GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccB in Pseudomonas fluorescens FW300-N1B4

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate Pf1N1B4_222 Methylcrotonyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.4)

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



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_222 Methylcrotonyl-CoA
           carboxylase carboxyl transferase subunit (EC 6.4.1.4)
          Length = 538

 Score =  427 bits (1099), Expect = e-124
 Identities = 234/541 (43%), Positives = 326/541 (60%), Gaps = 11/541 (2%)

Query: 1   MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60
           M +I S + P S  F  N A   +    +R+ L Q  +   AE + R ++RG+L  R+R+
Sbjct: 1   MPVIQSQVDPFSESFARNRAAMLAGIEQVRQ-LEQNLRSKAAEAKPRFDKRGQLLPRERL 59

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

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

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

Query: 238 HTRISGVADYFANDDREALAIVRDIVAHLGPRQRANW-ELRDPEPPRYDPREIYGILPRD 296
           H + +G A+Y A +D + +  VR+I++ L    +  W   R  E P Y   E+ G++P D
Sbjct: 237 HAQTAGTAEYLAENDADGVRQVREIMSLLPWNDQLPWLPERRWEEPLYPIDELLGLIPDD 296

Query: 297 FRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKG 356
            ++ YDVRE+IARI D S   EFK  +    +CG   ++G   G + NNG +  + A K 
Sbjct: 297 PKKPYDVREIIARIADASNFLEFKGEFDQQTICGHLQLQGRACGFIGNNGPITPKGASKA 356

Query: 357 AHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGS 416
           A FI+LC     PL+F  N TGFMVG + E  G+ K GAK++ AV+ A VPK T+++GGS
Sbjct: 357 AQFIQLCDQSQTPLLFFHNTTGFMVGTESEQQGVIKHGAKMIQAVANARVPKLTIVVGGS 416

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

Query: 477 FMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPV---QPTRFGVF 533
                  K + +    Y SA LWDDG+IDP +TR +L   L    EA V   QP  FGV 
Sbjct: 477 LEQVTAQKLDSQSTALYGSANLWDDGLIDPRDTRTLLGYLLDICHEAEVRSLQPNSFGVA 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: 776
Number of extensions: 39
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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