GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SM_b21124
          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:

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