GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Acidovorax sp. GW101-3H11

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2881
          Length = 496

 Score =  319 bits (817), Expect = 2e-91
 Identities = 202/511 (39%), Positives = 293/511 (57%), Gaps = 41/511 (8%)

Query: 6   LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65
           +E RN+TK F  V+ L  V   ++ G ++ L+GENGAGKSTLMK+L+G     T  GE+ 
Sbjct: 5   VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTT--GEVV 62

Query: 66  YEGAVR----NFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTF 121
            +GAVR      RA   +E  GI++IHQE  L   L+IA+NIFLG+E+     +  +   
Sbjct: 63  VDGAVRAPGGGSRA---AEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAMR 119

Query: 122 NRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEA 181
            +TRE L KVGL   P+T +  + V ++QLVEIA+AL+++ +LLI+DEPTA+L   ++E 
Sbjct: 120 EKTREALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETER 179

Query: 182 LLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN- 240
           L  L+   +  G+T I I+HKL+EV +  D++ V+RDG+ V        E +  V  R  
Sbjct: 180 LFALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLV------AREATASVTRRQM 233

Query: 241 ---MVGRDLEDRYPPR-----DVPIGETI--LEVKNWNAYHQQHRDRQVLHDINVTVRKG 290
              MVGR+L D +PP+     D     T+  L V  W               ++  VR+G
Sbjct: 234 ANLMVGRELADLFPPKLPAPQDGAPAITVRGLTVPGW------------AEGVDFEVRRG 281

Query: 291 EVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDR 350
           E++G AGL+GAGRTE    + G     R  G V I G+PV + + R A   GL Y++EDR
Sbjct: 282 EILGFAGLVGAGRTELFEGLLG--LRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDR 339

Query: 351 KHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLS 410
           K  GL ++  +  N TL  L   +K   +D   E     +      IR+  +     +LS
Sbjct: 340 KGKGLHVHFGLRPNLTLMALERYAK-PWLDPAAEQAALREAVQEFGIRTGSLEVRASSLS 398

Query: 411 GGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPE 470
           GGNQQK+ L+K L   P V++LDEPTRG+DVGAK EIY ++ +LA  G  V++ISSE+ E
Sbjct: 399 GGNQQKLALAKVLHPGPSVVVLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELME 458

Query: 471 LLGNCDRIYVMNEGRIVAELPKGEASQESIM 501
           L+G C R+ VM  GR+   L +   ++E ++
Sbjct: 459 LIGLCHRVAVMRAGRLQTTLQEPHLTEEELI 489


Lambda     K      H
   0.316    0.135    0.374 

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: 588
Number of extensions: 32
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 512
Length of database: 496
Length adjustment: 34
Effective length of query: 478
Effective length of database: 462
Effective search space:   220836
Effective search space used:   220836
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 (21.6 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