Alignments for a candidate for HSERO_RS03640 in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Pseudomonas simiae WCS417

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__WCS417:GFF2673
          Length = 510

 Score =  487 bits (1253), Expect = e-142
 Identities = 274/507 (54%), Positives = 357/507 (70%), Gaps = 15/507 (2%)

Query: 1   MTQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ 60
           M+  PLL+M+GI K+F     L  + L + PGEIHALMGENGAGKSTLMK+LSG +  D 
Sbjct: 1   MSLEPLLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADP 60

Query: 61  G-EILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAA 119
           G EI + G+ +   DP  ++A GI +IYQEL++ PN+SVA N+++G ELR R   ID   
Sbjct: 61  GGEIRIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELR-RGWTIDRKG 119

Query: 120 MRSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERET 179
           M +    VL++LGA F  +     LSIAE+Q VEIARAL   ++I++MDEPT  LS RET
Sbjct: 120 MEAGCIEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRET 179

Query: 180 EQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMM 239
           ++LF ++++LR +GLAIIYISHRMAE+YAL+DRV+VLRDG ++GEL RD + +E +V+MM
Sbjct: 180 DRLFALIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMM 239

Query: 240 VGRSLSEFY--QHQRIAPADAAQLPTVMQVRALAGGK-IRPASFDVRAGEVLGFAGLVGA 296
           VGR LS FY  +H    P +      VM+VR +A GK +R  SFD+ AGEVLG AGLVGA
Sbjct: 240 VGRDLSGFYKKEHAAYNPGN-----VVMRVRDMADGKRVRHCSFDLHAGEVLGIAGLVGA 294

Query: 297 GRTELARLLFGADPRSGGDILLEGRPV-HIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVA 355
           GRTELARL+F ADPR+ G + + G+ V  +  P  A+RAG+ Y+ EDRK QGLFL M+VA
Sbjct: 295 GRTELARLIFAADPRTSGTLEVVGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSVA 354

Query: 356 ANATMNVASRHTRLGLVRSRSLG-GVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLAR 414
            N  +         G V  R      +  AI+ L+++VA  +   G LSGGNQQKVLLAR
Sbjct: 355 DNINVCACVPDAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLAR 414

Query: 415 WLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVM 474
            LE+ P VLILDEPTRGVDI +KSEIY+++++LA  G+ +VVISSELPE+IG CDRVL+M
Sbjct: 415 LLEVKPHVLILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLIM 474

Query: 475 REGMITGELAGA---AITQENIMRLAT 498
           REG +  E+ GA   AI+QE I+ LAT
Sbjct: 475 REGQLVAEVGGASGQAISQERIIDLAT 501



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 70/245 (28%), Positives = 120/245 (48%), Gaps = 13/245 (5%)

Query: 275 IRPASFDVRAGEVLGFAGLVGAGRTELARLLFGA---DPRSGGDILLEGRPVHIDQPRAA 331
           ++     V  GE+    G  GAG++ L ++L GA   DP  GG+I + G+ +    P  A
Sbjct: 22  LKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADP--GGEIRIAGQLIPTFDPATA 79

Query: 332 MRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLG-LVRSRSLGGVARAAIQRLNV 390
              GIA + ++     L   ++VA N  +    R  R G  +  + +       +QRL  
Sbjct: 80  KALGIAVIYQELS---LCPNLSVAENIYLG---RELRRGWTIDRKGMEAGCIEVLQRLGA 133

Query: 391 KVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQ 450
           +   P T V  LS   +Q V +AR L    K+L++DEPT  +       ++ L+ +L SQ
Sbjct: 134 EFT-PATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLFALIKQLRSQ 192

Query: 451 GVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPASH 510
           G+A++ IS  + E+  + DRV V+R+G   GEL   A++ E ++++    ++       H
Sbjct: 193 GLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMMVGRDLSGFYKKEH 252

Query: 511 SSPTP 515
           ++  P
Sbjct: 253 AAYNP 257


Lambda     K      H
   0.320    0.135    0.378 

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: 786
Number of extensions: 39
Number of successful extensions: 12
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: 521
Length of database: 510
Length adjustment: 35
Effective length of query: 486
Effective length of database: 475
Effective search space:   230850
Effective search space used:   230850
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