GapMind for catabolism of small carbon sources

 

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

Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate WP_101590190.1 BJEO58_RS14660 ATP-grasp domain-containing protein

Query= SwissProt::I3R7G3
         (601 letters)



>NCBI__GCF_900169175.1:WP_101590190.1
          Length = 454

 Score =  408 bits (1048), Expect = e-118
 Identities = 208/447 (46%), Positives = 298/447 (66%), Gaps = 4/447 (0%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           +  ++LVANRGEIA R+ R C+ LG+ TVAVYS+AD++  HVR AD    IG A A+ SY
Sbjct: 4   VIKRILVANRGEIACRIFRTCDLLGIETVAVYSDADENSKHVRMADRTVRIGEALASSSY 63

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           LD E+V+ AA  +  DAIHPGYGFL+EN+EFARK+++   TWVGP  ++M+ + EK  AR
Sbjct: 64  LDIEAVLRAASDSGVDAIHPGYGFLSENSEFARKIQELGLTWVGPDPESMDSMSEKVPAR 123

Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180
           +LM +A VPVVPGT+   D+ +     A + GYP+ +KA  GGGG G+ VV S+ E++  
Sbjct: 124 ALMLEAGVPVVPGTSGSVDTLDHALLSAQEIGYPMVLKATAGGGGLGMSVVTSDAELEKS 183

Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240
           ++  +R+ E  F N SVY+EKY+E+ +HIEVQ+L      V  +G+R+CS+QRRHQKV+E
Sbjct: 184 YDATRRKAERAFGNGSVYLEKYIESAKHIEVQVLGLNSDKVAVIGDRECSVQRRHQKVLE 243

Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE--DGEFYFMEVNTRIQVEHTV 298
           EAP+P LSE  R+ +   A++     +Y  AGTVEF+ +    EFYF+E+NTR+QVEH V
Sbjct: 244 EAPAPTLSESERDWLYVMAQKVAEKVKYRGAGTVEFIFDRMTREFYFLEMNTRLQVEHPV 303

Query: 299 TEEVTGLDVVKWQLRVAAGEELDFSQ-DDVEIEGHSMEFRINAEAPEKEFAPATGTLSTY 357
           TE VTGLD+V+ Q+ +AAG+ELD ++ D    +GH++EFR+ AE P + F P  G ++T+
Sbjct: 304 TELVTGLDLVELQIHIAAGQELDLARLDRPTPQGHAIEFRVYAEDPVR-FLPGPGEITTW 362

Query: 358 DPPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTV 417
             P G G+R+D     GD +   YD ++AKL V   DR+ VL     A  EFD+ G +T 
Sbjct: 363 AEPSGPGVRVDSGYDVGDIVTPYYDPLLAKLCVHDVDRDHVLHALGEAAQEFDVSGPKTN 422

Query: 418 IPFHRLMLTDEAFREGSHTTKYLDEVL 444
           +     ++ D +F +G + T+ L  V+
Sbjct: 423 LALVEGIVGDPSFVDGEYDTEMLTRVV 449


Lambda     K      H
   0.312    0.132    0.371 

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: 666
Number of extensions: 31
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: 601
Length of database: 454
Length adjustment: 35
Effective length of query: 566
Effective length of database: 419
Effective search space:   237154
Effective search space used:   237154
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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