GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA 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)



>FitnessBrowser__Putida:PP_2455
          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:

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