GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacD in Burkholderia phytofirmans PsJN

Align L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 (characterized)
to candidate BPHYT_RS25650 BPHYT_RS25650 dihydroxy-acid dehydratase

Query= SwissProt::Q1JUQ1
         (583 letters)



>FitnessBrowser__BFirm:BPHYT_RS25650
          Length = 588

 Score =  298 bits (762), Expect = 5e-85
 Identities = 193/542 (35%), Positives = 299/542 (55%), Gaps = 27/542 (4%)

Query: 24  YRSWMKNQGIPDHEFDGRPIIGICNTWSELTPCNAHFRKLAEHVKRGISEAGGFPVEFPV 83
           +R++++  G+ D     +P + I +T+ E TPC+    +++++V+ GI+  GG P+    
Sbjct: 21  HRAFLRATGLDDESMQ-KPFVAIVDTFGENTPCSMSLNQVSDNVRLGIAAGGGVPIRGSA 79

Query: 84  FSNGE------SNLRPSAMLTRNLASMDVEEAIRGNPIDAVVLLAGCDKTTPALLMGAAS 137
            S  +      S +R S +++R + +  VE  +R +  DA++ +AGCDKT P +LMG   
Sbjct: 80  ISVSDGTSMNHSGMRMS-LVSREVVADSVELFVRAHNYDALIGVAGCDKTLPGILMGMVR 138

Query: 138 CDVPAIVVSGGPMLNGKLEGKNIG-SGTAVWQLHEAL---------KAGEIDVHHFLSAE 187
            +VP + + GG ML G   G+  G +GT + +    L         + G++      + E
Sbjct: 139 VNVPGVFLFGGAMLPGVAPGQLPGGAGTGLQRQSTILTTIEAVGTTQRGDMSRAQLDAIE 198

Query: 188 AGMSRSAGTCNTMGTASTMACMAEALGVALPHNAAIPAVDSRRYVLAHMSGIRIVEMALE 247
              + +AG+C    TA+TMA +AE LG+A   +A +PAV S R  +A  +G  ++ +  +
Sbjct: 199 KQCTPTAGSCPGQFTANTMAMVAETLGLAPLGSAMVPAVYSERIAIARRAGETVMRILTQ 258

Query: 248 GLVLSK-ILTRAAFENAIRANAAIGGSTNAVIHLKAIAGRIGVPLELEDWMRIGRDTPTI 306
           G  L + ++T  + ENA  A AA GGSTNA +H+ AIA   G+   L+D  R+    P I
Sbjct: 259 GGPLPRDLVTMESLENACAAVAATGGSTNAALHIPAIANEAGIRFALDDVQRVFAKIPLI 318

Query: 307 VDLMPSGRFPMEEFYYAGGLPAVLRRLGEGGLLPNPDALTVNGKSLWDNVREAPNYDEEV 366
            DL P GR+  ++ ++AGG+PAVL  L  GG L + D     G +L + +      D  V
Sbjct: 319 GDLQPGGRYLAQDLHHAGGVPAVLNALLAGGFL-HGDVPAFGGGTLAEALSAFSGPDGIV 377

Query: 367 IRPLDRPLIADGGIRILRGNLAPRGAVLKPSAASPELLKHRGRAVVFENLDHYKATINDE 426
           +RP D PL  +GG+ ILRGNLAP GA LK   A  + L   G   VFE  +   A +   
Sbjct: 378 VRPCDEPLGENGGLVILRGNLAPDGACLK--IAGLKSLSFTGAVRVFECEEDCMAVV--A 433

Query: 427 ALDIDASSVMVLKNCGPRGYPGMAEVGNMGLPPKLLRQGVKDMVR-ISDARMSGTAYGTV 485
           A D     V+V++N GP+G PGM E+  +G+   +  QG+ + V  ++D R SG   G  
Sbjct: 434 ARDYREGDVLVIRNEGPKGGPGMREM--LGVTAAIYGQGMGEKVALLTDGRFSGATRGMC 491

Query: 486 VLHVAPEAAAGGPLAAVRNGDWIELDCEAGTLHLDITDDELHRRLSDVDPTAAPGVAGQL 545
           + +V PEAAAGGP+  +RN D + +D  AG L +D++DDEL RR +D    A+  +AG L
Sbjct: 492 IGYVGPEAAAGGPIGLLRNDDRVHIDARAGILRVDLSDDELARRRADAPARASRRLAGVL 551

Query: 546 GK 547
            K
Sbjct: 552 EK 553


Lambda     K      H
   0.319    0.136    0.412 

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: 942
Number of extensions: 54
Number of successful extensions: 7
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: 583
Length of database: 588
Length adjustment: 37
Effective length of query: 546
Effective length of database: 551
Effective search space:   300846
Effective search space used:   300846
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 (21.7 bits)
S2: 53 (25.0 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