GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Sphingomonas koreensis DSMZ 15582

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate Ga0059261_2250 Ga0059261_2250 ABC-type multidrug transport system, ATPase component

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__Korea:Ga0059261_2250
          Length = 307

 Score =  117 bits (292), Expect = 8e-31
 Identities = 91/295 (30%), Positives = 143/295 (48%), Gaps = 10/295 (3%)

Query: 3   ATLRFDNIGKVFPGVR-ALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRV 61
           A +  + + KV+ G + ALD VSF V  GQ+ GL+G NGAGKSTL+ IL G     +GR 
Sbjct: 4   AAIEIEGLSKVYQGGKQALDDVSFTVPRGQIFGLLGPNGAGKSTLINILAGLVNKTAGRA 63

Query: 62  MIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFV 121
            I G ++      +  A GI  ++QE+ + P  T  E L +       G     +A+R  
Sbjct: 64  SIWGFDIDQHPRNAKRAIGI--VNQEILFDPFFTPVETLEI-----QAGLYGVPKAQRRS 116

Query: 122 RERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFK 181
            E L A+ +    +A  R LS   ++ + + KA++ +  V+ LDEPT+ +     + L+ 
Sbjct: 117 MELLRAVHLEDKAHAYSRTLSGGMKRRLMVAKAMVHSPPVLVLDEPTAGVDIELRQQLWA 176

Query: 182 LVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLE--GVTRDTIVSEMVG 239
            VR L      ++  +H ++E  ELCD   I   G+ IA+ PT E  G T++  V   V 
Sbjct: 177 YVRSLNERGVTVVLTTHYLEEAEELCDRIAIINHGKLIANEPTRELVGKTQEKAVEVTVD 236

Query: 240 REISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSE 294
           R+I+ + +       EV+     +  +A  Q  + EV        FG+V     E
Sbjct: 237 RDIAAVPDSRCFQKIEVKGDRTLVITYAKDQANAGEVLGAVQAAGFGIVDVSTRE 291



 Score = 71.6 bits (174), Expect = 4e-17
 Identities = 59/246 (23%), Positives = 118/246 (47%), Gaps = 22/246 (8%)

Query: 265 GHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDGKPIKV--RSA 322
           G       SF V RG+I G  G  GAG+S L++++ G  +K  G   + G  I    R+A
Sbjct: 18  GKQALDDVSFTVPRGQIFGLLGPNGAGKSTLINILAGLVNKTAGRASIWGFDIDQHPRNA 77

Query: 323 GEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAETADRFIKL 382
             AI              GIV    + +          ++ G++   K +  + +  ++ 
Sbjct: 78  KRAI--------------GIVNQEILFDPFFTPVETLEIQAGLYGVPKAQRRSME-LLRA 122

Query: 383 LKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKHEIYNVIYQ 442
           + ++  +     R LSGG +++ ++++ +      V++LDEPT G+D+  + +++  +  
Sbjct: 123 VHLEDKAHAYS-RTLSGGMKRRLMVAKAMVHSP-PVLVLDEPTAGVDIELRQQLWAYVRS 180

Query: 443 LAERGCAIVMISSELPEVLGVSDRIVVMRQGR-ISGELTRK--DATEQSVLSLALPQSST 499
           L ERG  +V+ +  L E   + DRI ++  G+ I+ E TR+    T++  + + + +   
Sbjct: 181 LNERGVTVVLTTHYLEEAEELCDRIAIINHGKLIANEPTRELVGKTQEKAVEVTVDRDIA 240

Query: 500 ALPGTQ 505
           A+P ++
Sbjct: 241 AVPDSR 246


Lambda     K      H
   0.320    0.136    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: 327
Number of extensions: 17
Number of successful extensions: 4
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: 512
Length of database: 307
Length adjustment: 31
Effective length of query: 481
Effective length of database: 276
Effective search space:   132756
Effective search space used:   132756
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