GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Burkholderia phytofirmans PsJN

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate BPHYT_RS31740 BPHYT_RS31740 ABC transporter permease

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>FitnessBrowser__BFirm:BPHYT_RS31740
          Length = 316

 Score =  276 bits (706), Expect = 4e-79
 Identities = 152/311 (48%), Positives = 214/311 (68%), Gaps = 19/311 (6%)

Query: 1   MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVAL--ITFLAIG 58
           M+ F+QQ+INGL LG++Y +IA+GYTMVYGI+G+INFAHG++ M+GA VAL  IT L   
Sbjct: 1   MDIFIQQIINGLVLGSVYAIIALGYTMVYGILGIINFAHGDVLMVGAMVALSAITVLQDH 60

Query: 59  SLGITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYV 118
              +  VP  L+ +++A+ +  A+ G+T+E++AYRPLR +PRLAPLI+AIG+SI LQ   
Sbjct: 61  FPELGHVPTLLIALILAAAV-CAMVGYTIEKVAYRPLRRAPRLAPLITAIGVSILLQTAA 119

Query: 119 QILQGARSKPLQPILP-GNLTLMD------GAVSVSYVRLATIVITIALMYGFTQLITRT 171
            I+ G        +LP   L L+       GAV +S   +A +V+   +M G   L+ RT
Sbjct: 120 MIIWGRNPLAFPQLLPTAPLNLIQASENHPGAV-ISLTEIAIVVVAFFVMAGLLLLVHRT 178

Query: 172 SLGRAQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLA 231
            LGRA RA  ++  +A L+GVN   VIS TF++G+ALAA+AG+M+   YG   FY+GF+ 
Sbjct: 179 KLGRAMRAIAENPNVASLMGVNPGFVISATFMIGSALAALAGVMIASEYGNAHFYMGFIP 238

Query: 232 GVKAFTAAVLGGIGSLPGAMLGGVVIGLIEAFWSGYM--------GSEWKDVATFTILVL 283
           G+KAFTAAVLGGIG+L GAM+GGV++GL+E   +GY+        GS ++DV  F +L+ 
Sbjct: 239 GLKAFTAAVLGGIGNLGGAMVGGVILGLVEQLGAGYIGTLTGGVFGSNYQDVFAFVVLIA 298

Query: 284 VLIFRPTGLLG 294
           VL+FRP+GLLG
Sbjct: 299 VLVFRPSGLLG 309


Lambda     K      H
   0.329    0.144    0.425 

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: 390
Number of extensions: 18
Number of successful extensions: 4
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: 301
Length of database: 316
Length adjustment: 27
Effective length of query: 274
Effective length of database: 289
Effective search space:    79186
Effective search space used:    79186
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 (21.8 bits)
S2: 48 (23.1 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