GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Amycolatopsis halophila YIM 93223

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_034270915.1 AMYHA_RS11770 acetyl-CoA carboxylase

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



>NCBI__GCF_000504245.1:WP_034270915.1
          Length = 532

 Score =  466 bits (1198), Expect = e-135
 Identities = 257/543 (47%), Positives = 343/543 (63%), Gaps = 19/543 (3%)

Query: 1   MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60
           M+++ + +   + DF        +   +L    A+  +GGG +   RH +RGKL  R+RI
Sbjct: 1   MTVVRTSVDAAAEDFAEYRDAMLTKLDELETEHAKAIEGGGEKYTERHRKRGKLLARERI 60

Query: 61  DTLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPL 120
           + LID DS FLE+  LAA+   D +V  A +V GIG V G   MIIA+D TVKGG+  P 
Sbjct: 61  ELLIDEDSPFLELSPLAAWGS-DYKV-GASMVTGIGVVEGVECMIIASDPTVKGGSMNPW 118

Query: 121 TVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQ 180
           +VKK  RA +IA +NRLP I LV+SGGA LP Q E+F      GR F +  + S E +P 
Sbjct: 119 SVKKGFRAADIAAQNRLPTINLVESGGADLPTQKEIFIPG---GRTFRDLTRASKERVPT 175

Query: 181 IACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTR 240
           +A V G+ TAGGAY+P MSD VV+VK    +FLGGPPLVK ATGEE   E LGGA++H R
Sbjct: 176 VALVFGNSTAGGAYLPGMSDYVVMVKEQAKVFLGGPPLVKMATGEESDDESLGGAEMHAR 235

Query: 241 ISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEP------PRYDPREIYGILP 294
            SG+ADY A D+ +A+ + R I+      +R NW  + P P      PRYD  ++ GI+P
Sbjct: 236 TSGLADYLAVDEEDAIRLGRSII------KRLNWNKQGPSPKPSYSEPRYDAEDLLGIVP 289

Query: 295 RDFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILAN-NGILFSESA 353
            D +  +D REVIAR+VDGS   EFK  YG++LV G+A I G+PVGILAN  G+LFSE +
Sbjct: 290 TDLKVPFDPREVIARVVDGSDFDEFKPLYGSSLVTGWADIHGYPVGILANARGVLFSEES 349

Query: 354 LKGAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVII 413
            K   FI+L    + PL+FL N TG+MVGK YE  GI K GA ++ AVS + VP  +V++
Sbjct: 350 QKATQFIQLANQSDTPLLFLHNTTGYMVGKNYEQNGIIKHGAMMINAVSNSTVPHISVLM 409

Query: 414 GGSFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEE 473
           G S+GAG+YGMCGRAY PR L+ WP+A+ +VMGG Q A VL  + R +  +RGQ    ++
Sbjct: 410 GASYGAGHYGMCGRAYDPRFLFAWPSAKSAVMGGQQLAGVLSIVARASAESRGQAYDEDQ 469

Query: 474 QERFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTR-FGV 532
                A +  + E E  P + S  L+DDG+IDP +TR VL + L+A    PV+  R +GV
Sbjct: 470 DAAMRAMVEGQIEAESVPTFLSGMLYDDGIIDPRDTRTVLGMSLSAIHNGPVEGARGYGV 529

Query: 533 FRM 535
           FRM
Sbjct: 530 FRM 532


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: 780
Number of extensions: 44
Number of successful extensions: 6
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: 532
Length adjustment: 35
Effective length of query: 500
Effective length of database: 497
Effective search space:   248500
Effective search space used:   248500
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 24 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