GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Pseudomonas simiae WCS417

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 GFF3463 PS417_17730 ribonucleotide-diphosphate reductase subunit alpha

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__WCS417:GFF3463
          Length = 502

 Score =  407 bits (1045), Expect = e-118
 Identities = 219/495 (44%), Positives = 324/495 (65%), Gaps = 3/495 (0%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           M  +L++++I KR+PGV ALK ++++   GE+HA++GENGAGKSTLMKI+ GV   DEG+
Sbjct: 1   MSSLLKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQ 60

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYRE 120
           I+ +G+  ++    +AI AGI  VFQE S++  L+  ENIF+G E      +  K+   E
Sbjct: 61  ILIDGQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHELSNRFGLLRKREMVE 120

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           A + + +  G+ ID +  +   S+A QQ VEIA+A+   A++L+LDEPT++LT  E E L
Sbjct: 121 ASEALFKRLGVTIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAELL 180

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           FE+++ LK +GVA+IFISH LEEIF++CD++SVLRDG  +G   + +   + +VEMMVGR
Sbjct: 181 FEIMRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVEMMVGR 240

Query: 241 KLE-KFYIKEAHEPGEVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETI 298
           +L   F  K   E G ++LEVK++   R   +  F L +GEILGFAGLVG+GRTEL   +
Sbjct: 241 RLACSFPPKPTRERGPLLLEVKDIQLVRNGPHNRFQLHKGEILGFAGLVGSGRTELALGM 300

Query: 299 FGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDR 358
            G  P    ++++ G+++ ++ P  A+  GIGL+PE RK  GLI   SI  N+SL +L +
Sbjct: 301 MGALPSVSKDVWLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISLNNLPK 360

Query: 359 IKKGP-FISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILI 417
            +     I   RE    +  +K   I+    + +V  LSGGNQQKVV+A+W+     +L+
Sbjct: 361 YQNASGLIDKNRECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHHCDVLV 420

Query: 418 LDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIID 477
            DEPTRGIDVGAKA+IY +M  L ++G  +IMISSELPE++ M DR+AV   G +  +++
Sbjct: 421 FDEPTRGIDVGAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAVFHKGAIVKLLE 480

Query: 478 AKEASQEKVMKLAAG 492
           A   + ++VM+ A G
Sbjct: 481 ASAVNPQEVMRHATG 495



 Score = 75.5 bits (184), Expect = 4e-18
 Identities = 62/246 (25%), Positives = 108/246 (43%), Gaps = 10/246 (4%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           +LEVK I     G H       + + GE+    G  G+G++ L   + G       ++  
Sbjct: 258 LLEVKDIQLVRNGPHN----RFQLHKGEILGFAGLVGSGRTELALGMMGALPSVSKDVWL 313

Query: 64  EGRGVRWNHPSEAINAGIVTVFQELS---VMDNLSVAENIFMGDEEK---RGIFIDYKKM 117
            G  +  + P++A+  GI  + +      ++ + S+ ENI + +  K       ID  + 
Sbjct: 314 RGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISLNNLPKYQNASGLIDKNRE 373

Query: 118 YREAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKET 177
               E  MK+        E ++   S   QQ V IAR +     VL+ DEPT  +     
Sbjct: 374 CASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHHCDVLVFDEPTRGIDVGAK 433

Query: 178 EKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMM 237
            +++ +++SL E+G AII IS  L EI  +CD+V+V   G  +       +  ++++   
Sbjct: 434 AQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAVFHKGAIVKLLEASAVNPQEVMRHA 493

Query: 238 VGRKLE 243
            G   E
Sbjct: 494 TGGSSE 499


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: 695
Number of extensions: 36
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: 502
Length adjustment: 34
Effective length of query: 460
Effective length of database: 468
Effective search space:   215280
Effective search space used:   215280
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