GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2881
          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:

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