GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Paraburkholderia bryophila 376MFSha3.1

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Burk376:H281DRAFT_02712
          Length = 505

 Score =  402 bits (1033), Expect = e-116
 Identities = 231/512 (45%), Positives = 323/512 (63%), Gaps = 18/512 (3%)

Query: 9   TKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPG 68
           T  P L +RNI +TFPGV+AL +V L   AGEV AL GENGAGKSTLMKIL+G Y  DPG
Sbjct: 5   TGVPFLEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPG 64

Query: 69  GECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDM 127
           G   ++GQ V +     AR LGV +IYQEL++  NL+V ENI+L R  + R GL+ R  M
Sbjct: 65  GTILVEGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRM 124

Query: 128 VRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETD 187
            R     LA +  D  PA  V+ LS+ Q+Q++EIA+A+   ++ ++MDEPT  LS HET 
Sbjct: 125 YREAREVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETS 184

Query: 188 RLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247
            L  ++++LR   +A++YISHR+ EI ELADRVTVLRDG  VGT   A +++  LV++MV
Sbjct: 185 VLLGIVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMV 244

Query: 248 GRDLSGFYTKTHGQAVEREVM----LSVRDVADGR-RVKGCSFDLRAGEVLGLAGLVGAG 302
            R+LS  Y +    A    V+    LS++ V     R++  SF L  GEVLG+AGLVG+G
Sbjct: 245 ARELSELYGEPQSHASRDPVLEVRALSLKPVRKAEPRIRDISFTLHRGEVLGIAGLVGSG 304

Query: 303 RTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFL 362
           RTE+  ++FG  A T G V+I     S          P  AI +GI ++TEDRK QGL L
Sbjct: 305 RTEIMEMIFGMRACT-GSVKIEGKPVS-------IRNPHDAIRSGIGFVTEDRKAQGLIL 356

Query: 363 DQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQK 422
             +V EN +L    R +     +     R      +  LGI+    +  V  LSGGNQQK
Sbjct: 357 GMTVRENFSLTHLERYS-PFQFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQK 415

Query: 423 VMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCD 482
           +++++ +   P+VLI+DEPTRG+D+GAK+E++ LI  LA  G+ +++ISS+L EV+ + D
Sbjct: 416 IVIAKWVARSPKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSD 475

Query: 483 RVLVMREGTLAGEVRPAGSAAETQERIIALAT 514
           R+L +REG ++GE+     A  +QE+++ALAT
Sbjct: 476 RILTVREGRISGEL---SRAQASQEKVMALAT 504


Lambda     K      H
   0.320    0.136    0.382 

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: 643
Number of extensions: 32
Number of successful extensions: 8
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: 540
Length of database: 505
Length adjustment: 35
Effective length of query: 505
Effective length of database: 470
Effective search space:   237350
Effective search space used:   237350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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