GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS16930 in Klebsiella michiganensis M5al

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS07240 BWI76_RS07240 D-ribose
           transporter ATP-binding protein
          Length = 494

 Score =  436 bits (1121), Expect = e-127
 Identities = 228/490 (46%), Positives = 328/490 (66%), Gaps = 4/490 (0%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L  + I K FPGV+ALD VS  V  G VH LMGENGAGKSTL+K L G Y+PD G + + 
Sbjct: 6   LEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVK 65

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124
           G  V+F     ++ +GI++IHQEL  VP +TVAEN+ LG+ P   G+V+ R+  R  ++ 
Sbjct: 66  GEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYGFVDHRQLARQTQDL 125

Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184
           L+ + + L  +  + +LSIA +QMVEI KA+  NA ++ +DEPTS+L+  E   LF ++R
Sbjct: 126 LDKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTIIR 185

Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244
           DLR   +A+IYISH+MDEI+ + D  ++FRDG  + S  T E  TR +++++MVGRE++ 
Sbjct: 186 DLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTE-FTRQSLITQMVGRELTQ 244

Query: 245 IYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADH 304
           ++      +GE     + +         +F VRRGEI+G  GLVGAGRSE+M  ++G + 
Sbjct: 245 LFPKFNNAIGEEVLTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGMEK 304

Query: 305 KKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVG 364
              GE+L+DG P+ + S   AI  G+ L  EDRK+ G+  + +V EN++I     Y+   
Sbjct: 305 ADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYIGKT 364

Query: 365 MFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRW-LAEPDLKVVILDE 423
            F+   K AE     I+ L IKTP+  Q I  LSGGNQQK +++RW LA+P  K++ILDE
Sbjct: 365 GFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQP--KILILDE 422

Query: 424 PTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKD 483
           PTRGIDVGAK EIY++I +LA RG A++M+SSELPE+LG+SDR++VM +GRI+G L ++D
Sbjct: 423 PTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEGRITGILDKED 482

Query: 484 ATEQSVLSLA 493
           A ++++LSLA
Sbjct: 483 ADQETILSLA 492



 Score = 86.3 bits (212), Expect = 2e-21
 Identities = 68/250 (27%), Positives = 119/250 (47%), Gaps = 14/250 (5%)

Query: 255 EVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDG 314
           E    +K   G       S  VR G +    G  GAG+S LM  + G      G + + G
Sbjct: 7   EAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVKG 66

Query: 315 KPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAE 374
           +P++ +   +A+R GI +     +E  +V   TV+ENI +   R  ++ G F+D ++ A 
Sbjct: 67  EPVQFQDTMDALRSGISMI---HQELNLVPHMTVAENIWLG--REPMKYG-FVDHRQLAR 120

Query: 375 TADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSR---WLAEPDLKVVILDEPTRGIDVG 431
                +  L I+  + R  +  LS  +QQ   +++   W A+    +VI+DEPT  +   
Sbjct: 121 QTQDLLDKLNIRLSADRL-VGELSIASQQMVEIAKAVSWNAD----IVIMDEPTSALTES 175

Query: 432 AKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLS 491
               ++ +I  L ++G AI+ IS ++ E+  ++D I V R G   G     + T QS+++
Sbjct: 176 EVAHLFTIIRDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLIT 235

Query: 492 LALPQSSTAL 501
             + +  T L
Sbjct: 236 QMVGRELTQL 245


Lambda     K      H
   0.320    0.136    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: 642
Number of extensions: 26
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: 512
Length of database: 494
Length adjustment: 34
Effective length of query: 478
Effective length of database: 460
Effective search space:   219880
Effective search space used:   219880
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