GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS05250 in Pseudomonas putida KT2440

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit

Query= uniprot:D8J111
         (520 letters)



>lcl|FitnessBrowser__Putida:PP_2455 PP_2455 ribose ABC transporter -
           ATP-binding subunit
          Length = 524

 Score =  368 bits (945), Expect = e-106
 Identities = 213/477 (44%), Positives = 302/477 (63%), Gaps = 6/477 (1%)

Query: 38  LDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQAL 97
           L      L AGEV AL GENGAGKSTL K++SG+    +G +   G+        +A+ L
Sbjct: 31  LGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYRGQAYAPGSRGEAERL 90

Query: 98  GIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLD-MDPST 156
           G+ ++ QELNL+  L+ A+N+F+   P +    +I    L + A A  AR+ LD +DP T
Sbjct: 91  GVRMVMQELNLLPTLTVAENLFLDNLPSRFG--WISHKRLRQLATAAMARVGLDAIDPDT 148

Query: 157 PVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYI 216
           PVGEL +  QQMVEIA+ L  D  VLI+DEPTA L   E+A LF  I  L+A+GV IVYI
Sbjct: 149 PVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQIERLRARGVAIVYI 208

Query: 217 SHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRALDGEQRIPPDTSRNDV 276
           SH+++EL+++A R+ V+RDGK +   P+Q  S   ++++MVGR L GE            
Sbjct: 209 SHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGREL-GEHIDLGRRQLGAP 267

Query: 277 VLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIII-HGG 335
           +L+V  L RG  +R+VSF +R GEI G +GL+GAGRTE+ R I+GAD  ++G I +    
Sbjct: 268 LLKVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPP 327

Query: 336 KAV-IKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREA 394
           +AV I SP  AV  GI  ++EDRK  GL +   + ANIAL ++G  +R G +D  A +  
Sbjct: 328 QAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLDSEAEKAL 387

Query: 395 AQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEI 454
           A+  ++ + I++   +Q    LSGGNQQK+VI +WL RDC +L FDEPTRGIDVGAK +I
Sbjct: 388 AERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDI 447

Query: 455 YKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLA 511
           Y LL  LA QGKA+V++SS+L E++ +  R+ V+  GR+    AR   +Q++++  A
Sbjct: 448 YGLLAELARQGKALVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQLLAAA 504



 Score = 92.4 bits (228), Expect = 4e-23
 Identities = 67/258 (25%), Positives = 127/258 (49%), Gaps = 10/258 (3%)

Query: 261 LDGEQRIPPDTSRNDVVLEVRGLNRGRA---IRDVSFTLRKGEILGFAGLMGAGRTEVAR 317
           L GE  +P     N+VVL   GL +  A   + +VS +LR GE+L   G  GAG++ +++
Sbjct: 2   LPGESAMP--ALANEVVLAASGLGKTYAQPVLGEVSLSLRAGEVLALTGENGAGKSTLSK 59

Query: 318 AIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSM 377
            I G +    G +   G      S  +A   G+  + ++     L   + V  N+ L ++
Sbjct: 60  LISGLEVPTTGHMTYRGQAYAPGSRGEAERLGVRMVMQE---LNLLPTLTVAENLFLDNL 116

Query: 378 GRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDIL 437
              +R G++  + +R+ A   + ++ +     +     L  G+QQ + IA+ L+ DC +L
Sbjct: 117 P--SRFGWISHKRLRQLATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVL 174

Query: 438 FFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGEL 497
             DEPT  +     + ++  ++ L  +G AIV IS  L E+ R++ R++V+ +G++  + 
Sbjct: 175 ILDEPTAMLTAREVALLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDE 234

Query: 498 ARADATQEKIMQLATQRE 515
                +  +++ L   RE
Sbjct: 235 PIQRYSSAELVNLMVGRE 252


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: 687
Number of extensions: 31
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: 524
Length adjustment: 35
Effective length of query: 485
Effective length of database: 489
Effective search space:   237165
Effective search space used:   237165
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:

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:

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:

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, or view the source code.

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