GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Coprobacter fastidiosus NSB1

Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_022601570.1 NSB1T_RS24085 acyl-CoA carboxylase subunit beta

Query= SwissProt::I3R7F1
         (516 letters)



>NCBI__GCF_000473955.1:WP_022601570.1
          Length = 511

 Score =  619 bits (1597), Expect = 0.0
 Identities = 313/505 (61%), Positives = 382/505 (75%), Gaps = 6/505 (1%)

Query: 12  EKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHRNHKFGMEETKL 71
           E+   A   GG DRI  QH  GK+TARERI+  LD  +F E D+F  HR   +GM+  ++
Sbjct: 13  ERNRAAEMAGGADRIGKQHAAGKLTARERIELLLDPASFNELDKFVVHRCKDYGMDGARI 72

Query: 72  PGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEVGAPVIGLNDSA 131
           PGDGV++G+G ++GR VFV+A+DFTVFGG+L    A KI KV D A++ GAPVI LNDS 
Sbjct: 73  PGDGVVSGYGRIEGRLVFVYAYDFTVFGGTLSAENARKIMKVQDLALKNGAPVIALNDSG 132

Query: 132 GARIQEGVQSLGGFGEIFRRNTEASGVVPQISAIMGPCAGGAVYSPALTDFTFMVRDTSH 191
           GARIQEGV+SL G+  IF RNT ASGV+PQISAI+GPCAGGA YSPALTDF FMVR  SH
Sbjct: 133 GARIQEGVESLSGYAGIFFRNTMASGVIPQISAILGPCAGGACYSPALTDFIFMVRGYSH 192

Query: 192 MFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQALDDIRHLLSYLPQNN 251
           MF+TGPDV+K VT E V  +ELGGA TH S SGVAHF  D+E++ + +IR LLS+LP NN
Sbjct: 193 MFVTGPDVVKAVTHELVGKEELGGAVTHASVSGVAHFLGDSEKEVILEIRELLSFLPANN 252

Query: 252 VEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEGSFFGVQEDFAKNIVV 311
           +ED P V   DD  R    L E++PD P  PYD+ +V+  V+D+G FF V  DFAKNIV+
Sbjct: 253 MEDAPCVPCRDDIRREVTGLREVIPDDPNIPYDMKEVIVPVVDDGYFFEVMPDFAKNIVI 312

Query: 312 GFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIPILSFVDVPGFLPGTD 371
           GF RL G +VGIVANQP   AG LDI+AS+K ARFIRFCD FNIP+++F DVPGFLPGT 
Sbjct: 313 GFARLGGRTVGIVANQPAFLAGVLDIDASDKAARFIRFCDCFNIPLVTFEDVPGFLPGTV 372

Query: 372 QEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMASKHLGADVNYAWPTAEIAV 431
           QEHNGIIRHGAK++YA++EATVP +T+ITRKAYGGAY VMASK  GAD+N A+P AEIAV
Sbjct: 373 QEHNGIIRHGAKVVYAFAEATVPKVTLITRKAYGGAYIVMASKLTGADINLAFPNAEIAV 432

Query: 432 MGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAADRGFVDDVIEPGDTRNR 491
           MG +GAVNIL+R+    AD  + +R EL EEYRE FANP+ AA+ G++D+VI P  TR +
Sbjct: 433 MGAEGAVNILFRN----AD--NEKRAELTEEYRERFANPFRAAELGYIDEVILPEQTRAK 486

Query: 492 LIADLRMLKSKRKSQPDKKHGNIPL 516
           LIA L M ++K  S P KKHGN+PL
Sbjct: 487 LIAALEMAQNKNVSNPPKKHGNMPL 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: 801
Number of extensions: 28
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: 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 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