GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA in Sinorhizobium meliloti 1021

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate SM_b21124 SM_b21124 methylcrotonoyl-CoA carboxylase biotinylated subunit

Query= reanno::PS:Dsui_0516
         (663 letters)



>lcl|FitnessBrowser__Smeli:SM_b21124 SM_b21124 methylcrotonoyl-CoA
           carboxylase biotinylated subunit
          Length = 662

 Score =  495 bits (1274), Expect = e-144
 Identities = 292/672 (43%), Positives = 395/672 (58%), Gaps = 30/672 (4%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60
           MF K+LIANRGEIACR+I+TAR++GI+TVAVYS+AD DAL V +ADEA+ IG A + ESY
Sbjct: 1   MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60

Query: 61  LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120
           L +  I+ A +  GA+A+HPGYGFLSENA+F+  + E G+ F+GP   +I  MG K  +K
Sbjct: 61  LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120

Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180
            L   + V  +PGY+          + A++IGYPV+IKA AGGGGKG+R      +    
Sbjct: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180

Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240
             +   EA ++FGD  V +E+Y+ +PRHIE+QV GD HGN V+L ERDCS+QRRHQKVIE
Sbjct: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240

Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGAT----KEFYFLEMNTRLQV 296
           EAP+P +  E+R+AMG+ AV  A+A+ Y  AGTVEF+           FYF+EMNTRLQV
Sbjct: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300

Query: 297 EHPVTELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRL 356
           EHPVTE ITG+DLVE  +RVA GE LP  QAD+ +NGWA E R+ AEDP RGFLP+TGRL
Sbjct: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360

Query: 357 VKFQPPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIR 416
            +   P   +G  RVD+GV  G  I+ YYD +IAKLIVHG +R  A+ R++DAL    I 
Sbjct: 361 TELSFP---EGTSRVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIG 417

Query: 417 GISSNIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDP---ALLIGVAAFVH 473
           G  +N  F   L +   F+SG  DTG I +E  +   A + P D+    A +    A   
Sbjct: 418 GTVTNRDFLIRLTEEHDFRSGHPDTGLIDREIER-LTAPVAPGDEALALAAIFSTGALDP 476

Query: 474 RRYIDRAAQV-SGQLPGHERKVGDEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYEL--- 529
            R  D  + + S Q+ G   ++    VVI + +    V     G            L   
Sbjct: 477 NRSTDPWSSLGSWQIWGDAHRM----VVIEHADVRATVTLASRGRDQFAVRAGASTLPVL 532

Query: 530 -LSDWRQGQSLFNGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEK 588
            L  +  G  L      G++  ++  R R    LFH G      V          L   +
Sbjct: 533 VLDRFEGGARL---EVAGQKRLIRFSRDREALTLFHGGRNLVFHVPD-------GLTGGQ 582

Query: 589 AAPDLSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVT 648
           ++      L++PMPGL++ V V  G  V  G+ L V+EAMKME  L A ++  +  + V 
Sbjct: 583 SSEIADDELVAPMPGLVKLVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIANVHVA 642

Query: 649 AGSSLSVDEIII 660
            G+ +S   +++
Sbjct: 643 EGAQVSEGTVLV 654


Lambda     K      H
   0.319    0.135    0.391 

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: 1079
Number of extensions: 51
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 663
Length of database: 662
Length adjustment: 38
Effective length of query: 625
Effective length of database: 624
Effective search space:   390000
Effective search space used:   390000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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