GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Marinobacter algicola DG893

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_007154498.1 MDG893_RS14185 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= reanno::PS:Dsui_0516
         (663 letters)



>NCBI__GCF_000170835.1:WP_007154498.1
          Length = 667

 Score =  481 bits (1237), Expect = e-140
 Identities = 296/678 (43%), Positives = 400/678 (58%), Gaps = 36/678 (5%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60
           MF KILIANRGEIACR+I+TA +MGI+ VAVYS+AD DA  V MADEA  IGPAAS ESY
Sbjct: 1   MFSKILIANRGEIACRIIQTAHRMGIRVVAVYSDADADARHVAMADEAFNIGPAASSESY 60

Query: 61  LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120
           L ADKII   K++GA+AVHPGYGFLSEN +F+   E   I FIGP   +IA MG K  +K
Sbjct: 61  LKADKIIEVAKESGAQAVHPGYGFLSENTQFAEACEANNIVFIGPPSSAIAAMGSKSAAK 120

Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180
            +   A V  +PGY+     P+   + A+K G+P+++KA AGGGGKG+RV     +  + 
Sbjct: 121 AIMETAGVPLVPGYHGDDQSPETLRKEAEKCGFPLLLKAVAGGGGKGMRVVERMEDFDDA 180

Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240
            ++   E++N+FG+  + IE+Y+ +PRH+EIQV  D  G  VYL ERDCS+QRRHQKV+E
Sbjct: 181 LAAAKRESKNAFGNPDMLIERYLTQPRHVEIQVFCDKSGKGVYLAERDCSVQRRHQKVLE 240

Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300
           EAP+P +  E RK+MGE AV  A+A++Y  AGTVEF+       F+F+EMNTRLQVEHPV
Sbjct: 241 EAPAPGLSDETRKSMGEAAVKAAQAIDYVGAGTVEFLYD-VDGSFFFMEMNTRLQVEHPV 299

Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360
           TE++TG DLVE  ++VA+G+ LPL QA V+  G A+E RI AEDP + FLP+TG L    
Sbjct: 300 TEMVTGQDLVEWQLKVAWGDALPLEQAQVKTRGHALEARIYAEDPDQDFLPATGNLRYLS 359

Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420
            P E    VRVDTGV +G +IS++YD MIAKLIV   +R+QAI RM  AL  + I G+ +
Sbjct: 360 TPDE-SAHVRVDTGVTEGDDISIHYDPMIAKLIVWDETRDQAINRMVQALEHYRIAGVKT 418

Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRA 480
           NI F  AL     F+     TGFI       F  S +  D    L+  A FV  +   ++
Sbjct: 419 NIRFLHALADAQPFREADLTTGFIEDHRELLFPKSRL--DTHKALVLAAGFVLEQ--RKS 474

Query: 481 AQVSGQLPGHERKVGDEWVVIRNGERHPVVAKPIE-------GGYLVTYNGEKYELLSDW 533
            +V    P       + W +  N E     A+P++           V    ++Y++    
Sbjct: 475 REVISTDPWSPFGRQNSWRM--NSE----YAQPLQLQVGEDIHELKVLERDDRYQVF--- 525

Query: 534 RQGQSLFNGTCNGEEFTLQ--VERHRMTYQLFHWGTRADMMVMSARAAELLALMP----- 586
             G S++N T   ++  LQ  +  HR++    H     D +V+         ++      
Sbjct: 526 -VGDSVYNLTAKLDDDYLQAVINGHRIS---VHGNLHNDQLVLFYEGDTFQCILYRETYG 581

Query: 587 -EKAAPDLSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKI 645
            E+ A + S  L +PM G +  V   VG  V AG+ L ++EAMKME+ +KA  D  V  I
Sbjct: 582 FEEMAGEGS--LAAPMNGAIVAVQTKVGDTVTAGQSLVIMEAMKMEHAIKAPADGVVTDI 639

Query: 646 SVTAGSSLSVDEIIIEFE 663
               G  +S    +I  E
Sbjct: 640 FFAEGDQVSEGAELIAIE 657


Lambda     K      H
   0.319    0.135    0.391 

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: 1068
Number of extensions: 41
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: 663
Length of database: 667
Length adjustment: 38
Effective length of query: 625
Effective length of database: 629
Effective search space:   393125
Effective search space used:   393125
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 (21.7 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