Alignments for a candidate for HSERO_RS05250 in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Pseudomonas fluorescens FW300-N2C3

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23205
          Length = 517

 Score =  459 bits (1182), Expect = e-134
 Identities = 249/487 (51%), Positives = 330/487 (67%), Gaps = 4/487 (0%)

Query: 27  NVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPV 86
           NV K FPGV+AL + Q  +  G V ALMGENGAGKSTLMKI++G+YQ D+G++ L GKPV
Sbjct: 31  NVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPV 90

Query: 87  EITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFA 146
               P  A   GI +IHQELNLM H+S A+NI+IGRE    + + +D  E++R  A +  
Sbjct: 91  TFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHM-VDHGEMHRCTARLLE 149

Query: 147 RMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDL 206
           R+R+ +DP   VG L++A +QMVEIAKA+S+DS +LIMDEPT+A+   E+A LF II DL
Sbjct: 150 RLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFSIIADL 209

Query: 207 QAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRALDGEQR 266
           ++QG GI+YI+HKM+E+  IAD V+V RDG YI          D++ISMMVGR L   Q 
Sbjct: 210 KSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS--QL 267

Query: 267 IPP-DTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPL 325
            P  +    ++VL VR L+     + VSF L  GEILG AGLMG+GRT VA AIFG  P 
Sbjct: 268 FPVREQPIGELVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGVTPS 327

Query: 326 EAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGF 385
             GEI + G    I  P  A+  G   L+EDRK  GL   + V  N+ ++ +  +   GF
Sbjct: 328 TGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGF 387

Query: 386 MDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRG 445
           + Q+A+R   +   ++L +KTPS+EQ    LSGGNQQK ++A+WL+ +  IL  DEPTRG
Sbjct: 388 IQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRG 447

Query: 446 IDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQE 505
           IDVGAK+EIY+L+  LA +G A++MISSELPEVL MS RV+VM EG + G L R++ATQE
Sbjct: 448 IDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQE 507

Query: 506 KIMQLAT 512
           ++MQLA+
Sbjct: 508 RVMQLAS 514



 Score =  101 bits (251), Expect = 8e-26
 Identities = 62/221 (28%), Positives = 117/221 (52%), Gaps = 6/221 (2%)

Query: 43  FELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGII 102
           F+L AGE+  + G  G+G++ + + + GV     G+I LDG+PV I++P  A   G  ++
Sbjct: 296 FDLHAGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFALL 355

Query: 103 HQELNLMNH---LSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDMDPSTP-- 157
            ++  L      LS  +N+ +   P      FI +  L      +  ++R+   PS    
Sbjct: 356 TEDRKLSGLFPCLSVLENMEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKT-PSLEQC 414

Query: 158 VGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYIS 217
           +  L+   QQ   +A+ L  + R+LI+DEPT  ++    AE++R+I  L ++G+ ++ IS
Sbjct: 415 IDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMIS 474

Query: 218 HKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
            ++ E+  ++DRV VM +G  + T+   E + + ++ +  G
Sbjct: 475 SELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 515



 Score = 86.7 bits (213), Expect = 2e-21
 Identities = 70/253 (27%), Positives = 120/253 (47%), Gaps = 12/253 (4%)

Query: 269 PDTSRND-VVLEVRGLNRGR----AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGAD 323
           PD S ++  +LEV  +++G     A+ DV   +R G +L   G  GAG++ + + I G  
Sbjct: 17  PDVSLDEPYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIY 76

Query: 324 PLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRV 383
             +AGE+ + G      +P  A+  GI  + ++     L   M +  NI +    +   +
Sbjct: 77  QPDAGELRLRGKPVTFDTPLAALQAGIAMIHQE---LNLMPHMSIAENIWIGRE-QLNGL 132

Query: 384 GFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPT 443
             +D   +       + +L IK    E+Q   LS   +Q + IAK +  D DIL  DEPT
Sbjct: 133 HMVDHGEMHRCTARLLERLRIKLDP-EEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPT 191

Query: 444 RGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADAT 503
             I     + ++ ++  L  QGK I+ I+ ++ EV  ++  V V  +G   G L RAD+ 
Sbjct: 192 SAITETEVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIG-LQRADSM 250

Query: 504 Q-EKIMQLATQRE 515
             + ++ +   RE
Sbjct: 251 DGDSLISMMVGRE 263


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: 649
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: 517
Length adjustment: 35
Effective length of query: 485
Effective length of database: 482
Effective search space:   233770
Effective search space used:   233770
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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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