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_6034 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6034
          Length = 517

 Score =  371 bits (952), Expect = e-107
 Identities = 211/477 (44%), Positives = 292/477 (61%), Gaps = 6/477 (1%)

Query: 38  LDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQAL 97
           L      L  GEV AL GENGAGKSTL KI+ G+    +G +   G+        QA+ L
Sbjct: 24  LTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTGQMRFQGRDYRPGSRSQAEEL 83

Query: 98  GIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLD-MDPST 156
           GI ++ QELNL+  LS A+N+F+   P  + G +I   +L + A    A++ LD +DP T
Sbjct: 84  GIRMVMQELNLLPTLSVAENLFLDNLP--SHGGWISRKQLRKAAIEAMAQVGLDAIDPDT 141

Query: 157 PVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYI 216
            VGEL +  QQMVEIA+ L  D  VLI+DEPTA L   E+  LF  I  LQA+GV I+YI
Sbjct: 142 LVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVSIIYI 201

Query: 217 SHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRALDGEQRIPPDTSRNDV 276
           SH+++EL ++A R++V+RDG  +   PM   + + ++++MVGR L GE            
Sbjct: 202 SHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGREL-GEHIDMGPRKIGAP 260

Query: 277 VLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGK 336
            L V+GL R   +RDVSF +R GEI G +GL+GAGRTE+ R IFGAD  ++G + +    
Sbjct: 261 ALTVKGLTRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGADTADSGTVALGASA 320

Query: 337 AV--IKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREA 394
            V  I+SPADAV HGI  ++EDRK  GL +   + ANIAL +M   +  GF++       
Sbjct: 321 QVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGNMPVISSGGFVNNGDEMSL 380

Query: 395 AQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEI 454
           AQ  +  + I++ S  Q    LSGGNQQK+VI +WL RDC ++ FDEPTRGIDVGAK +I
Sbjct: 381 AQRQINAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCTVMLFDEPTRGIDVGAKFDI 440

Query: 455 YKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLA 511
           Y LL  L  QGKA+V++SS+L E++ +  R+ V+  GR+     R   TQ+ ++  A
Sbjct: 441 YALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDLLAAA 497



 Score = 82.8 bits (203), Expect = 3e-20
 Identities = 61/244 (25%), Positives = 118/244 (48%), Gaps = 8/244 (3%)

Query: 275 DVVLEVRGLNRGRA---IRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEII 331
           + VL V G+ +  A   +  +  TL +GE+L   G  GAG++ +++ I G      G++ 
Sbjct: 7   NAVLSVSGIGKTYAQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTGQMR 66

Query: 332 IHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAI 391
             G      S + A   GI  + ++     L   + V  N+ L ++   +  G++ ++ +
Sbjct: 67  FQGRDYRPGSRSQAEELGIRMVMQE---LNLLPTLSVAENLFLDNLP--SHGGWISRKQL 121

Query: 392 REAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAK 451
           R+AA   + Q+ +     +     L  G+QQ + IA+ L+ DC +L  DEPT  +     
Sbjct: 122 RKAAIEAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREV 181

Query: 452 SEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLA 511
             +++ +  L  +G +I+ IS  L E+ R++ R+ V+ +G +      A+   E+++ L 
Sbjct: 182 EMLFEQITRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLM 241

Query: 512 TQRE 515
             RE
Sbjct: 242 VGRE 245


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: 655
Number of extensions: 38
Number of successful extensions: 8
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: 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