GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Marinobacter adhaerens HP15

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate GFF1025 HP15_1004 3-methylcrotonyl CoA carboxylase, beta subunit

Query= metacyc::MONOMER-17283
         (535 letters)



>FitnessBrowser__Marino:GFF1025
          Length = 535

 Score =  745 bits (1924), Expect = 0.0
 Identities = 363/535 (67%), Positives = 428/535 (80%)

Query: 1   MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60
           M+I+ S I P S +FQAN        ADLR++++ I+QGGG   + RH  RGKL  R+RI
Sbjct: 1   MTILQSKINPRSEEFQANQESMAQAVADLRDKVSTIQQGGGPSYQERHIARGKLLPRERI 60

Query: 61  DTLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPL 120
           + L+D  S FLEIG  AAYNVYDEEVPAAG++ G+GRV+G   MIIANDATVKGG+Y+PL
Sbjct: 61  NRLLDDGSPFLEIGQFAAYNVYDEEVPAAGVIAGVGRVSGTECMIIANDATVKGGSYYPL 120

Query: 121 TVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQ 180
           TVKKHLRAQEIA +NRLPCIYLVDSGGA LP Q EVFPDR+HFGRIFYNQA+MSA+ IPQ
Sbjct: 121 TVKKHLRAQEIALQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFYNQARMSADDIPQ 180

Query: 181 IACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTR 240
           IA VMG CTAGGAYVPAM+DE +IV+  GTIFL GPPLVKAATGE VTAE+LGGADVH +
Sbjct: 181 IAVVMGLCTAGGAYVPAMADESIIVRNQGTIFLAGPPLVKAATGEVVTAEDLGGADVHCK 240

Query: 241 ISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQS 300
           ISGVAD++A +D  AL I R  V++L  R+  + E+R P+ P YD  EIYGI+  D R+ 
Sbjct: 241 ISGVADHYAENDAHALEIARRSVSNLNRRKPTDVEIRKPKAPLYDAEEIYGIVGTDLRKQ 300

Query: 301 YDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFI 360
           +DVR+VIAR VDGS   EFK  YG TLV GFAHI G+PVGI+ANNGILFSE+A KGAHF+
Sbjct: 301 FDVRDVIARTVDGSEFDEFKRYYGQTLVTGFAHIHGYPVGIIANNGILFSEAAQKGAHFV 360

Query: 361 ELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAG 420
           ELCC RNIPL+FLQNITGFMVG++YE+ GIAK GAK+V AV+CANVPK TV+IGGSFGAG
Sbjct: 361 ELCCQRNIPLLFLQNITGFMVGQKYESEGIAKHGAKMVMAVACANVPKITVLIGGSFGAG 420

Query: 421 NYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAP 480
           NYGMCGRAY P  LWMWPNARISVMGG QAA V+ T+RR+ +  +GQ+ + EE+  F  P
Sbjct: 421 NYGMCGRAYSPDFLWMWPNARISVMGGEQAAGVMATVRREGMERKGQEWSAEEEAEFKKP 480

Query: 481 ILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535
           I+  YE +GHPYYASARLWDDGVIDP +TR V+AL L+A    P +PTRFGVFRM
Sbjct: 481 IIDTYEHQGHPYYASARLWDDGVIDPAQTREVVALSLSATLNRPAKPTRFGVFRM 535


Lambda     K      H
   0.322    0.139    0.423 

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: 966
Number of extensions: 46
Number of successful extensions: 2
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: 535
Length of database: 535
Length adjustment: 35
Effective length of query: 500
Effective length of database: 500
Effective search space:   250000
Effective search space used:   250000
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 (21.9 bits)
S2: 52 (24.6 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