GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylG in Herbaspirillum seropedicae SmR1

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 HSERO_RS22220 HSERO_RS22220 D-ribose transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS22220 HSERO_RS22220 D-ribose
           transporter ATP-binding protein
          Length = 505

 Score =  398 bits (1022), Expect = e-115
 Identities = 214/498 (42%), Positives = 330/498 (66%), Gaps = 11/498 (2%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P+L +  I KRF GV AL+ V     PGEV A++GENGAGKSTL+KI+ G++QPDEG I 
Sbjct: 11  PVLSLSGIGKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDEGSIH 70

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI--FIDYKKMYRE 120
             GR VR+    +A+  GI  V QE  + + LSVAENI++G +   G    ID+++M  E
Sbjct: 71  LGGREVRFASAQDAMRGGITAVHQETVMFEELSVAENIWIGRQPLCGTPRRIDWRRMEDE 130

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           A         +++    ++   S+A +  VEIARA+ ++A+V+I+DEPT++L+  E  +L
Sbjct: 131 ARALFAR-LEVDLPVRARVKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALSHHEIGEL 189

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           + ++  L+  G A+IFISH+ +EI+ + D+ +VLRDG +I +  + ++T++++V +MVGR
Sbjct: 190 YRIIGQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQLVALMVGR 249

Query: 241 KLEKFYIKEAHEPGEV---VLEVKNLSG-ERFENVSFSLRRGEILGFAGLVGAGRTELME 296
           ++ + + + A    +    VLEVK+LS    F++VSF++R GEILGF GLVGAGR+E+M 
Sbjct: 250 EVGQVFSRAASNTEDQTAPVLEVKHLSHPSEFDDVSFAVRPGEILGFYGLVGAGRSEVMH 309

Query: 297 TIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL 356
            +FG  P+  G ++I+G+ V++  P  AI  G+  VPEDR++ G +L + I  N++LP L
Sbjct: 310 ALFGLSPEAQGAVWIDGREVKLCSPAQAIAHGLAYVPEDRQRQGALLSLPIFQNITLPVL 369

Query: 357 DRIKKGPFISFKREKEL--ADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPK 414
             I  G F+   R +E+  A    +  +++ ++  + V  LSGGNQQKVVLAKWLA +P+
Sbjct: 370 PGI--GFFLRRHRRREIDIARRLCEQLELKASHFHQHVAQLSGGNQQKVVLAKWLATQPR 427

Query: 415 ILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAG 474
           +LILDEPT+GID+G+KA ++R + +L  +G+ VI++SSELPEV+ MSDRI VM  G++  
Sbjct: 428 VLILDEPTKGIDIGSKAAVHRFIGELVAQGLAVILVSSELPEVMGMSDRIVVMHQGRVQQ 487

Query: 475 IIDAKEASQEKVMKLAAG 492
           +    EAS E +   A+G
Sbjct: 488 VFSRAEASAEALAAAASG 505



 Score = 81.6 bits (200), Expect = 6e-20
 Identities = 60/237 (25%), Positives = 117/237 (49%), Gaps = 12/237 (5%)

Query: 265 GERFE------NVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEI 318
           G+RF+      +V F++R GE++   G  GAG++ L++ + G      G I++ G+ V  
Sbjct: 19  GKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDEGSIHLGGREVRF 78

Query: 319 NHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAI 378
               DA+  GI  V ++     +   +S+  N+ +           I ++R ++ A    
Sbjct: 79  ASAQDAMRGGITAVHQETV---MFEELSVAENIWIGRQPLCGTPRRIDWRRMEDEARALF 135

Query: 379 KTFDIRPAYPDR-KVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIM 437
              ++    P R +V  LS   +  V +A+ L+ + +++I+DEPT  +      E+YRI+
Sbjct: 136 ARLEVD--LPVRARVKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALSHHEIGELYRII 193

Query: 438 SQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494
            QL + G  VI IS +  E+  ++DR  V+  G+     +  + ++++++ L  G E
Sbjct: 194 GQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQLVALMVGRE 250


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: 600
Number of extensions: 32
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: 505
Length adjustment: 34
Effective length of query: 460
Effective length of database: 471
Effective search space:   216660
Effective search space used:   216660
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