GapMind for catabolism of small carbon sources

 

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

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate H281DRAFT_06137 H281DRAFT_06137 dihydroxyacid dehydratase (EC 4.2.1.9)

Query= reanno::WCS417:GFF2156
         (578 letters)



>FitnessBrowser__Burk376:H281DRAFT_06137
          Length = 583

 Score =  497 bits (1279), Expect = e-145
 Identities = 273/562 (48%), Positives = 365/562 (64%), Gaps = 9/562 (1%)

Query: 5   KPGLRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHFRQIA 64
           K GL S   +G    + F+ ++++K  G  D Q   +P+IGI NT S    C+ +  Q+ 
Sbjct: 18  KRGLTS---YGDQGFSLFLRKAFIKGAGYTD-QALDRPVIGIVNTGSGFNACHGNMPQLV 73

Query: 65  EHVKRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVLLTGC 124
           E VKRGV+ AGG PV+FP  S  ES   PT+M  RNL SMD EE IR  P+D VVL+ GC
Sbjct: 74  EAVKRGVMLAGGLPVDFPTISVHESFSSPTSMYLRNLMSMDTEEMIRAQPMDAVVLIGGC 133

Query: 125 DKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTITLDDFL 184
           DKT PA LMGAAS ++PAI +  G ML G H+ + +G+ T   +   + +A  I  ++  
Sbjct: 134 DKTVPAQLMGAASAEIPAIQLVTGSMLTGSHRSERVGACTDCRRYWGKFRASEIDQEEIN 193

Query: 185 AAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMRAVEM 244
                +  S GTC+ MGTASTMAC+AEALG ++P  A  PAV A R  +A  +G  AV++
Sbjct: 194 DVNNQLVASVGTCSVMGTASTMACIAEALGMTVPGGATPPAVTADRIRVAEQTGTTAVKL 253

Query: 245 VREDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWTRIGRGMP 304
             E L + KILT +AFENA+RV  AIGGSTNA++HL A+AGR+G ++ LD   R+G+  P
Sbjct: 254 ASERLTIDKILTPKAFENAMRVLLAIGGSTNAIVHLSAVAGRLGHKIGLDSLDRMGKETP 313

Query: 305 TIVDLQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPHPNALTVNGKSLGENTQDS-PIYG 363
            ++DL+P+G+  ME+F+ AGG+  +LR   E   + H +A+TV+G +LGE  + S P + 
Sbjct: 314 VLLDLKPTGQHYMEDFHKAGGVATLLR---ELKPLLHLDAMTVSGHTLGEQIEASGPGFS 370

Query: 364 QDEVIRTLDNPIRADGGICVLRGNLAPLGAVLKPSAASPALMQHRGRAVVFENFDMYKAR 423
           QD V+R+   PI   GG+ V+RGNLAP GA++K SAA P LM+H GRAVVFEN +    R
Sbjct: 371 QD-VVRSFSQPIYPQGGLAVVRGNLAPGGAIIKQSAADPKLMEHEGRAVVFENLEDLINR 429

Query: 424 INDPELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSGTAY 483
           ++D  LDV A+ +LV+KN GP G PGM E G + +P KL   GV DMVRISD RMSGTA+
Sbjct: 430 VDDESLDVKADDVLVLKNIGPVGAPGMPEAGYIPIPRKLARAGVKDMVRISDGRMSGTAF 489

Query: 484 GTVVLHVAPEAAAGGPLATVKEGDWIELDCANGRLHLDIPDAELAARMADLAPPQKLIVG 543
           GT+VLHV PEAAAGGP A V+ GD I L  +N  + L + D +L  R AD    +     
Sbjct: 490 GTIVLHVTPEAAAGGPFAYVQNGDRIRLSVSNREVSLLVSDEKLKQRAADKPIKRPTADR 549

Query: 544 GYRQLYIDHVLQADQGCDFDFL 565
           GYR+L++  V QAD+G DFDFL
Sbjct: 550 GYRKLFLQTVTQADEGVDFDFL 571


Lambda     K      H
   0.319    0.136    0.413 

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: 946
Number of extensions: 32
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: 578
Length of database: 583
Length adjustment: 36
Effective length of query: 542
Effective length of database: 547
Effective search space:   296474
Effective search space used:   296474
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: 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