GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfR in Pseudomonas putida KT2440

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>FitnessBrowser__Putida:PP_2455
          Length = 524

 Score =  313 bits (803), Expect = 7e-90
 Identities = 187/473 (39%), Positives = 271/473 (57%), Gaps = 7/473 (1%)

Query: 6   HQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGT 65
           ++ +L   GL K +     L  V  SLR GE++AL GENGAGKSTL K ++G+     G 
Sbjct: 13  NEVVLAASGLGKTY-AQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGH 71

Query: 66  IWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKR 125
           +   GQA +P +   A++LG+  V QE+NLLP ++VA+NLF+   P RFG +  K + + 
Sbjct: 72  MTYRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRLRQL 131

Query: 126 ATELMASYGF-SLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELL 184
           AT  MA  G  ++D   P+    +  QQ+V I R +     VLILDEPTA L  +EV LL
Sbjct: 132 ATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALL 191

Query: 185 FDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGR 244
           F  + +LR RGV++++++H L+++ +V+ RI VLR+G  V           ELV +M+GR
Sbjct: 192 FTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGR 251

Query: 245 ELDTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAE 304
           EL  H     GR  L   P+       +   +     EVR GEI G++GL+G+GRTE   
Sbjct: 252 ELGEHI--DLGRRQLG-APLLKVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGRTELLR 308

Query: 305 VIFGIKPADSGTALIKGKPQ--NLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILA 362
           +I+G   ADSG   +   PQ  ++ SP  A   GI    EDRK +G++   S+  NI L 
Sbjct: 309 LIYGADRADSGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIALG 368

Query: 363 LQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQ 422
                     +  + ++ +AER I+ + IR+   +Q +  LSGGNQQKV++ RWL    Q
Sbjct: 369 NLGAVSRAGVLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQ 428

Query: 423 FLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIM 475
            L+ DEPTRGIDVGA  +I  L+  L   G AL+V+SS+L EL+   DR+ ++
Sbjct: 429 VLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVL 481



 Score = 96.3 bits (238), Expect = 2e-24
 Identities = 70/242 (28%), Positives = 125/242 (51%), Gaps = 10/242 (4%)

Query: 259 LSDKPVAAFKNYGK---KGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSG 315
           L+++ V A    GK   +  +    L +R GE++ L G  G+G++  +++I G++   +G
Sbjct: 11  LANEVVLAASGLGKTYAQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTG 70

Query: 316 TALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILA-LQAQRGWLRPIS 374
               +G+     S  +A  LG+    ++     ++   +V EN+ L  L ++ GW   IS
Sbjct: 71  HMTYRGQAYAPGSRGEAERLGVRMVMQELN---LLPTLTVAENLFLDNLPSRFGW---IS 124

Query: 375 RKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGID 434
            K  +++A   + ++G+     + P+  L  G+QQ V ++R L+     LILDEPT  + 
Sbjct: 125 HKRLRQLATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLT 184

Query: 435 VGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAI 494
               A +   IE L A G+A++ IS  LEEL   A R++++RD K V + P+   S   +
Sbjct: 185 AREVALLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAEL 244

Query: 495 MN 496
           +N
Sbjct: 245 VN 246



 Score = 75.1 bits (183), Expect = 6e-18
 Identities = 62/206 (30%), Positives = 101/206 (49%), Gaps = 10/206 (4%)

Query: 28  VDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL--EGQAISPKNTAHAQQLG 85
           V F +R GEI  + G  GAG++ L++ + G   AD G I L    QA+S  +   A + G
Sbjct: 283 VSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQAVSIDSPKAAVRAG 342

Query: 86  IGTVYQE---VNLLPNMSVADNLFIGR--EPKRFGLLRRKEMEKRATE--LMASYGFSLD 138
           I  + ++     LL   S++ N+ +G      R G+L   E EK   E  + A    S  
Sbjct: 343 IALITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLD-SEAEKALAERQIQAMRIRSAG 401

Query: 139 VREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSL 198
            ++ +   S   QQ V I R ++   +VL+ DEPT  +D      ++ L+ +L  +G +L
Sbjct: 402 AQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQGKAL 461

Query: 199 IFVTHFLDQVYQVSDRITVLRNGSFV 224
           + V+  L ++  + DRI VL  G  +
Sbjct: 462 VVVSSDLRELMLICDRIAVLSAGRLI 487


Lambda     K      H
   0.321    0.138    0.391 

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: 592
Number of extensions: 30
Number of successful extensions: 8
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: 500
Length of database: 524
Length adjustment: 35
Effective length of query: 465
Effective length of database: 489
Effective search space:   227385
Effective search space used:   227385
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:

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