GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Pseudovibrio axinellae Ad2

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate WP_068001529.1 PsAD2_RS02130 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= SwissProt::Q5LUF3
         (681 letters)



>NCBI__GCF_001623255.1:WP_068001529.1
          Length = 670

 Score =  825 bits (2130), Expect = 0.0
 Identities = 426/686 (62%), Positives = 514/686 (74%), Gaps = 21/686 (3%)

Query: 1   MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60
           MF+KILIANRGEIACRVIKTA+ MGI TVA+YSDAD+ ALHV+MADEAVHIG P A +SY
Sbjct: 1   MFSKILIANRGEIACRVIKTAKAMGIKTVAVYSDADRDALHVEMADEAVHIGEPTAAKSY 60

Query: 61  IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120
           +VIDK++ A + TGA+AVHPGYGFLSE ++F E L+ EG++F+GP   AIE MGDKITSK
Sbjct: 61  LVIDKIIDACKQTGAEAVHPGYGFLSERAEFCERLKQEGIVFIGPNPKAIEVMGDKITSK 120

Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180
           + A EANVSTVPGYMGLIE   +A +I+ ++GYPVMIKASAGGGGKGMRIAWND+EA +G
Sbjct: 121 RFAAEANVSTVPGYMGLIETPQDAKRIAAEVGYPVMIKASAGGGGKGMRIAWNDEEAMDG 180

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240
           F  +K+EA NSFGDDRIFIEKF+  PRHIEIQV+ D HGN +YLGERECSIQRRNQKV+E
Sbjct: 181 FDRAKSEAINSFGDDRIFIEKFIENPRHIEIQVMGDKHGNAVYLGERECSIQRRNQKVIE 240

Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300
           EAPSP LDE TRR MGEQAVALAKAV Y SAGTVEF+    K+F+FLEMNTRLQVEHPVT
Sbjct: 241 EAPSPLLDEKTRRKMGEQAVALAKAVDYDSAGTVEFVAGQDKSFFFLEMNTRLQVEHPVT 300

Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360
           EL+TGVDLVEQMIRVAAGE LSI Q DVKL GW+IE+R+YAEDPYR FLPSIGRLT YRP
Sbjct: 301 ELVTGVDLVEQMIRVAAGEALSIKQEDVKLNGWSIESRIYAEDPYRNFLPSIGRLTHYRP 360

Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420
           P E         GK       G   VRNDTGV EG EISM+YDPMIAKL T A TRA AI
Sbjct: 361 PVE---------GK------HGNYLVRNDTGVVEGSEISMFYDPMIAKLVTHAATRAEAI 405

Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480
           E M  ALD F+V+GI HN+PFL+++M HP++ SG+++T FIA+EYP+GFE    P+ +  
Sbjct: 406 EGMSTALDEFQVDGIQHNVPFLASLMKHPRWRSGEISTGFIADEYPDGFEPAT-PDAEAN 464

Query: 481 RV-AAAAAAMHRVAEIRRTRVSGRMDNHERRVGTEWVVTLQG----ADFPVTIAADHDGS 535
            V A+ A +MH +   R   + GR+  H   V  EW V + G    A+    +AA     
Sbjct: 465 SVLASVALSMHLIERERLDHLPGRLRPHHGAVRREWAVRIDGETLKAELVEGLAATPVDL 524

Query: 536 TVSFDDGSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLKVHVRTPR 595
            +  D G++ RV S W PG+ L    V    + ++V  +  G+++  +G  +   V +PR
Sbjct: 525 DICVDGGANERVASSWAPGEMLWKGQVGERNVSVQVRAVDNGYQLDWQGFSVVAQVMSPR 584

Query: 596 QAELARLMPEKLPPDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAE 655
            AELA LMPEK+ PDTS +LLCPMPGL+V + V  GQEV+ G+ L  +EAMKMEN+LRAE
Sbjct: 585 IAELAALMPEKVAPDTSNLLLCPMPGLVVSLHVNEGQEVKAGEQLAIVEAMKMENVLRAE 644

Query: 656 KKGVVAKINASAGNSLAVDDVIMEFE 681
           +  VV+ I A+ G+SLAVD VIMEFE
Sbjct: 645 RDCVVSAIKAAPGDSLAVDAVIMEFE 670


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: 1237
Number of extensions: 40
Number of successful extensions: 4
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: 681
Length of database: 670
Length adjustment: 39
Effective length of query: 642
Effective length of database: 631
Effective search space:   405102
Effective search space used:   405102
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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