GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylG in Acidovorax sp. GW101-3H11

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 Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Ribose ABC
           transport system, ATP-binding protein RbsA (TC
           3.A.1.2.1)
          Length = 496

 Score =  372 bits (956), Expect = e-107
 Identities = 207/496 (41%), Positives = 316/496 (63%), Gaps = 6/496 (1%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           M   +E +++ K F  V  L GV     PG V+ ++GENGAGKSTLMKI+AG   P  GE
Sbjct: 1   MSVAVEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGE 60

Query: 61  IIYEGRGVRWNHPSEAINA-GIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYR 119
           ++ +G        S A  A GIV + QE ++ D+L++A+NIF+G E KRG+F+D K M R
Sbjct: 61  VVVDGAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAM-R 119

Query: 120 EAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEK 179
           E  +    + G+ +DP+ ++ K  +A +Q+VEIARA+ + A++LI+DEPT++LT  ETE+
Sbjct: 120 EKTREALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETER 179

Query: 180 LFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVG 239
           LF ++  LK  GV II+ISH+L+E+    D+V V+RDG  +  ++  ++T+ ++  +MVG
Sbjct: 180 LFALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVG 239

Query: 240 RKLEKFYIKE--AHEPGEVVLEVKNLSGERF-ENVSFSLRRGEILGFAGLVGAGRTELME 296
           R+L   +  +  A + G   + V+ L+   + E V F +RRGEILGFAGLVGAGRTEL E
Sbjct: 240 RELADLFPPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTELFE 299

Query: 297 TIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL 356
            + G RP+  G + I G+ V++  P DA   G+  + EDRK  GL +   +  N++L +L
Sbjct: 300 GLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMAL 359

Query: 357 DRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKIL 416
           +R  K P++    E+     A++ F IR    + +   LSGGNQQK+ LAK L   P ++
Sbjct: 360 ERYAK-PWLDPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGPSVV 418

Query: 417 ILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGII 476
           +LDEPTRG+DVGAK EIY ++ +LA++G+ VI+ISSEL E++ +  R+AVM  G+L   +
Sbjct: 419 VLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRLQTTL 478

Query: 477 DAKEASQEKVMKLAAG 492
                ++E+++  A G
Sbjct: 479 QEPHLTEEELIAHATG 494



 Score = 89.7 bits (221), Expect = 2e-22
 Identities = 71/245 (28%), Positives = 118/245 (48%), Gaps = 12/245 (4%)

Query: 256 VVLEVKNLSGER-----FENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIY 310
           V +E +N++ E         V F+L+ G + G  G  GAG++ LM+ + G+     GE+ 
Sbjct: 3   VAVEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVV 62

Query: 311 IEGK-RVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKR 369
           ++G  R        A  QGI L+ ++     L   ++I  N+ L     IK+G F+  K 
Sbjct: 63  VDGAVRAPGGGSRAAEAQGIVLIHQE---FNLADDLTIAQNIFLGH--EIKRGLFLDDKA 117

Query: 370 EKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGA 429
            +E    A+    + P  PD +V  L    +Q V +A+ LA   ++LI+DEPT  +  G 
Sbjct: 118 MREKTREALAKVGL-PLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGE 176

Query: 430 KAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKL 489
              ++ +M+ L   GV +I IS +L EV + +D + VM  G L         ++ ++  L
Sbjct: 177 TERLFALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANL 236

Query: 490 AAGLE 494
             G E
Sbjct: 237 MVGRE 241



 Score = 75.5 bits (184), Expect = 4e-18
 Identities = 57/226 (25%), Positives = 109/226 (48%), Gaps = 6/226 (2%)

Query: 21  KGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAG 80
           +GV  E   GE+    G  GAG++ L + + G+     G +   G+ V+   P +A   G
Sbjct: 272 EGVDFEVRRGEILGFAGLVGAGRTELFEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHG 331

Query: 81  IVTVFQELS---VMDNLSVAENI-FMGDEEKRGIFIDYKKMYREAEKFMKEEFGIEIDP- 135
           +  + ++     +  +  +  N+  M  E     ++D     + A +   +EFGI     
Sbjct: 332 LTYLSEDRKGKGLHVHFGLRPNLTLMALERYAKPWLD-PAAEQAALREAVQEFGIRTGSL 390

Query: 136 EEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAII 195
           E +    S   QQ + +A+ ++    V++LDEPT  +      +++ +V+ L E+G+A+I
Sbjct: 391 EVRASSLSGGNQQKLALAKVLHPGPSVVVLDEPTRGVDVGAKREIYHLVQRLAEQGLAVI 450

Query: 196 FISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241
            IS  L E+  +C +V+V+R G    T    +LT+E+++    G +
Sbjct: 451 VISSELMELIGLCHRVAVMRAGRLQTTLQEPHLTEEELIAHATGTR 496


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: 672
Number of extensions: 38
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 494
Length of database: 496
Length adjustment: 34
Effective length of query: 460
Effective length of database: 462
Effective search space:   212520
Effective search space used:   212520
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