GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PS:Dsui_0982
          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:

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