GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Burkholderia phytofirmans PsJN

Align ABC transporter permease (characterized, see rationale)
to candidate BPHYT_RS15605 BPHYT_RS15605 ABC transporter permease

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__BFirm:BPHYT_RS15605
          Length = 316

 Score =  394 bits (1011), Expect = e-114
 Identities = 199/316 (62%), Positives = 248/316 (78%), Gaps = 7/316 (2%)

Query: 1   MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60
           MDI +QQ++NGLVLGS+YA+IALGYTMVYGI+ +INFAHG+VLM+GA+ + S IG++Q  
Sbjct: 1   MDIFIQQVLNGLVLGSVYAIIALGYTMVYGILGIINFAHGDVLMVGAMVALSAIGVLQNH 60

Query: 61  MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120
            PG      L++A IIA +V A + + IE+VAYRPLR +PRLAPLITAIG+SILLQTLAM
Sbjct: 61  FPGLGNVPTLIIALIIAAIVCAAVGYTIERVAYRPLRKAPRLAPLITAIGVSILLQTLAM 120

Query: 121 IIWKPNYKPYPTMLPSSPFEI-------GGAFITPTQILILGVTAVALASLVYLVNHTNL 173
           +IW  N  P+P +LP+ P  +        GA I+ T+I+I+ V  + +  L+ LV+ T L
Sbjct: 121 MIWSRNPLPFPQLLPTDPLNVIKATDTTPGAVISMTEIVIIVVAFLVMGGLLLLVHKTKL 180

Query: 174 GRAMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGL 233
           GRAMRA AENP  ASLMGV P+ VISATF+IG+ LAA+AG+M AS YG A   MGF+PGL
Sbjct: 181 GRAMRAIAENPGNASLMGVNPNFVISATFMIGSALAALAGVMIASEYGNAHFYMGFIPGL 240

Query: 234 KAFTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIIL 293
           KAFTAAV GGIGNL GA+VGG++LGLIE +G+GYIG LTGG+ GS+Y D+FAFIVLII+L
Sbjct: 241 KAFTAAVLGGIGNLGGAMVGGVILGLIEQLGAGYIGNLTGGVFGSNYQDVFAFIVLIIVL 300

Query: 294 TLRPSGLLGERVADRA 309
             RPSGLLGERVADRA
Sbjct: 301 VFRPSGLLGERVADRA 316


Lambda     K      H
   0.327    0.142    0.419 

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: 330
Number of extensions: 10
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: 309
Length of database: 316
Length adjustment: 27
Effective length of query: 282
Effective length of database: 289
Effective search space:    81498
Effective search space used:    81498
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: 48 (23.1 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