GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccB in Bacteroides thetaiotaomicron VPI-5482

Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate 351445 BT1917 propionyl-CoA carboxylase beta chain (NCBI ptt file)

Query= SwissProt::I3R7F1
         (516 letters)



>lcl|FitnessBrowser__Btheta:351445 BT1917 propionyl-CoA carboxylase
           beta chain (NCBI ptt file)
          Length = 511

 Score =  609 bits (1570), Expect = e-179
 Identities = 300/506 (59%), Positives = 384/506 (75%), Gaps = 6/506 (1%)

Query: 11  REKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHRNHKFGMEETK 70
           +E+   A  GGG ++I  QH+ GKMTARERI+  LD GTF E D+   HR   +GM++ K
Sbjct: 12  QERDRIASLGGGVEKIEKQHESGKMTARERIEMLLDKGTFVELDKLMVHRCTNYGMDKNK 71

Query: 71  LPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEVGAPVIGLNDS 130
           +PGDG+++G+G++DGR VFV+A+DFTV+GGSL    A+KI KV   A++ GAP+I LNDS
Sbjct: 72  IPGDGIVSGYGKIDGRQVFVYAYDFTVYGGSLSASNAKKIVKVQQLALKNGAPIIALNDS 131

Query: 131 AGARIQEGVQSLGGFGEIFRRNTEASGVVPQISAIMGPCAGGAVYSPALTDFTFMVRDTS 190
            GARIQEG++SL G+ +IF +NT ASGV+PQISAI+GPCAGGA YSPALTDF FMV++ S
Sbjct: 132 GGARIQEGIESLSGYADIFYQNTMASGVIPQISAILGPCAGGACYSPALTDFIFMVKEKS 191

Query: 191 HMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQALDDIRHLLSYLPQN 250
           HMF+TGPDV+KTV  EEV+ +ELGGA TH+S SGV HF  +TEE+ L  IR LLS+LPQN
Sbjct: 192 HMFVTGPDVVKTVIHEEVSKEELGGAMTHSSKSGVTHFMCNTEEELLMSIRELLSFLPQN 251

Query: 251 NVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEGSFFGVQEDFAKNIV 310
           N+++  +    D+  R    L+ IVP  P  PYD+ D++  V+D G FF V  +FAKNI+
Sbjct: 252 NMDETKKQNCTDETNREDAVLDTIVPADPNVPYDMKDIIERVVDNGYFFEVMTNFAKNII 311

Query: 311 VGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIPILSFVDVPGFLPGT 370
           +GF RL G SVGIVANQP   AG LDI+AS+K +RFIRFCD FNIP+++F DVPGFLPG 
Sbjct: 312 IGFARLAGRSVGIVANQPAYLAGVLDIDASDKASRFIRFCDCFNIPLITFEDVPGFLPGY 371

Query: 371 DQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMASKHLGADVNYAWPTAEIA 430
            QE+NGIIRHGAK++YA++EATVP +TVITRKAYGGAY VM SK  GADVN+A+P+AEIA
Sbjct: 372 TQENNGIIRHGAKIVYAFAEATVPKLTVITRKAYGGAYIVMNSKQTGADVNFAYPSAEIA 431

Query: 431 VMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAADRGFVDDVIEPGDTRN 490
           VMG +GAVNIL+R       D + +  EL E Y+E+FA PY AA+ GF+D++I P  TR 
Sbjct: 432 VMGAEGAVNILFRKA-----DAETKGKEL-EAYKEKFATPYQAAELGFIDEIIYPRQTRK 485

Query: 491 RLIADLRMLKSKRKSQPDKKHGNIPL 516
           RLI  L M ++K ++ P KKHGN+PL
Sbjct: 486 RLIQALEMTENKMQTNPPKKHGNMPL 511


Lambda     K      H
   0.318    0.138    0.407 

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: 786
Number of extensions: 28
Number of successful extensions: 3
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: 516
Length of database: 511
Length adjustment: 35
Effective length of query: 481
Effective length of database: 476
Effective search space:   228956
Effective search space used:   228956
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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 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