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_03422 H281DRAFT_03422 dihydroxyacid dehydratase (EC 4.2.1.9)

Query= reanno::BFirm:BPHYT_RS19730
         (577 letters)



>FitnessBrowser__Burk376:H281DRAFT_03422
          Length = 592

 Score =  574 bits (1480), Expect = e-168
 Identities = 288/563 (51%), Positives = 397/563 (70%), Gaps = 4/563 (0%)

Query: 4   SNQTKKPLRSQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAHF 63
           + +T + LRS  W+G+ D   F HRS     G    ++ G+PVI + NTWSE+  C+ HF
Sbjct: 3   NRKTSEQLRSYRWYGVNDLRSFGHRSRTAQMGYHASDYMGKPVIAVVNTWSEINSCHTHF 62

Query: 64  RELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVIL 123
           ++  E VK+G+ +AGG P+E PVM+L E   +PT ML+RN  +M+ EE ++  P DG +L
Sbjct: 63  KQRVEEVKRGIWQAGGFPVEMPVMTLAEPFQKPTTMLYRNFLAMETEEILKSYPFDGCVL 122

Query: 124 LVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQ 183
           + GCDKTTP LLMGA S NLP++ +  GPML G + G+ +GSG+  W+   E+RAG +T+
Sbjct: 123 MGGCDKTTPGLLMGAISMNLPSIFLPAGPMLRGNWNGRTLGSGSDTWKYWAELRAGKITE 182

Query: 184 EEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRR 243
           +E+   ES + RS GHCMTMGTASTM S  E+LG+ LP  ++IPAVD+R    A L G+R
Sbjct: 183 DEWKGIESGIARSPGHCMTMGTASTMTSAAEALGLTLPGFSSIPAVDSRHAQFASLTGQR 242

Query: 244 IVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDW-ELG 302
           IV+MV  D+    ILT ++F+NA+ T  A+ GSTNA+VHL+A+A+R G++L+   + EL 
Sbjct: 243 IVEMVWTDVKPSDILTAKSFDNAVTTVLAMSGSTNAIVHLVAVARRAGIDLTTARFDELS 302

Query: 303 SNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAAN 362
              P + NL+PSG+YLMEDF+YAGGL A+L +LG+  L+    +TVNG TL +N+  A  
Sbjct: 303 RITPVIGNLRPSGQYLMEDFFYAGGLRALLLELGD--LIDGSQMTVNGSTLGENIAGAEI 360

Query: 363 YDEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELHA 422
           +++ VI     P     G+AVL GNLAP+GAVIKP+A  A LL HRGRAVVF++  ++ A
Sbjct: 361 FNDDVIRKRGNPVVASDGLAVLTGNLAPDGAVIKPAAMEAHLLNHRGRAVVFKDYADMAA 420

Query: 423 KIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSGTA 482
           +ID E LDI    ++VL+ AGP G PG  E G +P+P+K+L++G+ DMVRISD RMSGT+
Sbjct: 421 RIDMEDLDITADSVIVLQHAGPVGAPGMPEWGQLPIPQKLLKQGVRDMVRISDARMSGTS 480

Query: 483 YGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQAPEAP-K 541
           YGA VLHV+PE+  GGPLA V+ GDMI+LDV  RRLHL+V+DEEL+ R+AAWQ P+ P +
Sbjct: 481 YGACVLHVAPESFVGGPLALVKDGDMIQLDVAARRLHLEVSDEELSARKAAWQPPKLPFE 540

Query: 542 RGYYKLYVEHVLQADQGADLDFL 564
           RG+  ++  HVLQA++G D DFL
Sbjct: 541 RGFGVMHQLHVLQANKGCDFDFL 563


Lambda     K      H
   0.318    0.135    0.401 

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: 986
Number of extensions: 46
Number of successful extensions: 5
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: 577
Length of database: 592
Length adjustment: 37
Effective length of query: 540
Effective length of database: 555
Effective search space:   299700
Effective search space used:   299700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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