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_0516 Dsui_0516 acetyl-CoA carboxylase, biotin carboxylase subunit

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



>lcl|FitnessBrowser__PS:Dsui_0516 Dsui_0516 acetyl-CoA carboxylase,
           biotin carboxylase subunit
          Length = 663

 Score = 1313 bits (3399), Expect = 0.0
 Identities = 663/663 (100%), Positives = 663/663 (100%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60
           MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY
Sbjct: 1   MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60

Query: 61  LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120
           LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK
Sbjct: 61  LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120

Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180
           KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG
Sbjct: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180

Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240
           FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE
Sbjct: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240

Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300
           EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV
Sbjct: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300

Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360
           TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ
Sbjct: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360

Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420
           PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS
Sbjct: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420

Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRA 480
           NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRA
Sbjct: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRA 480

Query: 481 AQVSGQLPGHERKVGDEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYELLSDWRQGQSLF 540
           AQVSGQLPGHERKVGDEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYELLSDWRQGQSLF
Sbjct: 481 AQVSGQLPGHERKVGDEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYELLSDWRQGQSLF 540

Query: 541 NGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDLSKFLLSP 600
           NGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDLSKFLLSP
Sbjct: 541 NGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDLSKFLLSP 600

Query: 601 MPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSLSVDEIII 660
           MPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSLSVDEIII
Sbjct: 601 MPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSLSVDEIII 660

Query: 661 EFE 663
           EFE
Sbjct: 661 EFE 663


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: 1543
Number of extensions: 45
Number of successful extensions: 1
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: 663
Length adjustment: 38
Effective length of query: 625
Effective length of database: 625
Effective search space:   390625
Effective search space used:   390625
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