GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Caulobacter crescentus NA1000

Align propionyl-CoA carboxylase (EC 6.4.1.3) (characterized)
to candidate CCNA_03320 CCNA_03320 biotin carboxylase

Query= BRENDA::Q9X4K7
         (530 letters)



>FitnessBrowser__Caulo:CCNA_03320
          Length = 1078

 Score =  241 bits (614), Expect = 1e-67
 Identities = 172/530 (32%), Positives = 256/530 (48%), Gaps = 47/530 (8%)

Query: 5    EEQQPDIHTTAGKLADLRRRIEEATHAGSARAVEKQHAKGKLTARERIDLLLDEGSFVEL 64
            E  + D+      LA++  R           AV K+   G  TARE ID L+D GSF+E 
Sbjct: 555  ETVEQDLDALRPDLAEVVARHRHTLDEARPEAVAKRRKTGHRTARENIDDLVDPGSFLEY 614

Query: 65   DEFA-----RHRSTNFGLDANRPYGDGVVTGYGTVDGR-------PVAVFSQDFTVFGGA 112
               A     R RST   L AN P  DG++TG GTV+G          A  + DFTV  G 
Sbjct: 615  GALAIAAQKRRRSTE-DLIANTP-ADGLITGIGTVNGALFPPDKARTAALAYDFTVLAGT 672

Query: 113  LGEVYGQKIVKVMDFALKTGCPVVGINDSGGARI--QEGVASLGAYGEIFRRNTHASGVI 170
             G +  +K  ++M        PVV   + GG R    +  A  G     FR     SG++
Sbjct: 673  QGAMNHRKSDRLMALIADQKLPVVWFAEGGGGRPGDTDTTAVAGLDVPTFRSFAQLSGLV 732

Query: 171  PQISLVVGPCAGGAVYSPAITDFTVMVDQTSHMFITGPDVIKTVTGEDVGF---EELGGA 227
            P+I++V G C  G      +++  ++  + S++ + GP +I+   G  +G    EE+G +
Sbjct: 733  PKIAIVAGRCFAGNAAIAGLSEI-IIATRDSNLGMGGPAMIE---GGGLGVFRPEEIGPS 788

Query: 228  RTHNSTSGVAHHMAGDEKDAVEYVKQLLSYLPSNNLSEPPAFPEEADLAVTDEDAELDTI 287
              H   +GV   +A DE  A    KQ LSY           F          +   L   
Sbjct: 789  -AHQWKNGVIDILADDEAHATRLAKQALSY-----------FQGTLSTWTAPDQRRLRHA 836

Query: 288  VPDSANQPYDMHSVIEHVLDDAEFFETQPLFAPNILTGFGRVEGRPVGIVANQPMQFAGC 347
            +P++  + YD+  +I H++D+  F E +  FA  ++TG  R+EGRP+G++AN P    G 
Sbjct: 837  IPENRLRVYDVRGLINHLVDEGSFLELRGGFAAGMVTGLIRIEGRPMGLIANDPRHLGGA 896

Query: 348  LDITASEKAARFVRTCDAFNVPVLTFVDVPGFLPGVDQEHDGIIRRGAKLIFAYAEATVP 407
            +D   +EKAARF++ CDAF +PVL+  D PGF+ G D E    +RR ++   A A+   P
Sbjct: 897  IDCEGAEKAARFLQLCDAFALPVLSLCDTPGFMVGPDSEDAAAVRRVSRQFIAGAKLRSP 956

Query: 408  LITVITRKAFG-GAYDVMGSKHLGADLNLAWPTAQIAVMGAQGAVNILHRRTIADAGDDA 466
            L T++TRK +G GA  + G          AWPT +   MG +GAV + +R+ +     +A
Sbjct: 957  LFTIVTRKGYGLGAQAMAGGSFHSPAFIAAWPTGEFGGMGLEGAVKLGYRKEL-----EA 1011

Query: 467  EATRARLIQEYEDALLNPYTA------AERGYVDAVIMPSDTRRHIVRGL 510
            E    +    Y+  +   Y A      A    +DAVI P+DTRR ++ GL
Sbjct: 1012 ETDPVKQKALYDQLVARLYAAGKATSMAAALEIDAVIDPADTRRWVIGGL 1061


Lambda     K      H
   0.318    0.136    0.398 

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: 1378
Number of extensions: 78
Number of successful extensions: 9
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: 530
Length of database: 1078
Length adjustment: 40
Effective length of query: 490
Effective length of database: 1038
Effective search space:   508620
Effective search space used:   508620
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 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