GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Azospirillum thiophilum BV-S

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_045586135.1 AL072_RS14875 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= metacyc::MONOMER-13589
         (666 letters)



>NCBI__GCF_001305595.1:WP_045586135.1
          Length = 666

 Score =  827 bits (2135), Expect = 0.0
 Identities = 425/670 (63%), Positives = 513/670 (76%), Gaps = 10/670 (1%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60
           MF+KILIANRGEIACRVI+TAR+MGI+TVAVYSDAD+NALHV MADEA+HIGPP + QSY
Sbjct: 1   MFEKILIANRGEIACRVIRTARRMGIKTVAVYSDADKNALHVEMADEAVHIGPPASAQSY 60

Query: 61  IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120
           ++ID+I++A K +GA+AVHPGYGFLSE+  F  AL AAG+ FIGP + A+ AMGDKI SK
Sbjct: 61  LLIDRIVDACKRTGAQAVHPGYGFLSEKPGFQEALAAAGIAFIGPDAHAMRAMGDKIESK 120

Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180
           KLAK AGVSTVPGY+G+IAD +EAV I+ +IGYPVMIKASAGGGGKGMR+AW++ E +EG
Sbjct: 121 KLAKAAGVSTVPGYLGVIADDEEAVMIARDIGYPVMIKASAGGGGKGMRVAWNDEEAREG 180

Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240
           F S+ NEA +SF DDR+F+EK++ QPRHIEIQ+LAD  G C+YLHERECSIQRR+QKVIE
Sbjct: 181 FRSATNEARSSFADDRVFVEKYIQQPRHIEIQLLADGQGTCLYLHERECSIQRRHQKVIE 240

Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300
           EAPSPFLD ATRKAMGEQA ALA AV Y SAGTVEFIVD ++NFYFLEMNTRLQVEHPVT
Sbjct: 241 EAPSPFLDAATRKAMGEQAVALANAVQYKSAGTVEFIVDAERNFYFLEMNTRLQVEHPVT 300

Query: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360
           ELITG+DLVE MIRVAAGEKL   Q D+ +NGWA+E+R+YAEDP+RNFLPS GRLT YRP
Sbjct: 301 ELITGLDLVELMIRVAAGEKLTIGQDDVTLNGWAIEARVYAEDPFRNFLPSTGRLTNYRP 360

Query: 361 PVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGI 420
           P         VR DTGV+EGGEISMYYDPMIAKLCTW  TR+AAI  MR ALD + + G+
Sbjct: 361 PAAD----PHVRVDTGVFEGGEISMYYDPMIAKLCTWGSTRDAAIGGMREALDQYYIRGV 416

Query: 421 GHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNRVAEI 480
            HN+PF+ ++M + RFV G +TT FIAEEYP+GF  + L       + A AA ++R    
Sbjct: 417 SHNIPFLASLMANQRFVDGRLTTNFIAEEYPNGFHASDLPPEDPAVLVAVAAVIHRSLND 476

Query: 481 RRTRISGTMNNHERHVGVDWVVALQGESYHVSIAA-----DREGSTVSFSDGSSLRVTSD 535
           R  +ISG M   +  V  DWVV L G ++ V + A      R G TV  + G    V SD
Sbjct: 477 RDIQISGKMAGSKVTVRDDWVVVLDGTAHPVHLHAAAGSPQRIGYTVDIA-GRHHTVWSD 535

Query: 536 WTPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKLPPD 595
           W  G+PL    VDG  + +++ ++ +G+RL   G+   V V TP+ A L  LMP K PPD
Sbjct: 536 WQIGEPLFRGTVDGSHVCVQIDRVGIGYRLHHSGSQAIVKVLTPKAAALDALMPVKAPPD 595

Query: 596 TSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAPGAS 655
            SK+LL PMPGL+V + V+EG E++ G+ LA VEAMKMENILRA + GTV KI AAPG+S
Sbjct: 596 MSKFLLSPMPGLLVSLAVSEGQEIKAGEVLAVVEAMKMENILRASQDGTVAKIHAAPGSS 655

Query: 656 LRVDDVIMEF 665
           L VD  I+EF
Sbjct: 656 LAVDQKIVEF 665


Lambda     K      H
   0.318    0.134    0.386 

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: 1205
Number of extensions: 44
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: 666
Length of database: 666
Length adjustment: 38
Effective length of query: 628
Effective length of database: 628
Effective search space:   394384
Effective search space used:   394384
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: 54 (25.4 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