GapMind for catabolism of small carbon sources

 

Aligments 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)



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