GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Acidovorax sp. GW101-3H11

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate Ac3H11_2058 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= reanno::Phaeo:GFF1302
         (334 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2058
          Length = 360

 Score =  233 bits (593), Expect = 7e-66
 Identities = 136/336 (40%), Positives = 193/336 (57%), Gaps = 31/336 (9%)

Query: 4   IKLESVTKNFGPVE----VIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGT 59
           I   ++TK +G        +  +   +  G  T  +GPSGCGK+T LR+IAGLE  TSG 
Sbjct: 8   IVFRNITKRYGTDSSAALAVKGISFEVPRGTLTTILGPSGCGKTTTLRMIAGLESPTSGE 67

Query: 60  IRIDGEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAA 119
           I I G+D T + PA+R ++M+FQSYAL+PHM+V +N+ + ++M+G P ++ + +   A  
Sbjct: 68  IFIGGKDVTTLGPAQRNVSMMFQSYALFPHMNVVENVMYGLRMSGQPKEQARAKAVEALR 127

Query: 120 ALNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISEL 179
            + L  + DR P +LSGGQ+QRVA+ RA+V EP   LFDEPLSNLDA LR  MR EI  L
Sbjct: 128 GVGLVGFDDRLPSELSGGQQQRVALARALVLEPEVLLFDEPLSNLDARLRREMREEIRAL 187

Query: 180 HKRLATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKM 239
            +RL+ T+ YVTHDQ EAM ++D+I+V+  G+I Q GSP  LY  P + FVAGF+G   +
Sbjct: 188 QQRLSLTVAYVTHDQAEAMAVSDQIIVMNQGLIAQKGSPRALYETPHSEFVAGFMGEAML 247

Query: 240 ---------NLLTGP------QAAQHNAATIGIRPEHLSIS-ETEGMWAGTIGVSEHLGS 283
                     +  GP       A +     + +RPE   I+ + EG+    +  S +LG+
Sbjct: 248 FPAVADADGTVALGPLVLRPRVAVKSGPVKVAVRPEAWRITRQGEGLLPARLAKSAYLGA 307

Query: 284 ----------DTFFHVQCDAFDDPLTVRASGELDLG 309
                      + F V  D  DD L V    +L LG
Sbjct: 308 VHEYTFETALGSIFVVSSD-LDDVLAVGDDVQLGLG 342


Lambda     K      H
   0.320    0.138    0.400 

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: 310
Number of extensions: 10
Number of successful extensions: 1
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: 334
Length of database: 360
Length adjustment: 29
Effective length of query: 305
Effective length of database: 331
Effective search space:   100955
Effective search space used:   100955
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: 49 (23.5 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