Alignments for a candidate for rbsA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Pseudomonas putida KT2440

Align Ribose ABC transporter ATPase; SubName: Full=Sugar ABC transporter ATP-binding protein; SubName: Full=Sugar ABC transporter ATPase (characterized, see rationale)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit

Query= uniprot:A0A1N7TZ92
         (517 letters)



>FitnessBrowser__Putida:PP_2455
          Length = 524

 Score =  767 bits (1981), Expect = 0.0
 Identities = 401/514 (78%), Positives = 438/514 (85%)

Query: 1   MSSSAPNAVLSVSGIGKTYAQPVLSDITLTLNRGEVLALTGENGAGKSTLSKIIGGLVTP 60
           M + A   VL+ SG+GKTYAQPVL +++L+L  GEVLALTGENGAGKSTLSK+I GL  P
Sbjct: 8   MPALANEVVLAASGLGKTYAQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVP 67

Query: 61  TTGHMQFNGQDFRPGSRTQAEELGVRMVMQELNLLPTLTVAENLFLDNLPSHCGWISRKQ 120
           TTGHM + GQ + PGSR +AE LGVRMVMQELNLLPTLTVAENLFLDNLPS  GWIS K+
Sbjct: 68  TTGHMTYRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISHKR 127

Query: 121 LRKAAIEAMAQVGLDAIDPDTLVGSLGIGHQQMVEIARNLIGDCHVLILDEPTAMLTARE 180
           LR+ A  AMA+VGLDAIDPDT VG LGIGHQQMVEIARNLIGDCHVLILDEPTAMLTARE
Sbjct: 128 LRQLATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTARE 187

Query: 181 VEMLFEQITRLQARGVAIIYISHRLEELARVAQRIAVLRDGKLVCVEPMANYNSEQLVTL 240
           V +LF QI RL+ARGVAI+YISHRLEEL RVAQRI VLRDGKLVC EP+  Y+S +LV L
Sbjct: 188 VALLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNL 247

Query: 241 MVGRELGEHIDLGPRTIGGPALTVKGLTRSDKVRDVSFEVRAGEIYGISGLIGAGRTELL 300
           MVGRELGEHIDLG R +G P L V  L R DKVR+VSFEVRAGEI+GISGLIGAGRTELL
Sbjct: 248 MVGRELGEHIDLGRRQLGAPLLKVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGRTELL 307

Query: 301 RLIFGADLADSGTVALGSPAQVVSIRSPVDAVGHGIALITEDRKGEGLLLTQSISANIAL 360
           RLI+GAD ADSG +ALG P Q VSI SP  AV  GIALITEDRKGEGLLLTQSISANIAL
Sbjct: 308 RLIYGADRADSGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIAL 367

Query: 361 GNMPEISGGGVVNSRDETALAKRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERDC 420
           GN+  +S  GV++S  E ALA+RQI AMRIRS+   Q+V ELSGGNQQKVVIGRWLERDC
Sbjct: 368 GNLGAVSRAGVLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDC 427

Query: 421 SVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLI 480
            V+LFDEPTRGIDVGAKFDIY LL EL RQGKALVVVSSDLRELMLICDRI VLSAGRLI
Sbjct: 428 QVLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVLSAGRLI 487

Query: 481 ETFERDSWTQDELLAAAFAGYQKRDALLNDAVLR 514
           +TF RD W+QD+LLAAAFAGYQKRDALL+DA  R
Sbjct: 488 DTFARDHWSQDQLLAAAFAGYQKRDALLHDAAPR 521


Lambda     K      H
   0.319    0.136    0.382 

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: 902
Number of extensions: 34
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 517
Length of database: 524
Length adjustment: 35
Effective length of query: 482
Effective length of database: 489
Effective search space:   235698
Effective search space used:   235698
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 (21.7 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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Steps (tab-delimited)
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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