GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS05250 in Klebsiella michiganensis M5al

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BWI76_RS19640 BWI76_RS19640 galactose/methyl galactoside ABC transporter ATP-binding protein MglA

Query= uniprot:D8J111
         (520 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS19640 BWI76_RS19640
           galactose/methyl galactoside ABC transporter ATP-binding
           protein MglA
          Length = 506

 Score =  437 bits (1123), Expect = e-127
 Identities = 225/502 (44%), Positives = 336/502 (66%), Gaps = 8/502 (1%)

Query: 15  SSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQR 74
           S  S   ++ + N+ K FPGV ALDN   ++    +HALMGENGAGKSTL+K L G+YQ+
Sbjct: 6   SERSGEYLLEMTNINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQK 65

Query: 75  DSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDE 134
           DSG IL  G+ ++    ++A   GI ++HQELNL+   S   N+++GR P K  G+F+D+
Sbjct: 66  DSGSILFQGQEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK--GVFVDQ 123

Query: 135 DELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNA 194
           D++ R   AIF  + +D+DP   VG L+V++ QM+EIAKA S++++++IMDEPT++L   
Sbjct: 124 DKMYRDTKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEK 183

Query: 195 EIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIIS 254
           E+  LF+IIR L+ +G GIVYISHKM+E+ Q+ D ++++RDG++IAT P++   MD II+
Sbjct: 184 EVNHLFKIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIA 243

Query: 255 MMVGRALDGEQRIP-PDTSRNDVVLEVRGLN--RGRAIRDVSFTLRKGEILGFAGLMGAG 311
           MMVGR+L+  QR P  +    +V+LEVR L   R  +IRD+SF L KGEILG AGL+GA 
Sbjct: 244 MMVGRSLN--QRFPNKENKPGEVILEVRNLTSLRQPSIRDISFDLHKGEILGIAGLVGAK 301

Query: 312 RTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQAN 371
           RT++   +FG      G I +HG K    S  +A+ HG   ++E+R+  G+   +D+  N
Sbjct: 302 RTDIVETLFGIREKAGGTIRLHGKKINNHSANEAINHGFALVTEERRSTGIYAYLDIGFN 361

Query: 372 IALSSMGRF-TRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWL 430
             +S++ ++  +VG +D   ++   Q  +  + +KTP    Q   LSGGNQQK++I +WL
Sbjct: 362 SLISNIKKYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGQHTQIGSLSGGNQQKVIIGRWL 421

Query: 431 LRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCE 490
           L   +IL  DEPTRGIDVGAK EIY+L+  LA++ K I++ISSE+PE+L ++ R+LVM  
Sbjct: 422 LTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKDKGIIIISSEMPELLGITDRILVMSN 481

Query: 491 GRITGELARADATQEKIMQLAT 512
           G + G +     TQ +I++LA+
Sbjct: 482 GLVAGIVETKTTTQNEILRLAS 503



 Score = 73.2 bits (178), Expect = 2e-17
 Identities = 59/247 (23%), Positives = 117/247 (47%), Gaps = 16/247 (6%)

Query: 275 DVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEI 330
           + +LE+  +N+     +A+ +V+  +R   I    G  GAG++ + + +FG    ++G I
Sbjct: 11  EYLLEMTNINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSI 70

Query: 331 IIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVG-FMDQR 389
           +  G +    S  +A+ +GI  + ++     L +   V  N+ L   GR+   G F+DQ 
Sbjct: 71  LFQGQEIDFHSAKEALENGISMVHQE---LNLVLQRSVMDNMWL---GRYPTKGVFVDQD 124

Query: 390 AIREAAQMYVRQLAIKTPSVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTRGID 447
            +    +    +L I    ++ +AR+  LS    Q I IAK    +  I+  DEPT  + 
Sbjct: 125 KMYRDTKAIFDELDI---DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181

Query: 448 VGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKI 507
               + ++K++  L E+G  IV IS ++ E+ ++   + ++ +G+            +KI
Sbjct: 182 EKEVNHLFKIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKI 241

Query: 508 MQLATQR 514
           + +   R
Sbjct: 242 IAMMVGR 248


Lambda     K      H
   0.320    0.135    0.372 

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: 620
Number of extensions: 26
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: 520
Length of database: 506
Length adjustment: 35
Effective length of query: 485
Effective length of database: 471
Effective search space:   228435
Effective search space used:   228435
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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 preprint 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