GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Burkholderia phytofirmans PsJN

Align L-alanine and D-alanine permease (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter

Query= reanno::WCS417:GFF1065
         (472 letters)



>FitnessBrowser__BFirm:BPHYT_RS15500
          Length = 461

 Score =  410 bits (1054), Expect = e-119
 Identities = 204/455 (44%), Positives = 296/455 (65%), Gaps = 5/455 (1%)

Query: 18  LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77
           LKR L  RHI+L+ALG  IG GLFLGSA  ++ AGP+++L Y IGG+   +IMR LGEM 
Sbjct: 10  LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGIIAFMIMRQLGEMV 69

Query: 78  VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTPRWIW 137
              PVAGSFS +A  Y G   GFL+GWNYW L+++  +AE+TAV  Y+  W+P  P W+ 
Sbjct: 70  AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYWWPGVPTWVS 129

Query: 138 ALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197
           AL     + +INL  VKA+GE EFWFA+IK+V +I M++ G  ++  G G  G    I+N
Sbjct: 130 ALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGHG--GPQASITN 187

Query: 198 LWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVFWRILLF 257
           LW+HGGF P+G  G+ M L ++MF++ G+E+IG+TA EA  PQK+IP A+  V +RIL+F
Sbjct: 188 LWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVNQVIYRILIF 247

Query: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317
           Y+ +L V+LS+YPWNE+   GSPFVM F ++G    A ++N VV+TAALS  N G+++  
Sbjct: 248 YICSLTVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVYANS 307

Query: 318 RMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKVFVWVTSIATF 377
           RMLY LA+ G AP    K    GVP  A+ LS  A    V++NYL+P +    + ++   
Sbjct: 308 RMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMALVVA 367

Query: 378 GAIWTWLMILLAQLKFRKSLSPAEQAGLKYRMWLYPVSSYLALAFLLLVVGLMAYFPDTR 437
             +  W +I L  LK RK++  A +  L ++ + +PVS+++ LAF+ L++ ++A  P   
Sbjct: 368 ALVLNWALISLTHLKSRKAMVAAGET-LVFKSFWFPVSNWICLAFMALILVILAMTPGLS 426

Query: 438 IALYVGPVFLVLLTVLFYVFKLQPTQVAQGEARPV 472
           +++++ P +LV++    YVFK +   V QG AR V
Sbjct: 427 VSVWLVPAWLVVMWA-GYVFKRRRAAV-QGGARVV 459


Lambda     K      H
   0.328    0.142    0.447 

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: 665
Number of extensions: 30
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: 472
Length of database: 461
Length adjustment: 33
Effective length of query: 439
Effective length of database: 428
Effective search space:   187892
Effective search space used:   187892
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: 51 (24.3 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