GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Klebsiella michiganensis M5al

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 BWI76_RS00275 BWI76_RS00275 ribose ABC transporter ATP-binding protein RbsA

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS00275 BWI76_RS00275 ribose ABC
           transporter ATP-binding protein RbsA
          Length = 501

 Score =  445 bits (1144), Expect = e-129
 Identities = 231/494 (46%), Positives = 335/494 (67%), Gaps = 3/494 (0%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           M+ +L++K I K FPGV AL G S+  YPG V A+VGENGAGKST+MK++ G+Y  D G 
Sbjct: 1   MEALLQLKGIDKAFPGVKALSGASLNVYPGRVMALVGENGAGKSTMMKVLTGIYARDAGS 60

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDE-EKRGIFIDYKKMYR 119
           +++ G+   +N P  +  AGI  + QEL+++  L++AENIF+G E   R   ID+K MY 
Sbjct: 61  LLWLGKETTFNGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120

Query: 120 EAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEK 179
           EA+K + +   +  + ++ +G  SI  QQMVEIA+ +  ++KV+I+DEPT +LT  ETE 
Sbjct: 121 EADKLLAK-LNLRFNSQKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETES 179

Query: 180 LFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVG 239
           LF V++ LK +G  I++ISHR++EIFEICD V+V RDG++I    + +L ++ ++EMMVG
Sbjct: 180 LFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLDEDLLIEMMVG 239

Query: 240 RKLEKFYIKEAHEPGEVVLEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRTELMETIF 299
           RKLE  Y +    PG V L+V NL G   EN+SF LR+GEILG AGL+GAGRTELM+ ++
Sbjct: 240 RKLEDQYPRLDKAPGAVRLKVDNLCGSGVENISFILRQGEILGVAGLMGAGRTELMKVLY 299

Query: 300 GFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRI 359
           G  P+  G + ++G+ V    P D +  GI  + EDRK+ GL+L MS+  N+SL +L   
Sbjct: 300 GALPRSSGSVTLDGREVVARSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYF 359

Query: 360 KK-GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILIL 418
            + G  +  K E++     I+ F+++    ++ +  LSGGNQQKV +A+ L  +PK+LIL
Sbjct: 360 SRGGGSLKHKDEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLIL 419

Query: 419 DEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDA 478
           DEPTRG+DVGAK EIY++++Q   EG+ +I++SSE+PEVL MSDRI VM  G L G    
Sbjct: 420 DEPTRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRIMVMHEGHLGGEFTR 479

Query: 479 KEASQEKVMKLAAG 492
           ++A+QE +M  A G
Sbjct: 480 EQATQEVLMAAAVG 493



 Score = 94.4 bits (233), Expect = 8e-24
 Identities = 60/231 (25%), Positives = 117/231 (50%), Gaps = 14/231 (6%)

Query: 20  LKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINA 79
           ++ +S     GE+  + G  GAG++ LMK++ G      G +  +GR V    P + +  
Sbjct: 268 VENISFILRQGEILGVAGLMGAGRTELMKVLYGALPRSSGSVTLDGREVVARSPQDGLAN 327

Query: 80  GIVTVFQE---------LSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFMKEEFG 130
           GIV + ++         +SV +N+S+    +     + G  + +K   +    F++  F 
Sbjct: 328 GIVYISEDRKRDGLVLGMSVKENMSLTALRYFS---RGGGSLKHKDEQQAVSDFIRL-FN 383

Query: 131 IEIDP-EEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKE 189
           ++    E+ +G  S   QQ V IAR +  + KVLILDEPT  +     +++++++   K 
Sbjct: 384 VKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKA 443

Query: 190 KGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           +G++II +S  + E+  + D++ V+ +G   G  + E  T+E ++   VG+
Sbjct: 444 EGLSIILVSSEMPEVLGMSDRIMVMHEGHLGGEFTREQATQEVLMAAAVGK 494


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: 676
Number of extensions: 34
Number of successful extensions: 8
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: 501
Length adjustment: 34
Effective length of query: 460
Effective length of database: 467
Effective search space:   214820
Effective search space used:   214820
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