GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS31740 BPHYT_RS31740 ABC
           transporter permease
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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