GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TIPa in Azospirillum brasilense Sp245

Align Tonoplast intrinsic protein-a (transports water, urea, glycerol and gases (CO2 and NH3) (characterized)
to candidate AZOBR_RS03835 AZOBR_RS03835 aquaporin Z

Query= TCDB::Q9XG70
         (247 letters)



>FitnessBrowser__azobra:AZOBR_RS03835
          Length = 246

 Score = 99.4 bits (246), Expect = 6e-26
 Identities = 74/218 (33%), Positives = 107/218 (49%), Gaps = 20/218 (9%)

Query: 24  EFICTFLFVFAGVGSAMAANKLNGDPLVSLFFVAMAHALVVAVTISAGFRISGGHLNPAV 83
           EF+ TF  VF G GSA+ +     +  + L  V++A  L V     +   ISG HLNPAV
Sbjct: 10  EFLGTFWLVFGGCGSAVLSAAFP-EVGIGLTGVSLAFGLTVLTMAYSVGHISGCHLNPAV 68

Query: 84  TLGLCMGGHITVFRSILYWIDQLLASVAACALLNYLTAGLETPVHTLANGVS---YGQ-- 138
           T+GL  GG       + Y I Q++ +  A A++ Y+ A  +      A G++   YG+  
Sbjct: 69  TVGLWAGGRFPAKDILPYVIAQVVGAFLA-AMVLYVIATGKADWSLAAKGLAANGYGEHS 127

Query: 139 --------GIIMEVILTFSLLFTVYTTIVDPKKGILEGMGPLLTGLVVGANIMAGGPFSG 190
                   G+++EV+LTF  L  +   +    +    G  PL  GL +    +   P + 
Sbjct: 128 PGAYNLTSGLLIEVVLTFMFLIVI---LGSTDRRAPAGFAPLAIGLALTLIHLISIPVTN 184

Query: 191 ASMNPARSFGPAFVSGIWT--DHWVYWVGPLIGGGLAG 226
            S+NPARS GPA V G W     W +WV PL+GG L G
Sbjct: 185 TSVNPARSTGPALVVGGWALQQLWAFWVAPLVGGLLGG 222



 Score = 25.8 bits (55), Expect = 9e-04
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 10/73 (13%)

Query: 21  LIVEFICTFLFVFAGVGSAMAANKLNGDPLVSLFFVAMAHALVVAVTISAGFRISGGHLN 80
           L++E + TF+F+   +GS          PL     + + H + + VT ++        +N
Sbjct: 137 LLIEVVLTFMFLIVILGSTDRRAPAGFAPLAIGLALTLIHLISIPVTNTS--------VN 188

Query: 81  PAVTLG--LCMGG 91
           PA + G  L +GG
Sbjct: 189 PARSTGPALVVGG 201


Lambda     K      H
   0.327    0.142    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: 215
Number of extensions: 19
Number of successful extensions: 6
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: 247
Length of database: 246
Length adjustment: 24
Effective length of query: 223
Effective length of database: 222
Effective search space:    49506
Effective search space used:    49506
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 46 (22.3 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