GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA in Dechlorosoma suillum PS

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate Dsui_0982 Dsui_0982 acetyl/propionyl-CoA carboxylase, alpha subunit

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



>lcl|FitnessBrowser__PS:Dsui_0982 Dsui_0982 acetyl/propionyl-CoA
           carboxylase, alpha subunit
          Length = 667

 Score =  514 bits (1323), Expect = e-150
 Identities = 314/679 (46%), Positives = 411/679 (60%), Gaps = 35/679 (5%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60
           MF KILIANRGEIACRVIKTAR++GI+TVAVYSEAD +A  V +ADEAV +GPAA++ESY
Sbjct: 1   MFSKILIANRGEIACRVIKTARRLGIRTVAVYSEADANARHVRLADEAVLLGPAAARESY 60

Query: 61  LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120
           LVA+KI+ A ++TGA+A+HPGYGFLSENA+F+      G+ FIGP   +I  MG K  +K
Sbjct: 61  LVAEKILDAARRTGAQAIHPGYGFLSENADFAEACAAAGVVFIGPPASAIRAMGSKSAAK 120

Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180
            L  +A V   PGY+     P+   + A  IGYPV+IKA+AGGGGKG+R+     +    
Sbjct: 121 ALMEKAAVPLTPGYHGDNQEPEFLKQQADAIGYPVLIKAAAGGGGKGMRLVDKGEDFIAA 180

Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240
            +SC  EAR+SFG+D+V +EKY+  PRHIEIQV GDS GN VYL ERDCS+QRRHQKV+E
Sbjct: 181 LASCQREARSSFGNDQVLVEKYITRPRHIEIQVFGDSQGNCVYLFERDCSVQRRHQKVLE 240

Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300
           EAP+P + PE R+ MGE AVA A+AV Y  AGTVEF ++     FYF+EMNTRLQVEHPV
Sbjct: 241 EAPAPGMTPERRRQMGEAAVAAAKAVGYVGAGTVEF-IANQDGSFYFMEMNTRLQVEHPV 299

Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360
           TE+ITG DLVE  +RVA GE LPL Q  +QI G A+E RI AED  +GFLPSTGRL+   
Sbjct: 300 TEMITGQDLVEWQLRVAAGEALPLRQEQLQIRGHALEARIYAEDAGKGFLPSTGRLLHLV 359

Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420
           PPAE    VRVDTGV +G EI+ +YD MIAKLIV    RE A+ARMR AL  + + G+++
Sbjct: 360 PPAE-GLNVRVDTGVEEGDEITPHYDPMIAKLIVWDEDREAALARMRQALADYRVVGVTT 418

Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRA 480
           NI F + L+    F     DTG I ++    F  S     D  L   VA  +  R  D A
Sbjct: 419 NIDFLSRLVSCPAFAGADLDTGLIERQQDFLFPESPEVPRDVILTATVAELLRER--DLA 476

Query: 481 AQVSGQLPGHERKVGDEWVV--IRNGERHPVVAK----------PIEGGYLVTYNGEKYE 528
           AQ         R+ GD W     R+G R  + A+           ++ G  V Y GE ++
Sbjct: 477 AQ-------QGRRSGDPWSPWNRRDGWRMNIAARRTVSFRVGETQVDVG--VAYAGEDWQ 527

Query: 529 LLSDWRQGQSLFNGTCNG-EEFTLQVERHRMTYQLFHWGTRADMMVMSA----RAAELLA 583
           L    R    L  G     +   +++E  R+   +     +  + + S        + L 
Sbjct: 528 L--TLRNDTLLVRGRLLAHDRLAVELEDRRLMASVVAVAEKRHVFLNSGTYVIERHDPLH 585

Query: 584 LMPEKAAPDLSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVK 643
           L+  +A       L +PMPG +  +    G   K G  L ++EAMKME+ + A +   +K
Sbjct: 586 LV--EAGGAQGGGLTAPMPGKVVALLAQPGPVAK-GTPLLILEAMKMEHTITAPKQGNLK 642

Query: 644 KISVTAGSSLSVDEIIIEF 662
                 G  ++    +++F
Sbjct: 643 GFRYAVGEQVADGAELVDF 661


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: 1053
Number of extensions: 44
Number of successful extensions: 5
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: 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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