GapMind for catabolism of small carbon sources

 

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

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate H281DRAFT_03840 H281DRAFT_03840 urea carboxylase

Query= SwissProt::Q5LUF3
         (681 letters)



>FitnessBrowser__Burk376:H281DRAFT_03840
          Length = 1199

 Score =  392 bits (1007), Expect = e-113
 Identities = 226/556 (40%), Positives = 319/556 (57%), Gaps = 49/556 (8%)

Query: 1   MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60
           MF KILIANRG IACR+++T R++ ++ V+++S+AD+ + HV  A  A  +G  PA  +Y
Sbjct: 1   MFEKILIANRGAIACRILRTLRELNVTGVSVFSEADRASRHVSEAPIAHELGDGPAAMTY 60

Query: 61  IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120
           +   K++   R  G QA+HPGYGFLSEN+ F EA EA G+ F+GP    + A G K T++
Sbjct: 61  LDSTKILEIARCEGVQAIHPGYGFLSENAAFGEACEAAGIAFIGPTPAQLRAFGLKHTAR 120

Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180
           +IA E  V  + G  GL+ED   A+  +  IGYPVM+K++AGGGG GMR+ W+  E    
Sbjct: 121 EIAGEQGVPMLNG-TGLLEDLPAALNAAESIGYPVMLKSTAGGGGIGMRVCWHADELSAH 179

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240
           F + K    N+F D  +F+EK++ + RH+E+QV  D  G+ I LG R+CS+QRRNQKV+E
Sbjct: 180 FDAVKRLGENNFSDSGVFLEKYIERARHLEVQVFGDGKGDAIALGVRDCSVQRRNQKVLE 239

Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDG-QKNFYFLEMNTRLQVEHPV 299
           E P+P L E   +A+ + AV LAKAV Y SAGTVEF+ D   + FYFLE+NTRLQVEH V
Sbjct: 240 ETPAPCLPEGIAQALCDAAVKLAKAVDYRSAGTVEFVYDSTAQQFYFLEVNTRLQVEHGV 299

Query: 300 TELITGVDLVEQMIRVAAG--EPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTR 357
           TE + GVDLV  MI +AAG   PL+     +   G AI+ RLYAEDP R F+PS G LT 
Sbjct: 300 TEQVWGVDLVRWMIELAAGTLAPLNELAASLTPRGHAIQARLYAEDPGRDFIPSPGLLTH 359

Query: 358 YRPPAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRA 417
              P              Q D     +A+R DT +  G E+  Y+DPM+AK+  W+PTR 
Sbjct: 360 VAFP--------------QADG----SALRIDTWIESGCEVPPYFDPMLAKIIAWSPTRE 401

Query: 418 AAIEAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFI---------------- 461
            A  A+  AL +  + G+  N  +L  ++D   F SG+  T  +                
Sbjct: 402 EARHALNDALQNTRIFGVETNRDYLRQILDDEPFASGEPWTRCLEGLKYRASTIEVVSGG 461

Query: 462 ----AEEYP--EGFEGVNLPET---DLRRVAAAAAAMHRVAEIRRTRVSGRMDNHERRVG 512
                +++P  +GF  V +P +   D R +      +    E     ++  M     R  
Sbjct: 462 TQTTVQDFPGRQGFWAVGIPPSGPMDDRAMRLGNRLLGNAPEAAALEIT--MSGPTLRFN 519

Query: 513 TEWVVTLQGADFPVTI 528
           T+ V+ + GA+ PV +
Sbjct: 520 TDAVIAITGAEIPVLL 535



 Score = 26.9 bits (58), Expect = 0.006
 Identities = 19/61 (31%), Positives = 27/61 (44%)

Query: 621  GLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAEKKGVVAKINASAGNSLAVDDVIMEF 680
            G + +V V+ G  V     L  IE+MKME  + A   G V +I    G+ +     I   
Sbjct: 1137 GSLWQVKVKPGDVVAADDILLIIESMKMEISVCAPCAGTVGEIYVGPGSPVRAGQRIAVI 1196

Query: 681  E 681
            E
Sbjct: 1197 E 1197


Lambda     K      H
   0.317    0.134    0.387 

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: 1876
Number of extensions: 92
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 681
Length of database: 1199
Length adjustment: 43
Effective length of query: 638
Effective length of database: 1156
Effective search space:   737528
Effective search space used:   737528
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: 56 (26.2 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