Alignments for a candidate for HSERO_RS05250 in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Pseudomonas fluorescens FW300-N2E2

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf6N2E2_523 Inositol transport system ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523
          Length = 517

 Score =  464 bits (1194), Expect = e-135
 Identities = 255/515 (49%), Positives = 340/515 (66%), Gaps = 18/515 (3%)

Query: 13  AASSSSSVPVIALR--------------NVCKRFPGVLALDNCQFELAAGEVHALMGENG 58
           A++++SS P +  R              NV K FPGV+AL + Q  +  G V ALMGENG
Sbjct: 3   ASATASSAPAMTFRPDVIPDEPYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENG 62

Query: 59  AGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNI 118
           AGKSTLMKI++G+YQ D+G++ L GKPV    P  A   GI +IHQELNLM H+S A+NI
Sbjct: 63  AGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENI 122

Query: 119 FIGREPRKAMGLFIDEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFD 178
           +IGRE    + + +D  E++R  A +  R+R+ +DP   VG L++A +QMVEIAKA+S+D
Sbjct: 123 WIGREQLNGLHM-VDHGEMHRCTARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYD 181

Query: 179 SRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKY 238
           S +LIMDEPT+A+   E+A LF II DL++QG GI+YI+HKM+E+  IAD V+V RDG Y
Sbjct: 182 SDILIMDEPTSAITETEVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAY 241

Query: 239 IATVPMQETSMDTIISMMVGRALDGEQRIPP-DTSRNDVVLEVRGLNRGRAIRDVSFTLR 297
           I          D++ISMMVGR L   Q  P  +    D+VL VR L+     + VSF L 
Sbjct: 242 IGLQRADSMDGDSLISMMVGRELS--QLFPVREQPIGDLVLSVRDLSLDGIFKGVSFDLH 299

Query: 298 KGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDR 357
            GEILG AGLMG+GRT VA AIFG  P   GEI++ G    I  P  A+  G   L+EDR
Sbjct: 300 AGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEILLDGQPVRISDPHMAIEKGFALLTEDR 359

Query: 358 KHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLS 417
           K  GL   + V  N+ ++ +  +   GF+ Q+A+R   +   ++L +KTPS+EQ    LS
Sbjct: 360 KLSGLFPCLSVLENMEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLS 419

Query: 418 GGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPE 477
           GGNQQK ++A+WL+ +  IL  DEPTRGIDVGAK+EIY+L+  LA +G A++MISSELPE
Sbjct: 420 GGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPE 479

Query: 478 VLRMSHRVLVMCEGRITGELARADATQEKIMQLAT 512
           VL MS RV+VM EG + G L R +ATQE++MQLA+
Sbjct: 480 VLGMSDRVMVMHEGDLMGTLNRGEATQERVMQLAS 514



 Score =  102 bits (254), Expect = 3e-26
 Identities = 63/221 (28%), Positives = 118/221 (53%), Gaps = 6/221 (2%)

Query: 43  FELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGII 102
           F+L AGE+  + G  G+G++ + + + GV     G+ILLDG+PV I++P  A   G  ++
Sbjct: 296 FDLHAGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEILLDGQPVRISDPHMAIEKGFALL 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 SELPEVLGMSDRVMVMHEGDLMGTLNRGEATQERVMQLASG 515



 Score = 86.3 bits (212), Expect = 3e-21
 Identities = 72/259 (27%), Positives = 120/259 (46%), Gaps = 17/259 (6%)

Query: 268 PPDTSRNDVV------LEVRGLNRGR----AIRDVSFTLRKGEILGFAGLMGAGRTEVAR 317
           P  T R DV+      LEV  +++G     A+ DV   +R G +L   G  GAG++ + +
Sbjct: 11  PAMTFRPDVIPDEPYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMK 70

Query: 318 AIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSM 377
            I G    +AGE+ + G      +P  A+  GI  + ++     L   M +  NI +   
Sbjct: 71  IIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQE---LNLMPHMSIAENIWIGRE 127

Query: 378 GRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDIL 437
            +   +  +D   +       + +L IK    E+Q   LS   +Q + IAK +  D DIL
Sbjct: 128 -QLNGLHMVDHGEMHRCTARLLERLRIKLDP-EEQVGNLSIAERQMVEIAKAVSYDSDIL 185

Query: 438 FFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGEL 497
             DEPT  I     + ++ ++  L  QGK I+ I+ ++ EV  ++  V V  +G   G L
Sbjct: 186 IMDEPTSAITETEVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIG-L 244

Query: 498 ARADATQ-EKIMQLATQRE 515
            RAD+   + ++ +   RE
Sbjct: 245 QRADSMDGDSLISMMVGRE 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: 653
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: 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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