GapMind for catabolism of small carbon sources

 

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

Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate H281DRAFT_05560 H281DRAFT_05560 putative acyl-CoA dehydrogenase

Query= SwissProt::P33224
         (541 letters)



>FitnessBrowser__Burk376:H281DRAFT_05560
          Length = 572

 Score =  337 bits (864), Expect = 7e-97
 Identities = 204/529 (38%), Positives = 285/529 (53%), Gaps = 15/529 (2%)

Query: 3   WQTHTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLA 62
           + TH V NQ    +  N +  D  L  AV RE A W +   +++G+  G     EL RLA
Sbjct: 19  YSTHVVKNQAASASGFNAFDGDVILKSAVERE-APWAASRCSALGKLAGDEAVQELARLA 77

Query: 63  NVNPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFM 122
           N N PEL  +D  G R+D V FHP+WH LM     + V +LAW    +   F ARA    
Sbjct: 78  NRNLPELKTHDRYGNRIDWVEFHPSWHELMSLAWRHEVPSLAWTAKEQQPHF-ARAVLSY 136

Query: 123 LHAQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGM 182
           L  QVE G+ CP  M +A+      M     + W        Y+        K  ++IG 
Sbjct: 137 LWNQVEQGTGCPTGMAYASHAGF--MAEPALKIWAEKACGTVYEFSRREVSLKPSVVIGY 194

Query: 183 GMTEKQGGSDVMSNTTRAERLEDGSYR--------LVGHKWFFSVPQSDAHLVLAQTAGG 234
            MTEKQGGSD+    T A       Y         L GHKWF SVPQSD    LA+ AG 
Sbjct: 195 AMTEKQGGSDLRETQTTAVYSHSAGYHGETAHWYELTGHKWFCSVPQSDGFFTLAKVAGE 254

Query: 235 LSCFFVPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKM 294
           ++CFF+PR LPDG  N   ++RLKDK GN+SNAS EVE+   +   +G EG GIR IL  
Sbjct: 255 VTCFFLPRTLPDGSYNRFFVQRLKDKCGNKSNASSEVEYSGTMAIRVGEEGRGIREILSH 314

Query: 295 GGMTRFDCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTAL 354
             +TR D A+GS  +MR+A  LA+ HA  R+ FG+ L  +P+M +VL+ MA+++E  T L
Sbjct: 315 AHLTRLDFAVGSAGLMRQALGLALNHASTRNGFGSSLADRPMMTNVLADMAVEVEAATLL 374

Query: 355 LFRLARAWDR-RADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPR 413
             R+A+A D    D ++  +AR+ TP AKF  C R      EA++  GG G+ EE+ + R
Sbjct: 375 ALRIAKATDHIDTDEQQKAFARVATPMAKFFNCSRAPAVAYEALQCHGGNGFIEENPMAR 434

Query: 414 LYREMPVNSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQ 473
           LYRE P+NS+WEG+ N+MC+DV R + KQA   + L     +V+GQ   FD  +  +   
Sbjct: 435 LYREAPLNSVWEGTANMMCMDVRRAMLKQASCREALIAELQDVRGQHAGFDSFIDSMGPL 494

Query: 474 LRKPAEE--LGREITHQLFLLGCGAQMLKYASPPMAQAWCQVMLDTRGG 520
           L +  ++  L R  T  +     GA++L++++  +  A+ +  L    G
Sbjct: 495 LDRVVKDEFLARPATEAIARAVQGAELLRHSTSEVVDAFMKTRLTGPSG 543


Lambda     K      H
   0.324    0.138    0.428 

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: 660
Number of extensions: 33
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: 541
Length of database: 572
Length adjustment: 36
Effective length of query: 505
Effective length of database: 536
Effective search space:   270680
Effective search space used:   270680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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