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

GapMind for catabolism of small carbon sources

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

Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate H281DRAFT_05793 H281DRAFT_05793 putative acyl-CoA dehydrogenase

Query= SwissProt::P33224
         (541 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_05793 H281DRAFT_05793
           putative acyl-CoA dehydrogenase
          Length = 561

 Score =  459 bits (1182), Expect = e-134
 Identities = 255/531 (48%), Positives = 324/531 (61%), Gaps = 16/531 (3%)

Query: 4   QTHTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLAN 63
           QTH V NQ  PL + NL+ SD AL  A+ R+GA W  D L   G  L T E+L L  LAN
Sbjct: 8   QTHEVTNQVPPLADYNLFSSDAALSAALERDGAAWHRDALLRHGAALTTPETLALAELAN 67

Query: 64  VNPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFML 123
            + PEL  +   G R+D + FHPAWH L+  L    +H L +  D + GA  AR A + L
Sbjct: 68  RHTPELSTHSPTGERIDALEFHPAWHELLSLLRRKGLHALPFS-DPQPGAMAARCAGYFL 126

Query: 124 HAQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMG 183
           HAQ+E+GSLCP+TMTFA+ P+L Q  P  F+     L +   D   LP  QK   +IGMG
Sbjct: 127 HAQIESGSLCPLTMTFASIPVL-QREPQLFETLRDKLYAREQDPRDLPLTQKISAMIGMG 185

Query: 184 MTEKQGGSDVMSNTTRAERL----EDGSYRLVGHKWFFSVPQSDAHLVLAQTA--GGLSC 237
           MTEKQGGSDV SN T+A  +      G+Y LVGHKWFFS PQ DAHLVLA+T    GLSC
Sbjct: 186 MTEKQGGSDVRSNQTQARAIAAGGRGGAYELVGHKWFFSAPQCDAHLVLARTHDHAGLSC 245

Query: 238 FFVPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGM 297
           FFVPRF PDG +NA++++RLKDKLGNRSNAS EVEF DA G ++G EG G+  I++M   
Sbjct: 246 FFVPRFAPDGSKNAVQIQRLKDKLGNRSNASSEVEFLDAFGIMIGDEGRGVPTIIEMANY 305

Query: 298 TRFDCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFR 357
           TR DC +GS A+MR A   AI+HA  R  FG  L+ QPLMR+VL+ ++L+ E  T L  R
Sbjct: 306 TRLDCVIGSAALMRAALVQAIHHARHRSAFGRNLVDQPLMRNVLADLSLESEAATVLFMR 365

Query: 358 LARAWDRRADA-----KEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELP 412
           LA A+++  DA      E  W R+ TPAAK+ ICKR + F  EAMEV GG GY E   + 
Sbjct: 366 LAHAFEQSVDADSATSAERAWRRIVTPAAKYWICKRTLEFTGEAMEVWGGNGYVETGPMA 425

Query: 413 RLYREMPVNSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQ 472
           R YRE PVNSIWEGSGN+MCLDVLR + ++      L   +            A+ +L  
Sbjct: 426 RFYREAPVNSIWEGSGNVMCLDVLRAMEREPEAAQALFAQWQADAAAHAALSAALGKLAA 485

Query: 473 QLRKPAEE---LGREITHQLFLLGCGAQMLKYASPPMAQAWCQVMLDTRGG 520
            L  PAE+     R I  Q+ L+     ++K+A   +A+A+    L +  G
Sbjct: 486 TLNGPAEDREASARRIAQQIVLIAQATLLIKHAPAAVAEAFIATRLGSGCG 536


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: 685
Number of extensions: 25
Number of successful extensions: 6
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: 561
Length adjustment: 36
Effective length of query: 505
Effective length of database: 525
Effective search space:   265125
Effective search space used:   265125
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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources