GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuL in Sinorhizobium meliloti 1021

Align galactaro-1,5-lactonase (characterized)
to candidate SMa0717 SMa0717 hypothetical protein

Query= reanno::WCS417:GFF3393
         (291 letters)



>FitnessBrowser__Smeli:SMa0717
          Length = 569

 Score =  192 bits (488), Expect = 1e-53
 Identities = 115/283 (40%), Positives = 152/283 (53%), Gaps = 14/283 (4%)

Query: 13  VGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIARTDAGNWVAGMET 72
           +GE PVWV  E  LYWVDI    + R+   TG   +    ++++ +  T     +   + 
Sbjct: 293 LGEAPVWVEREKRLYWVDILHPAVHRFDPVTGKNESCNVAKLVSAVLPTRNEGLIVASQD 352

Query: 73  GFFQLTPHNDGSL-DTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNMGLNAAEGTL 131
           G      H D    D    A  E    + RLND + D  GR W GSM L++  +   G+L
Sbjct: 353 G----VEHFDFDRGDFNPFAEPEPGLPENRLNDAKVDPSGRLWVGSMRLDV--SRPTGSL 406

Query: 132 YRYTSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYDIDTGTPSNRRV 191
           YR TS         GF   NGLA+SPD  T Y  D+ P +  I+A+D+D   G+ +NRRV
Sbjct: 407 YRLTSAGEVTRAGSGFTVANGLAWSPDSSTFYFVDTVPGI--IYAYDFDAREGSIANRRV 464

Query: 192 FVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTVPVKKPTMCAFGGS 251
           FV + +  GRPDG AVDADG  W    D   ++R+ PDGRLDR++ +PV +PT  AFGG 
Sbjct: 465 FVTVPEAEGRPDGLAVDADGGVWCAIWDGWRVNRYRPDGRLDRAVELPVPRPTSVAFGGD 524

Query: 252 RLDTLFVTSIR-----DDQSEQSLSGGVFALNPGVVGLPEPTF 289
            L TLF+TS R        +E  LSGG+FA NPG  GLP   F
Sbjct: 525 ELATLFITSARTRLPASTLTEAPLSGGIFACNPGARGLPTSLF 567


Lambda     K      H
   0.321    0.137    0.443 

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: 556
Number of extensions: 35
Number of successful extensions: 5
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: 291
Length of database: 569
Length adjustment: 31
Effective length of query: 260
Effective length of database: 538
Effective search space:   139880
Effective search space used:   139880
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