GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Burkholderia phytofirmans PsJN

Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate BPHYT_RS18740 BPHYT_RS18740 acyl-CoA dehydrogenase

Query= SwissProt::P33224
         (541 letters)



>FitnessBrowser__BFirm:BPHYT_RS18740
          Length = 561

 Score =  462 bits (1189), Expect = e-134
 Identities = 257/526 (48%), Positives = 324/526 (61%), Gaps = 16/526 (3%)

Query: 4   QTHTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLAN 63
           QTH V NQ  PL + NL+ SD AL  A+ R+GAGW    L   G  L T E+L L  LAN
Sbjct: 8   QTHEVTNQVPPLADYNLFSSDAALSAALERDGAGWHRGALVRHGAALTTPETLALAELAN 67

Query: 64  VNPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFML 123
            + PEL+ +  +G R+D + FHP+WH L+  L    +H L + +  R GA VAR A + L
Sbjct: 68  RHEPELVTHSPRGERIDALEFHPSWHALLSLLRREGLHALPFSDPQR-GAMVARCAGYFL 126

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

Query: 184 MTEKQGGSDVMSNTTRAERL----EDGSYRLVGHKWFFSVPQSDAHLVLAQTAG--GLSC 237
           MTEKQGGSDV SN TRA          +YRLVGHKWFFS PQ DAHLVL +T    GLSC
Sbjct: 186 MTEKQGGSDVRSNQTRAYSTAGSGRGAAYRLVGHKWFFSAPQCDAHLVLGRTDEHEGLSC 245

Query: 238 FFVPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGM 297
           F+VPRF PDG++N ++++RLKDKLGNRSNAS EVEF DA G ++G EG G+  I++M   
Sbjct: 246 FYVPRFAPDGRKNNVQIQRLKDKLGNRSNASSEVEFLDAFGIMIGDEGRGVPTIIEMANY 305

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

Query: 358 LARAWDRRADA-----KEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELP 412
           LARA++   DA      E  W R+ TPAAK+ +CKR + F  EAMEV GG GY E   + 
Sbjct: 366 LARAFEESTDAASTSLAERAWRRIVTPAAKYWVCKRALEFTGEAMEVWGGNGYVETGPMA 425

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

Query: 473 QLRKPAEE---LGREITHQLFLLGCGAQMLKYASPPMAQAWCQVML 515
            L  PAE      R I  Q+ L+     +LK+A   +A+A+    L
Sbjct: 486 TLNGPAEHREASARRIAQQVVLIAQATLLLKHAPAEVAEAFVATRL 531


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: 682
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.

Links

Downloads

Related tools

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