GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Herbaspirillum aquaticum IEH 4430

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_088755445.1 CEJ45_RS12575 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= reanno::Dino:3607308
         (681 letters)



>NCBI__GCF_002213425.1:WP_088755445.1
          Length = 671

 Score =  529 bits (1362), Expect = e-154
 Identities = 312/696 (44%), Positives = 408/696 (58%), Gaps = 42/696 (6%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60
           MF KILIANRGEIACRV  TAR++GI TVA+YSDAD  A HV   DE+VH+GP+PA +SY
Sbjct: 1   MFTKILIANRGEIACRVAATARRLGIATVAVYSDADAQAKHVAACDESVHLGPAPAKESY 60

Query: 61  IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120
           +  DK++ A   TGA+A+HPGYGFLSEN  FA+A    G+ FIGPPA+AIEAMG K  +K
Sbjct: 61  LCADKIIAAALATGAQAIHPGYGFLSENAGFAQACADAGLVFIGPPASAIEAMGSKSAAK 120

Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180
            + ++A V  VPGY G   ++D     +  IGYPV++KASAGGGGKGMR+     +    
Sbjct: 121 ALMEKAAVPLVPGYHGQRQESDFLRTEADRIGYPVLLKASAGGGGKGMRVVERSEDFEVA 180

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240
             S K EA +SFGDDR+ +EK++T+PRHIEIQV AD HG+C+YL ER+CS+QRR+QKV+E
Sbjct: 181 LASCKREAISSFGDDRVLVEKYLTRPRHIEIQVFADGHGHCVYLFERDCSVQRRHQKVLE 240

Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVT 300
           EAP+P +    R AMGE + A A+AVGY  AGTVEFI + D  FYF+EMNTRLQVEHPVT
Sbjct: 241 EAPAPGMSCGRRAAMGEAAVAAARAVGYVGAGTVEFIANQDGTFYFMEMNTRLQVEHPVT 300

Query: 301 ELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYR- 359
           E+ITG+DLVE  +RVA+GE LP+ Q+ + + G AIE R+YAE+P + FLP+IG LTR R 
Sbjct: 301 EMITGLDLVEWQLRVASGEPLPLKQEQLRIQGHAIEARIYAENPEKGFLPAIGTLTRMRS 360

Query: 360 -PPVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPA 418
            P VE A   L A G       + P AVR D GV EG  IS +YDPMIAKL  WG DR A
Sbjct: 361 APAVEFA---LAAPG------ATQPAAVRIDAGVREGDAISPFYDPMIAKLIVWGADRDA 411

Query: 419 AIEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAAD 478
           A+  M  AL  ++V G+  N+ F+  ++    F   ++ T  I+      F       AD
Sbjct: 412 ALRNMARALAQYQVVGLATNIGFLQRLIAGQAFATADLDTGLIERHRDTLFPAPVAPTAD 471

Query: 479 LTRLAAAAAAMFRVAEIRRTRISGTLDNHERMVGTDWVVTAQDARFDVTIDADPGGSTVR 538
              LA AA         R  R   + D   +  G  W +  +  R  +  + D G S VR
Sbjct: 472 TLALATAALLQ------REQRNQDSRDPWAQTSG--WRLNTRLQRC-LNFEHDSGNSEVR 522

Query: 539 F------------ADGTAHRVTSRWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRGAD 586
                          G  H +       DS+  + +DG  +   V     G  + F G  
Sbjct: 523 IDYAGDGRQWQLQIGGNTHTLALHAANTDSV-RISLDGRTLQADVAWEGEGLHL-FDG-- 578

Query: 587 VKVHVRTPRQAELNDLMPEKLPPDT-SKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVEA 645
                R+     L D M      +     L  PMPG +V + V+ G  V +G  L  +EA
Sbjct: 579 -----RSQHSLRLPDPMAHAGHAEAEGGRLTAPMPGKIVALLVDQGASVTQGTPLLIMEA 633

Query: 646 MKMENILRAEKTATVTKINAGAGDSLAVDDVIMEFE 681
           MKME+ + A    TV  +    GD +A    +++F+
Sbjct: 634 MKMEHTIAAPSAGTVEALRYAVGDQVAEGAQLLDFK 669


Lambda     K      H
   0.318    0.134    0.392 

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: 1161
Number of extensions: 57
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 681
Length of database: 671
Length adjustment: 39
Effective length of query: 642
Effective length of database: 632
Effective search space:   405744
Effective search space used:   405744
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