GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Brevibacterium jeotgali SJ5-8

Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_101588272.1 BJEO58_RS04965 ATP-grasp domain-containing protein

Query= SwissProt::I3R7F1
         (516 letters)



>NCBI__GCF_900169175.1:WP_101588272.1
          Length = 1074

 Score =  239 bits (611), Expect = 3e-67
 Identities = 153/494 (30%), Positives = 240/494 (48%), Gaps = 10/494 (2%)

Query: 4    EDRIDELREKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHRNHK 63
            E  I+E+R + EEA K GG  ++A QH+ G++TARERI    D+G+F E      +  + 
Sbjct: 562  EQEIEEIRRRHEEAYKHGGAAKVARQHESGRLTARERIAALADEGSFDEIGPLAGYGEYD 621

Query: 64   FGMEETKLPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEVGAP 123
                   +     ++G G + GR   +   DF++ GGS      +K       A E+  P
Sbjct: 622  EDGNLLGVRPSNFLSGTGRIRGRRALLGVDDFSIRGGSGDAAVHQKQVFTEQLAGEMRVP 681

Query: 124  VIGLND--SAGARIQEGVQSLGGFGEI---FRRNTEASGVVPQISAIMGPCAGGAVYSPA 178
            ++ + D  S G  +++ + +   +  +   +    +    +P +S   GP  G       
Sbjct: 682  MVRVLDGASGGGSVKKVLTAQAMYLPVNPGWDHVVDNMSRIPVVSVCAGPTVGLGAARFV 741

Query: 179  LTDFTFMVRDTSHMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQALD 238
            ++ F  MV+    +F  GP V+K  TGE++  D LGG   H +   V  F  D EE A +
Sbjct: 742  MSHFGVMVQGIGQLFTAGPPVVKAATGEDLDKDGLGGEAVHRTNGTVERFVPD-EETAFE 800

Query: 239  DIRHLLSYLPQNNVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEGSF 298
             +R  LSYLP +  E PP  E  D  +R  + L   VP  PR+ Y I  +L+ V D GS 
Sbjct: 801  VVRDFLSYLPSSVDELPPVAENSDPVDRSEESLAAAVPRNPRQIYAIEPILHAVFDHGSV 860

Query: 299  FGVQEDFAKNIVVGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIPIL 358
            F   E +         RLDG  VG+V   P   A TL  E ++   R +  C++F++P++
Sbjct: 861  FRFAE-YGDGTYTALARLDGRPVGVVTADPSQGA-TLSREGAQAVERLVDICEAFHLPLV 918

Query: 359  SFVDVPGFLPGTDQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMASKHLGA 418
            S  D  G   G   E +  IR GA+ + A  +A +P   +I R+ YG     + ++H  A
Sbjct: 919  SLTDQAGMTIGLQAEKDATIRAGARAIAAIYQARIPQAEIILRRVYGVGGAGIVNRH-RA 977

Query: 419  DVNYAWPTAEIAVMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAADRGF 478
              ++AWP+ +   + PQG +   +R EL A DDP+ R  E+  E  E  ++ +  A+   
Sbjct: 978  VRSWAWPSGDWGSLPPQGGIEAAFRAELAAHDDPEKRLAEITHE-MELVSSRFRTAETFS 1036

Query: 479  VDDVIEPGDTRNRL 492
            V D+I+P  TR RL
Sbjct: 1037 VQDIIDPRTTRRRL 1050


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: 1401
Number of extensions: 76
Number of successful extensions: 8
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: 1074
Length adjustment: 40
Effective length of query: 476
Effective length of database: 1034
Effective search space:   492184
Effective search space used:   492184
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: 55 (25.8 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