GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Sphingomonas koreensis DSMZ 15582

Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate Ga0059261_2703 Ga0059261_2703 ABC-type multidrug transport system, ATPase component

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__Korea:Ga0059261_2703
          Length = 313

 Score =  101 bits (252), Expect = 2e-26
 Identities = 79/242 (32%), Positives = 115/242 (47%), Gaps = 23/242 (9%)

Query: 10  PLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKI 69
           P+L V  V   Y      L  V+  +  GE+  ++GPNGAGK+TL   I G++TP +G I
Sbjct: 3   PILSVRGVSKTYASGHKALGSVDLDINKGEIFALLGPNGAGKTTLISIICGIVTPSSGTI 62

Query: 70  TFKGKNIAGLKSNQIVRLGMCYVPQIANV--FPSLSVEENLEMGAFIR--NDSL--QPLK 123
              G +   +   +  R+ +  VPQ  +V  F ++          F R  ND+   Q LK
Sbjct: 63  VVDGHD--AISEPRAARMKIGLVPQELSVDMFETVQATTRYSRRLFGRPANDAYIDQVLK 120

Query: 124 DKIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVF 183
           D        L D+R  +   LSGG ++ + + KAL  EP +L LDEP+A +   L   ++
Sbjct: 121 DL------SLYDKRNSKVMELSGGMKRRVLIAKALAHEPDILFLDEPTAGVDVSLRRDMW 174

Query: 184 EQVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLGA 243
           + +  + + GT IIL      +A EMADR  V+  G         ELL     AEL    
Sbjct: 175 KLIGSLRERGTTIILTTHYIEEAEEMADRVGVINKG---------ELLLVEGKAELMKKL 225

Query: 244 GK 245
           GK
Sbjct: 226 GK 227


Lambda     K      H
   0.317    0.136    0.377 

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: 190
Number of extensions: 16
Number of successful extensions: 2
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: 247
Length of database: 313
Length adjustment: 25
Effective length of query: 222
Effective length of database: 288
Effective search space:    63936
Effective search space used:    63936
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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