Alignments for a candidate for HSERO_RS05250 in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Pseudomonas fluorescens FW300-N2E3

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21385
          Length = 521

 Score =  464 bits (1195), Expect = e-135
 Identities = 254/516 (49%), Positives = 344/516 (66%), Gaps = 19/516 (3%)

Query: 13  AASSSSSVPVIALR---------------NVCKRFPGVLALDNCQFELAAGEVHALMGEN 57
           A++++SS+P++ ++               NV K FPGV+AL + Q  +  G V ALMGEN
Sbjct: 3   ASATASSIPLVGVQPNAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGEN 62

Query: 58  GAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQN 117
           GAGKSTLMKI++G+YQ D+G++ L GKPV    P  A   GI +IHQELNLM H+S A+N
Sbjct: 63  GAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAEN 122

Query: 118 IFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSF 177
           I+IGRE      + ID  E++R  A +  R+R+++DP   VG L++A +QMVEIAKA+S+
Sbjct: 123 IWIGREQLNGFHM-IDHREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSY 181

Query: 178 DSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGK 237
           DS +LIMDEPT+A+ + E+A LF II DL+AQG GI+YI+HKM+E+  IAD V+V RDG 
Sbjct: 182 DSDILIMDEPTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGA 241

Query: 238 YIATVPMQETSMDTIISMMVGRALDGEQRIPP-DTSRNDVVLEVRGLNRGRAIRDVSFTL 296
           YI          D++ISMMVGR L   Q  P  +    D+++ VR L      + VSF L
Sbjct: 242 YIGLQRADSMDGDSLISMMVGRELS--QLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDL 299

Query: 297 RKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSED 356
             GEILG AGLMG+GRT VA AIFG  P + GEI + G    I  P  A+  G   L+ED
Sbjct: 300 HAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTED 359

Query: 357 RKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLL 416
           RK  GL   + V  N+ ++ +  +   GF+ Q+A+R   +   ++L +KTPS+EQ    L
Sbjct: 360 RKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTL 419

Query: 417 SGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELP 476
           SGGNQQK ++A+WL+ +  IL  DEPTRGIDVGAK+EIY+L+  LA +G A++MISSELP
Sbjct: 420 SGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELP 479

Query: 477 EVLRMSHRVLVMCEGRITGELARADATQEKIMQLAT 512
           EVL MS RV+VM EG + G L R++ATQE++MQLA+
Sbjct: 480 EVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLAS 515



 Score =  105 bits (263), Expect = 3e-27
 Identities = 63/224 (28%), Positives = 121/224 (54%), Gaps = 6/224 (2%)

Query: 43  FELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGII 102
           F+L AGE+  + G  G+G++ + + + G+   D G+I LDG+PV I++P  A   G  ++
Sbjct: 297 FDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALL 356

Query: 103 HQELNLMNH---LSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDMDPSTP-- 157
            ++  L      LS  +N+ +   P  A   FI +  L      +  ++R+   PS    
Sbjct: 357 TEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKT-PSLEQC 415

Query: 158 VGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYIS 217
           +  L+   QQ   +A+ L  + R+LI+DEPT  ++    AE++R+I  L ++G+ ++ IS
Sbjct: 416 IDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMIS 475

Query: 218 HKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261
            ++ E+  ++DRV VM +G  + T+   E + + ++ +  G ++
Sbjct: 476 SELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSV 519



 Score = 86.3 bits (212), Expect = 3e-21
 Identities = 70/246 (28%), Positives = 117/246 (47%), Gaps = 15/246 (6%)

Query: 277 VLEVRGLNRGR----AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIII 332
           +LE+  +++G     A+ DV   +R G +L   G  GAG++ + + I G    +AGE+ +
Sbjct: 27  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86

Query: 333 HGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGF--MDQRA 390
            G      +P  A+  GI  + ++     L   M +  NI +   GR    GF  +D R 
Sbjct: 87  RGKPVTFDTPLAALQAGIAMIHQE---LNLMPHMSIAENIWI---GREQLNGFHMIDHRE 140

Query: 391 IREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGA 450
           +       + +L I     E+Q   LS   +Q + IAK +  D DIL  DEPT  I    
Sbjct: 141 MHRCTAQLLERLRINLDP-EEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKE 199

Query: 451 KSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQ-EKIMQ 509
            + ++ ++  L  QGK I+ I+ ++ EV  ++  V V  +G   G L RAD+   + ++ 
Sbjct: 200 VAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIG-LQRADSMDGDSLIS 258

Query: 510 LATQRE 515
           +   RE
Sbjct: 259 MMVGRE 264


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: 629
Number of extensions: 30
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: 521
Length adjustment: 35
Effective length of query: 485
Effective length of database: 486
Effective search space:   235710
Effective search space used:   235710
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