATQEKIMQLAT 512
           S RV+VM EG + G L R++ATQE++MQLA+
Sbjct: 490 SDRVMVMHEGDLMGTLDRSEATQERVMQLAS 520



 Score =  100 bits (248), Expect = 2e-25
 Identities = 61/221 (27%), Positives = 117/221 (52%), Gaps = 6/221 (2%)

Query: 43  FELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGII 102
           F+L AGE+  + G  G+G++ + + + G+   D G+I LDG+ V I++P  A   G  ++
Sbjct: 302 FDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEIRLDGEVVRISDPHMAIEKGFALL 361

Query: 103 HQELNLMNH---LSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDMDPSTP-- 157
            ++  L      LS  +N+ +   P      FI +  L      +  ++R+   PS    
Sbjct: 362 TEDRKLSGLFPCLSVLENMEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKT-PSLEQC 420

Query: 158 VGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYIS 217
           +  L+   QQ   +A+ L  + R+LI+DEPT  ++    AE++R+I  L ++G+ ++ IS
Sbjct: 421 IDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMIS 480

Query: 218 HKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
            ++ E+  ++DRV VM +G  + T+   E + + ++ +  G
Sbjct: 481 SELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 521



 Score = 84.3 bits (207), Expect = 1e-20
 Identities = 66/244 (27%), Positives = 116/244 (47%), Gaps = 11/244 (4%)

Query: 277 VLEVRGLNRGR----AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIII 332
           +LE+  +++G     A+ DV   +R G +L   G  GAG++ + + I G    +AGE+ +
Sbjct: 32  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 91

Query: 333 HGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIR 392
            G   V ++P  A+  GI  + ++     L   M +  NI +    +   +  +D R + 
Sbjct: 92  RGKPVVFETPLAALQAGIAMIHQE---LNLMPHMSIAENIWIGRE-QLNGLHMIDHREMH 147

Query: 393 EAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKS 452
                 + +L I     E+    LS   +Q + IAK +  D DIL  DEPT  I     +
Sbjct: 148 RCTAKLLERLRINLDP-EELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVA 206

Query: 453 EIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQ-EKIMQLA 511
            ++ ++  L  QGK I+ I+ ++ EV  ++  V V  +G   G L RAD+   + ++ + 
Sbjct: 207 HLFSIIADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIG-LQRADSMDGDSLISMM 265

Query: 512 TQRE 515
             RE
Sbjct: 266 VGRE 269


Lambda     K      H
   0.320    0.135    0.372 

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: 642
Number of extensions: 31
Number of successful extensions: 7
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: 520
Length of database: 526
Length adjustment: 35
Effective length of query: 485
Effective length of database: 491
Effective search space:   238135
Effective search space used:   238135
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 (21.8 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