GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylG in Pseudomonas putida KT2440

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit

Query= TCDB::G4FGN3
         (494 letters)



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

 Score =  333 bits (853), Expect = 1e-95
 Identities = 190/471 (40%), Positives = 288/471 (61%), Gaps = 3/471 (0%)

Query: 23  VSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAGIV 82
           VS+    GEV A+ GENGAGKSTL K+I+G+  P  G + Y G+        EA   G+ 
Sbjct: 34  VSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYRGQAYAPGSRGEAERLGVR 93

Query: 83  TVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFMKEEFGIEIDPEEKLGKY 142
            V QEL+++  L+VAEN+F+ +   R  +I +K++ + A   M       IDP+  +G+ 
Sbjct: 94  MVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRLRQLATAAMARVGLDAIDPDTPVGEL 153

Query: 143 SIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAIIFISHRLE 202
            I  QQMVEIAR +     VLILDEPT+ LT +E   LF  ++ L+ +GVAI++ISHRLE
Sbjct: 154 GIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQIERLRARGVAIVYISHRLE 213

Query: 203 EIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEKFYIKEAHEPGEVVLEVKN 262
           E+  +  ++ VLRDG+ +  + I+  +  ++V +MVGR+L +       + G  +L+V  
Sbjct: 214 ELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGRELGEHIDLGRRQLGAPLLKVDK 273

Query: 263 L-SGERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYI--EGKRVEIN 319
           L  G++   VSF +R GEI G +GL+GAGRTEL+  I+G      G I +    + V I+
Sbjct: 274 LCRGDKVREVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQAVSID 333

Query: 320 HPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIK 379
            P  A+  GI L+ EDRK  GL+L  SI  N++L +L  + +   +  + EK LA+  I+
Sbjct: 334 SPKAAVRAGIALITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLDSEAEKALAERQIQ 393

Query: 380 TFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQ 439
              IR A   + V  LSGGNQQKVV+ +WL    ++L+ DEPTRGIDVGAK +IY ++++
Sbjct: 394 AMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAE 453

Query: 440 LAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLA 490
           LA++G  ++++SS+L E++ + DRIAV+S G+L         SQ++++  A
Sbjct: 454 LARQGKALVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQLLAAA 504



 Score = 86.3 bits (212), Expect = 2e-21
 Identities = 67/224 (29%), Positives = 110/224 (49%), Gaps = 5/224 (2%)

Query: 271 VSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIG 330
           VS SLR GE+L   G  GAG++ L + I G      G +   G+        +A   G+ 
Sbjct: 34  VSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYRGQAYAPGSRGEAERLGVR 93

Query: 331 LVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDR 390
           +V ++   L L+  +++  N+ L +L    +  +IS KR ++LA  A+    +    PD 
Sbjct: 94  MVMQE---LNLLPTLTVAENLFLDNLP--SRFGWISHKRLRQLATAAMARVGLDAIDPDT 148

Query: 391 KVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMI 450
            V  L  G+QQ V +A+ L     +LILDEPT  +     A ++  + +L   GV ++ I
Sbjct: 149 PVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQIERLRARGVAIVYI 208

Query: 451 SSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494
           S  L E+ +++ RI V+  GKL      +  S  +++ L  G E
Sbjct: 209 SHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGRE 252



 Score = 79.0 bits (193), Expect = 4e-19
 Identities = 57/222 (25%), Positives = 113/222 (50%), Gaps = 7/222 (3%)

Query: 20  LKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII--YEGRGVRWNHPSEAI 77
           ++ VS E   GE+  I G  GAG++ L+++I G  + D G I      + V  + P  A+
Sbjct: 280 VREVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQAVSIDSPKAAV 339

Query: 78  NAGIVTVFQEL---SVMDNLSVAENIFMGD--EEKRGIFIDYKKMYREAEKFMKEEFGIE 132
            AGI  + ++     ++   S++ NI +G+     R   +D +     AE+ ++      
Sbjct: 340 RAGIALITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLDSEAEKALAERQIQAMRIRS 399

Query: 133 IDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGV 192
              ++ +G+ S   QQ V I R + +  +VL+ DEPT  +       ++ ++  L  +G 
Sbjct: 400 AGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQGK 459

Query: 193 AIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIV 234
           A++ +S  L E+  ICD+++VL  G  I T + ++ ++++++
Sbjct: 460 ALVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQLL 501


Lambda     K      H
   0.318    0.138    0.385 

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: 601
Number of extensions: 31
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: 494
Length of database: 524
Length adjustment: 34
Effective length of query: 460
Effective length of database: 490
Effective search space:   225400
Effective search space used:   225400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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