GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00870 in Burkholderia phytofirmans PsJN

Align ABC-type branched-chain amino acid transport system, periplasmic component protein (characterized, see rationale)
to candidate BPHYT_RS28270 BPHYT_RS28270 ABC transporter substrate-binding protein

Query= uniprot:D8IUY1
         (378 letters)



>FitnessBrowser__BFirm:BPHYT_RS28270
          Length = 373

 Score =  399 bits (1025), Expect = e-116
 Identities = 201/366 (54%), Positives = 254/366 (69%), Gaps = 3/366 (0%)

Query: 11  IAASLALIPAFAMAQETQVV-KIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPITVGG 69
           + A+  +   F ++   QVV  IG S+PLTGPQA  GKDN+ G  +AI+ LN   +TV G
Sbjct: 6   MTAAALMAAGFTLSASAQVVVTIGHSAPLTGPQAPNGKDNENGARLAIDELNKSGVTVAG 65

Query: 70  KKIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAGIVVATV 129
           +K+ F + +EDDQADPK GV VAQKL D GV A+VGPYNSGV IPASRVYN   + +  V
Sbjct: 66  QKVTFKLDSEDDQADPKIGVQVAQKLVDSGVVAVVGPYNSGVAIPASRVYNTGNVPMLPV 125

Query: 130 ASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQGLAQEFIK 189
           ASNP +T+QGF  +FR+ ASD QLGG M  +AAK LK K  AVIDDRTAYGQG+A++F+K
Sbjct: 126 ASNPALTRQGFKNIFRIGASDEQLGGTMGQFAAKTLKAKTAAVIDDRTAYGQGVAEQFVK 185

Query: 190 VAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQMKQLGVDV 249
           VAKANGI +V  +FTN  ATDF +ILT+IK K PD +F GGYA QG P+ +QM+Q G+  
Sbjct: 186 VAKANGIQIVEQEFTNSSATDFLSILTTIKAKNPDVIFFGGYAAQGAPMAKQMRQRGLRA 245

Query: 250 PLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYNRPAETYAV 309
            L+GGDGICS +MG++ G+A    VYC QGG  L+K   G+ F  +Y+  YN   + YAV
Sbjct: 246 KLLGGDGICSADMGKVAGEA-ASIVYCAQGGIALEKTAAGREFLQKYKAAYNIDTQVYAV 304

Query: 310 SFYDGMMLIAQAM-KQANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQSPVTVYRFK 368
           S+YDG+ L+A AM K   + D  +    LAK +YKGVAG Y FD   DLK +P TVY  K
Sbjct: 305 SYYDGVKLLADAMVKAGTTTDKAKLTAQLAKENYKGVAGTYSFDEYGDLKGAPTTVYVIK 364

Query: 369 DGLPVP 374
           +GLP P
Sbjct: 365 NGLPTP 370


Lambda     K      H
   0.316    0.134    0.378 

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: 488
Number of extensions: 22
Number of successful extensions: 3
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: 378
Length of database: 373
Length adjustment: 30
Effective length of query: 348
Effective length of database: 343
Effective search space:   119364
Effective search space used:   119364
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: 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