GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Rhodobacter ovatus JA234

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_097030694.1 CRO07_RS10735 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= reanno::Dino:3607308
         (681 letters)



>NCBI__GCF_900207575.1:WP_097030694.1
          Length = 646

 Score =  469 bits (1207), Expect = e-136
 Identities = 283/687 (41%), Positives = 389/687 (56%), Gaps = 51/687 (7%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60
           MF+KILIANRGEIACRVI TAR++GI TVA++SDAD  ALHV +AD++ HIG +    SY
Sbjct: 1   MFRKILIANRGEIACRVIATARRLGISTVAVFSDADAAALHVALADDSRHIGGAQPADSY 60

Query: 61  IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120
           +  D+++ A   TGAEA+HPGYGFLSEN  F + +   G+ FIGP A+AI AMG K  +K
Sbjct: 61  LRADRIIQAALATGAEAIHPGYGFLSENPDFVDQVTAAGLTFIGPSADAIRAMGLKDAAK 120

Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180
            + ++A V  VPGY G   + D    ++ EIGYPV+IKA AGGGGKGMR     A+  + 
Sbjct: 121 ALMEKAGVPVVPGYHGEDQEPDHLAVMAAEIGYPVLIKAVAGGGGKGMRRVDRAADFADA 180

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240
             S++ EA  +FG+D + IEK++ QPRHIEIQ+  D   + ++L ER+CS+QRR+QKV+E
Sbjct: 181 LASARAEARTAFGNDAVLIEKYIDQPRHIEIQIFGD-GTDAVHLHERDCSLQRRHQKVIE 239

Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGD-----RNFYFLEMNTRLQV 295
           EAP+P +    R AMGE +   A+A+GY  AGT EFIVDG        F+F+EMNTRLQV
Sbjct: 240 EAPAPGMTPEMRAAMGEAAVRAARAIGYRGAGTCEFIVDGSDGLRPDRFWFMEMNTRLQV 299

Query: 296 EHPVTELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRL 355
           EHPVTE +TG+DLVE  +R+A+GE LP+TQ  + L G A E RLYAED    FLP+ GRL
Sbjct: 300 EHPVTEAVTGIDLVEWQLRIASGEPLPLTQAQIPLIGHAFEARLYAEDVPAGFLPATGRL 359

Query: 356 TRYRPPVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPD 415
              R           A+G            +R DTGV  G  IS +YDPMIAK+   GP 
Sbjct: 360 DHLR----------FADG------------IRADTGVRSGDRISPWYDPMIAKIVAHGPS 397

Query: 416 RPAAIEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLG 475
           R AA+  +  AL+  EV G   NL F++ +  HP F  G + T  I        +   + 
Sbjct: 398 RAAALNRLARALEDTEVAGTVTNLAFLSRLARHPGFAAGRVDTGLIARDIASLTDPAPVT 457

Query: 476 AADLTRLAAAAAAMFRVAEIRRTRISGTLDNHERM-VGTDWVVTAQDARFDVTIDADPGG 534
            A        A      A ++   +   L  H R+ +G D +  A      +T+D  PG 
Sbjct: 458 PAITAAALLTAELGTAAAPLQGFTLWSPLRRHARLRLGADEIAAA------ITLDG-PGR 510

Query: 535 STVRFADGTAHRVTSRWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRGADVKVHVRTP 594
           + V  A  T   +++R  P       E++G     +V  +     +  R   V+  +  P
Sbjct: 511 ARVELAGAT---LSARLKP----EGWEVEGTHPG-RVLCLPDAVHVFARSGTVRFTIPDP 562

Query: 595 RQAELNDLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMENILRA 654
                +D         T  + L PMPGLV ++ V  G+ V++G  L  +EAMKME++L A
Sbjct: 563 FDRGTDD-------GATGGLTLSPMPGLVREVAVRPGERVEKGDRLAVIEAMKMEHVLTA 615

Query: 655 EKTATVTKINAGAGDSLAVDDVIMEFE 681
            +  TV ++    G  +     ++  E
Sbjct: 616 ARDGTVAEVLVEPGAQVEAGAALVRLE 642


Lambda     K      H
   0.318    0.134    0.392 

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: 1184
Number of extensions: 53
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 681
Length of database: 646
Length adjustment: 38
Effective length of query: 643
Effective length of database: 608
Effective search space:   390944
Effective search space used:   390944
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