GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Sphingomonas koreensis DSMZ 15582

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Ga0059261_2703 Ga0059261_2703 ABC-type multidrug transport system, ATPase component

Query= uniprot:D8IUD1
         (522 letters)



>FitnessBrowser__Korea:Ga0059261_2703
          Length = 313

 Score = 95.5 bits (236), Expect = 2e-24
 Identities = 73/220 (33%), Positives = 115/220 (52%), Gaps = 12/220 (5%)

Query: 12  PLLTLSGIGKRYAA--PVLDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGM 69
           P+L++ G+ K YA+    L  +DLD+  G++ AL G NGAGK+TL  IICG+V  S+G +
Sbjct: 3   PILSVRGVSKTYASGHKALGSVDLDINKGEIFALLGPNGAGKTTLISIICGIVTPSSGTI 62

Query: 70  MLDGQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLPRRFGWIDRKKLAEAA 129
           ++DG  +   S  +A  + I +V QEL++    ++       +  R FG     + A  A
Sbjct: 63  VVDG--HDAISEPRAARMKIGLVPQELSVDMFETVQATTRYSR--RLFG-----RPANDA 113

Query: 130 RAQMEVVGLGELDPW-TPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELL 188
                +  L   D   + V +L  G ++ V IA+ L      L LDEPTA +       +
Sbjct: 114 YIDQVLKDLSLYDKRNSKVMELSGGMKRRVLIAKALAHEPDILFLDEPTAGVDVSLRRDM 173

Query: 189 FSRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLV 228
           +  I  LR  G  II  +H +EE + +ADR+ V+  G+L+
Sbjct: 174 WKLIGSLRERGTTIILTTHYIEEAEEMADRVGVINKGELL 213



 Score = 73.6 bits (179), Expect = 1e-17
 Identities = 53/227 (23%), Positives = 108/227 (47%), Gaps = 24/227 (10%)

Query: 264 PVLRIRGLGRA-----PVVHPASLALHAGEVLGIAGLIGSGRTELLRLIFGADRAEQGEI 318
           P+L +RG+ +        +    L ++ GE+  + G  G+G+T L+ +I G      G I
Sbjct: 3   PILSVRGVSKTYASGHKALGSVDLDINKGEIFALLGPNGAGKTTLISIICGIVTPSSGTI 62

Query: 319 FIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLANLGSVSRGG--ML 376
            +      +  R+ +  +K G             L+PQ +SV+     + + +R    + 
Sbjct: 63  VVDGHDAISEPRAAR--MKIG-------------LVPQELSVDM-FETVQATTRYSRRLF 106

Query: 377 DHAAESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCPIMLFDEPTRGI 436
              A  +     +K L +     ++   ELSGG +++V+IA+ L  +  I+  DEPT G+
Sbjct: 107 GRPANDAYIDQVLKDLSLYDKRNSKVM-ELSGGMKRRVLIAKALAHEPDILFLDEPTAGV 165

Query: 437 DIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRI 483
           D+  + D+++L   L  +G  +++ +  + E  ++ DR+ V++ G +
Sbjct: 166 DVSLRRDMWKLIGSLRERGTTIILTTHYIEEAEEMADRVGVINKGEL 212


Lambda     K      H
   0.320    0.137    0.390 

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: 378
Number of extensions: 23
Number of successful extensions: 5
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: 522
Length of database: 313
Length adjustment: 31
Effective length of query: 491
Effective length of database: 282
Effective search space:   138462
Effective search space used:   138462
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: 50 (23.9 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