GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Pseudomonas simiae WCS417

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate GFF3824 PS417_19580 acetyl-CoA carboxylase

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



>FitnessBrowser__WCS417:GFF3824
          Length = 538

 Score =  428 bits (1100), Expect = e-124
 Identities = 234/541 (43%), Positives = 322/541 (59%), Gaps = 11/541 (2%)

Query: 1   MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60
           M +I S I  +   F  N     +  A L + L         E + + ++RG+L  R+R+
Sbjct: 1   MPVIESLIDTHHAQFAQNREAMLAAIAHLHQ-LEHTLLAKAQEAKPKFDKRGQLLPRERL 59

Query: 61  DTLIDPDSSFLEIGALAAYNVYDEEVPAA---GIVCGIGRVAGRPVMIIANDATVKGGTY 117
             L+DP + FLE+ +LA Y ++D++  +A   G++ GIG V+G  ++++AN++ +KGGT 
Sbjct: 60  ALLLDPGAPFLELASLAGYKLHDDKDGSAAGGGLIAGIGYVSGVRMLVVANNSAIKGGTI 119

Query: 118 FPLTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEG 177
            P  +KK LR Q IA EN+LP + L +SGGA L   +E+F +     R F NQA+MSA G
Sbjct: 120 SPTGLKKSLRLQHIAMENKLPVVTLAESGGANLNYAAEIFVEG---ARSFANQARMSAMG 176

Query: 178 IPQIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADV 237
           +PQI  V GS TAGGAY P +SD VV+V+G   +FL GPPL+KAATGE  T EELGGA++
Sbjct: 177 LPQITVVHGSATAGGAYQPGLSDYVVVVRGRAKLFLAGPPLLKAATGEVATDEELGGAEM 236

Query: 238 HTRISGVADYFANDDREALAIVRDIVAHLGPRQRANW-ELRDPEPPRYDPREIYGILPRD 296
           H   +G A+Y A +D + + I RDIV  L           RD   P Y   E+ G++P D
Sbjct: 237 HAHTAGTAEYLAENDADGVRIARDIVGLLPWNDHLPMVPNRDYAEPLYPIEELLGLIPDD 296

Query: 297 FRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKG 356
            ++ YDVRE++AR+ DGSR  EFK  +    VCG  HI+G  VG++ NNG +  + A K 
Sbjct: 297 PKKPYDVREILARLADGSRFLEFKGEFDAHTVCGHLHIQGHAVGVIGNNGPITPKGATKA 356

Query: 357 AHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGS 416
           AHFI+LC     PL+FL N TGFMVG + E  G+ K GAK++ AV+ A VPK T+++GGS
Sbjct: 357 AHFIQLCDQSRTPLLFLHNTTGFMVGTESEQQGVIKHGAKMIQAVANARVPKLTIVVGGS 416

Query: 417 FGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQER 476
           +GAGNY MCGR   PR ++ WPN+R +VMGG QA  VL  +        G    P+  + 
Sbjct: 417 YGAGNYAMCGRGLDPRFIFAWPNSRTAVMGGAQAGKVLRIVTEAKQLKDGLVPDPKVLDM 476

Query: 477 FMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPV---QPTRFGVF 533
                  K + +    Y SA LWDDG+IDP +TR +L   L    EA V   Q   FGV 
Sbjct: 477 LEQVTAQKLDSQSTALYGSANLWDDGLIDPRDTRTLLGFLLDICHEAQVRELQANTFGVA 536

Query: 534 R 534
           R
Sbjct: 537 R 537


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: 821
Number of extensions: 43
Number of successful extensions: 4
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: 538
Length adjustment: 35
Effective length of query: 500
Effective length of database: 503
Effective search space:   251500
Effective search space used:   251500
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