GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Saccharomonospora cyanea NA-134

Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate WP_005458894.1 SACCYDRAFT_RS19840 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= BRENDA::Q9I299
         (655 letters)



>NCBI__GCF_000244975.1:WP_005458894.1
          Length = 660

 Score =  580 bits (1495), Expect = e-170
 Identities = 332/654 (50%), Positives = 425/654 (64%), Gaps = 25/654 (3%)

Query: 11  LLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYLRGD 70
           +LVANRGEIA RV+ + R LGI SVAV+SD D  ARHVAEAD+A  +G A  A SYL   
Sbjct: 5   VLVANRGEIAVRVIATLRRLGIRSVAVYSDADADARHVAEADVARRVGPADAARSYLSVP 64

Query: 71  RIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKALME 130
            I+AAA+ +GAQA+HPGYGFLSENA FA+ACE+AG++F+GPP AAIDAMG K  AK  + 
Sbjct: 65  DIVAAAVETGAQAVHPGYGFLSENAAFAKACEDAGIVFVGPPVAAIDAMGDKIRAKETVS 124

Query: 131 EAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEALSSA 190
            AGVP+VPG + +  D+++    A R+GYPVLLK +AGGGGKGM++V   AEL  A+ SA
Sbjct: 125 AAGVPVVPGAN-DVSDVDSVAAAAERVGYPVLLKPSAGGGGKGMRLVREPAELPAAVESA 183

Query: 191 QREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEEAPA 250
           QREA+ AFGD R+LVE+++  PRH+EIQV ADRHG  ++L ER+CS+QRRHQK+VEEAP+
Sbjct: 184 QREARGAFGDDRLLVERFVADPRHIEIQVLADRHGTVVHLGERECSLQRRHQKIVEEAPS 243

Query: 251 PGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERG--QFFFMEMNTRLQVEHPVTEA 308
             L A+ R  MG+AAV AA+++GYVGAGTVEF++      +FFF+EMNTRLQVEHPVTE 
Sbjct: 244 TLLDADTRARMGKAAVEAARSVGYVGAGTVEFIVSSSAPDEFFFLEMNTRLQVEHPVTEL 303

Query: 309 ITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREAA 368
           +TGLDLV WQ+RVA GE L  TQ+ V L+GHA+E R+YAEDP  DF+P  G ++   E A
Sbjct: 304 VTGLDLVEWQLRVAAGEPLTFTQDDVRLDGHAVEARVYAEDPARDFVPTGGTVLGLHE-A 362

Query: 369 AGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNLAF 428
           +GP  RVDSG+R+G  V+  YDPMLAK+IAWG  R  A  RL   LA+T+V G+ TN+ F
Sbjct: 363 SGPHVRVDSGLRQGTAVASHYDPMLAKVIAWGPDRTSALHRLDRALADTAVLGVPTNVPF 422

Query: 429 LRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAEAWLQSEPGHRRDDDPH 488
           LR +L HP   A  LDTG + R    L   P  + E F  AA +  L   P     D   
Sbjct: 423 LRTLLRHPDVVAGRLDTGLVERELSVLTADPDPV-EFFVAAALDRVLSLWPTGPVID--- 478

Query: 489 SPWSRNDGWRSALARESDLMLRCRDERRCVRLRHASPSQYRL--------------DGDD 534
            PW    GWR        + LR       VR+    P+Q R+              +G D
Sbjct: 479 -PWDVPSGWRLGGNAGVTMRLRVGAAEALVRV-EGLPAQARVVVDGAEAVSASAAREGAD 536

Query: 535 LVSRVDGVTRR-SAALRRGRQLFLEWEGELLAIEAVDPIAEAEAAHAHQGGLSAPMNGSI 593
           LV RV G  RR   A      ++   EG ++A+     +  + A     G +++PM G++
Sbjct: 537 LVVRVAGEYRRYRRAEACDGAVWYAREGRVVAVSERPNLLASHAESVAAGPVTSPMPGTV 596

Query: 594 VRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEGTPL 647
           + V VEPG TV+AG  L+V+EAMKMEH+I AP  GVV  L    G+ V    PL
Sbjct: 597 LVVKVEPGDTVKAGTPLLVVEAMKMEHTITAPVDGVVSQLDVRAGQQVALDEPL 650


Lambda     K      H
   0.319    0.135    0.397 

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: 1112
Number of extensions: 51
Number of successful extensions: 5
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: 655
Length of database: 660
Length adjustment: 38
Effective length of query: 617
Effective length of database: 622
Effective search space:   383774
Effective search space used:   383774
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. 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