GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Burkholderia phytofirmans PsJN

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate BPHYT_RS02510 BPHYT_RS02510 C4-dicarboxylate ABC transporter

Query= TCDB::Q848I3
         (444 letters)



>FitnessBrowser__BFirm:BPHYT_RS02510
          Length = 426

 Score =  516 bits (1328), Expect = e-151
 Identities = 255/413 (61%), Positives = 333/413 (80%)

Query: 4   RQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGI 63
           ++P++K LY QVIVAI IGI LGHFYP   V +KPLGDGFIKLIKMVI PIIFCTVV+GI
Sbjct: 2   KKPIHKVLYVQVIVAIIIGIALGHFYPNLAVDMKPLGDGFIKLIKMVIGPIIFCTVVTGI 61

Query: 64  AGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYV 123
           AGM++MK VG+ GG ALLYFEIVST AL++GL+  +V++PG G +ID +TLD   VA+Y 
Sbjct: 62  AGMEDMKKVGRVGGKALLYFEIVSTFALVLGLIATHVLKPGVGFNIDPATLDGKAVASYA 121

Query: 124 TAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRF 183
                Q+ V F++++IP+T+V AFA G+ILQ+L+ +++FG  L   G  GK V  FID  
Sbjct: 122 AKAHGQTTVDFLMHLIPDTLVSAFAQGEILQILLIALLFGAVLATAGEKGKVVTSFIDGL 181

Query: 184 AHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAI 243
           +HV+F I+ +I KLAPIGA GAMAFTIG YG+GSL+ + +L+  FY+T ++FV+VVLG I
Sbjct: 182 SHVLFGIVRIITKLAPIGAFGAMAFTIGKYGIGSLLPMLKLIGTFYLTSIVFVVVVLGII 241

Query: 244 CRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFN 303
            RA GF++L+ + YI+EE+LIVLGTSSSE+ALP++++K+E+LG  +SVVGLV+PTGYSFN
Sbjct: 242 ARAVGFNILRFVAYIKEEMLIVLGTSSSEAALPQLMLKLEKLGCSRSVVGLVVPTGYSFN 301

Query: 304 LDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAV 363
           LDGT+IY+TMA +FIAQAT+T +  T Q+TLL V +L+SKGA+GVTG+GFI LAATL+ V
Sbjct: 302 LDGTNIYMTMAVLFIAQATNTDLTWTQQLTLLAVTMLTSKGASGVTGAGFITLAATLAVV 361

Query: 364 GHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAEL 416
             +P++G+ LILGIDRFMSE RALTN+VGN VATVVV+ W KELD ++L A L
Sbjct: 362 PTIPLSGMVLILGIDRFMSECRALTNIVGNGVATVVVSAWEKELDRNKLNAAL 414


Lambda     K      H
   0.326    0.142    0.402 

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: 595
Number of extensions: 20
Number of successful extensions: 1
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: 444
Length of database: 426
Length adjustment: 32
Effective length of query: 412
Effective length of database: 394
Effective search space:   162328
Effective search space used:   162328
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 (21.6 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