GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:351445
          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.

Links

Downloads

Related tools

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