GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_3911 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3911
          Length = 517

 Score =  351 bits (900), Expect = e-101
 Identities = 200/490 (40%), Positives = 297/490 (60%), Gaps = 4/490 (0%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           +L V  I K +     L G+ +    GEV A+ GENGAGKSTL KII G+  P  G++ Y
Sbjct: 9   VLSVSGIGKTY-AQPVLAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQY 67

Query: 64  EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEK 123
           +G+  R    ++A   GI  V QEL+++  LSVAEN+F+ +   +G +I  K++ + A +
Sbjct: 68  QGQDYRPGSRAQAEALGIRMVMQELNLLPTLSVAENLFLDNLPSKGGWISRKQLRKAAIE 127

Query: 124 FMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEV 183
            M       IDP+  +G+  I  QQMVEIAR +     VLILDEPT+ LT +E E LFE 
Sbjct: 128 AMAHVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQ 187

Query: 184 VKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLE 243
           +  L+ +GV+II+ISHRLEE+  +  +++VLRDG  +  + + N   E++V +MVGR+L 
Sbjct: 188 ITRLQSRGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGRELG 247

Query: 244 KFYIKEAHEPGEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFR 302
           +     A + G  VL V  LS  ++  +VSF +R GEI G +GL+GAGRTEL+  IFG  
Sbjct: 248 EHIDMGARKIGAPVLTVNGLSRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGAD 307

Query: 303 PKRGGEIYI--EGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIK 360
               G I +    + + +  P+DA+  GI L+ EDRK  GL+L  SI  N++L ++  I 
Sbjct: 308 IADSGTIALGAPAQVINVRSPVDAVGHGIALITEDRKGEGLLLTQSIGANIALGNMPGIS 367

Query: 361 KGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDE 420
              F+   +E+ LA   I    IR + P + V  LSGGNQQKVV+ +WL     +L+ DE
Sbjct: 368 GAGFVDNDKERALAQRQIDAMRIRSSGPAQLVSELSGGNQQKVVIGRWLERDCSVLLFDE 427

Query: 421 PTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKE 480
           PTRGIDVGAK +IY ++ +L ++G  ++++SS+L E++ + DRI V+S G L    D   
Sbjct: 428 PTRGIDVGAKFDIYNLLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGSLIDTFDRDS 487

Query: 481 ASQEKVMKLA 490
            +Q++++  A
Sbjct: 488 WTQDELLAAA 497



 Score = 86.3 bits (212), Expect = 2e-21
 Identities = 66/224 (29%), Positives = 111/224 (49%), Gaps = 5/224 (2%)

Query: 271 VSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIG 330
           +  +L RGE+L   G  GAG++ L + I G      G++  +G+         A   GI 
Sbjct: 27  IDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQYQGQDYRPGSRAQAEALGIR 86

Query: 331 LVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDR 390
           +V ++   L L+  +S+  N+ L +L    KG +IS K+ ++ A  A+    +    PD 
Sbjct: 87  MVMQE---LNLLPTLSVAENLFLDNLP--SKGGWISRKQLRKAAIEAMAHVGLDAIDPDT 141

Query: 391 KVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMI 450
            V  L  G+QQ V +A+ L     +LILDEPT  +       ++  +++L   GV +I I
Sbjct: 142 LVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQSRGVSIIYI 201

Query: 451 SSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494
           S  L E+ +++ RIAV+  G L  +      + E+++ L  G E
Sbjct: 202 SHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGRE 245


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: 589
Number of extensions: 32
Number of successful extensions: 7
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: 494
Length of database: 517
Length adjustment: 34
Effective length of query: 460
Effective length of database: 483
Effective search space:   222180
Effective search space used:   222180
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