Alignments for a candidate for HSERO_RS03640 in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Pseudomonas putida KT2440

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__Putida:PP_2759
          Length = 512

 Score =  377 bits (967), Expect = e-109
 Identities = 207/496 (41%), Positives = 294/496 (59%), Gaps = 6/496 (1%)

Query: 4   TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63
           TP+L++RGI K+FGAT AL    L +  G +H L+GENGAGKSTL+KVL+G+H PD G +
Sbjct: 3   TPVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSL 62

Query: 64  LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 123
           LLDG+P     P      GI  I+QE  +    +V   +F G E R    L   +  R  
Sbjct: 63  LLDGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQQREA 122

Query: 124 TDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 183
              +    G    A+ L G LS AEQQ V+I RAL+ + R+++ DEP+ AL +RE E+L 
Sbjct: 123 ARLLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLL 182

Query: 184 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRS 243
            +V+RLRD+GLAI+YISH + E+ AL DRVTVLR+G  V E+       E+I ++MV R 
Sbjct: 183 RIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVNRE 242

Query: 244 LSEFYQHQRIAPADAAQLPTVMQVRALAGGKI-RPASFDVRAGEVLGFAGLVGAGRTELA 302
           + E Y    + PA A     ++ VR L   +  +     VR GE++G  GLVG+G  EL 
Sbjct: 243 VGELYPKVAV-PAGAL----LLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKELL 297

Query: 303 RLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNV 362
           R LFG  P   G++ L+G+P+ +  PR A+  G+A +PE+R+ QG+ L ++V  N T+  
Sbjct: 298 RSLFGLAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAA 357

Query: 363 ASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKV 422
            SR  RLGL+            I+RL +K       V +LSGGNQQKV LA+W      +
Sbjct: 358 LSRFVRLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSL 417

Query: 423 LILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGE 482
            +LDEP+ G+D+ AK EIY+L+  L  +G  V+++SS+LPE+IG+CDR+ VM  G I   
Sbjct: 418 YLLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAAR 477

Query: 483 LAGAAITQENIMRLAT 498
            A      + ++ +AT
Sbjct: 478 FAAGEANSDRLLAVAT 493



 Score =  110 bits (274), Expect = 2e-28
 Identities = 73/241 (30%), Positives = 124/241 (51%), Gaps = 9/241 (3%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           LL +RG+    G   A   + L +R GEI  L G  G+G   L++ L G+  PD GE+ L
Sbjct: 258 LLDVRGL----GRARAYQGIDLQVRRGEIVGLTGLVGSGAKELLRSLFGLAPPDSGEVRL 313

Query: 66  DGRPVALRDPGASRAAGINLIYQEL---AVAPNISVAANVFMGSELR-TRLGLIDHAAMR 121
           DG+P++LR P  + A G+ L+ +E     VA ++SV  N  + +  R  RLGL+  A  R
Sbjct: 314 DGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAALSRFVRLGLLSPARER 373

Query: 122 SRTDAVLRQLGA-GFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180
             T  ++ +L     GA     +LS   QQ+V +A+     S + ++DEP+  +      
Sbjct: 374 HTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLYLLDEPSVGIDVGAKV 433

Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240
           +++ ++  L  EG  ++ +S  + E+  L DR+ V+  G+        E +S+R++ +  
Sbjct: 434 EIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARFAAGEANSDRLLAVAT 493

Query: 241 G 241
           G
Sbjct: 494 G 494



 Score = 96.7 bits (239), Expect = 2e-24
 Identities = 76/245 (31%), Positives = 112/245 (45%), Gaps = 20/245 (8%)

Query: 268 RALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQ 327
           RAL G  +R     V AG V G  G  GAG++ L ++L G      G +LL+G+P     
Sbjct: 19  RALDGASLR-----VAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLLLDGQPHGHFS 73

Query: 328 PRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVA---SRHTRLG--LVRSRSLGGVAR 382
           PR   R GI ++ ++R          + A  T+  A       R G  L R       AR
Sbjct: 74  PRQVERLGIGFIHQER---------LLPARFTVGEALFFGHERRFGPLLDRRSQQREAAR 124

Query: 383 AAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQ 442
                  +++      +G+LS   QQ V + R L I P+VL+ DEP+  +       + +
Sbjct: 125 LLDDYFGLRLP-ANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLLR 183

Query: 443 LVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNV 502
           +V RL   G+A+V IS  L E+  +CDRV V+R G    E++    + E I RL  +  V
Sbjct: 184 IVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVNREV 243

Query: 503 PRTAP 507
               P
Sbjct: 244 GELYP 248


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: 707
Number of extensions: 37
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: 521
Length of database: 512
Length adjustment: 35
Effective length of query: 486
Effective length of database: 477
Effective search space:   231822
Effective search space used:   231822
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