GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Magnetospirillum magneticum AMB-1

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_011386591.1 AMB_RS21445 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= reanno::Smeli:SM_b21124
         (662 letters)



>NCBI__GCF_000009985.1:WP_011386591.1
          Length = 663

 Score =  505 bits (1300), Expect = e-147
 Identities = 303/660 (45%), Positives = 393/660 (59%), Gaps = 27/660 (4%)

Query: 1   MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60
           MF+K+LIANRGEIACR+I+TA+++GI+TVAVYSDAD DALHV++ADEA+ IG A +A+SY
Sbjct: 1   MFTKILIANRGEIACRVIKTAKKMGIKTVAVYSDADKDALHVSMADEAVHIGPAASAQSY 60

Query: 61  LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120
           L    IV A +  GAQA+HPGYGFLSE  +F EA+ +AG+ F+GP   AI AMG K  +K
Sbjct: 61  LVIDKIVDACKQTGAQAVHPGYGFLSEKREFQEALGKAGIAFIGPDAHAIFAMGDKIESK 120

Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180
            L   +GV  VPGY G  +DA      AREIGYPV++KA AGGGGKGMR      +    
Sbjct: 121 KLAREAGVNTVPGYLGVIKDADEAVKIAREIGYPVMLKASAGGGGKGMRLAWNDAEAHEG 180

Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240
             +A  EA+++FGD  V +E+++ +PRHIE+QV  D  G  ++L ER+CS+QRRHQKVIE
Sbjct: 181 FTSATNEAKTSFGDDRVFVEKFIEQPRHIEIQVLADGQGTTLYLGERECSIQRRHQKVIE 240

Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300
           EAP+P +T E R+AMG+ A   A+ + Y  AGTVEFI     G     FYF+EMNTRLQV
Sbjct: 241 EAPSPFLTPETRKAMGEQACALARIVNYKSAGTVEFIVGGATG----EFYFLEMNTRLQV 296

Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360
           EHPVTE ITG+DLVE  +RVASGE L   Q D+ +NGW+ EAR+YAEDP R FLP+TGRL
Sbjct: 297 EHPVTEMITGLDLVEQMIRVASGEKLSITQDDVKLNGWSMEARVYAEDPFRNFLPSTGRL 356

Query: 361 TELSFPEGTS--RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGG 418
           T    P  ++  RVD+GV +G  I+ +YDP+IAKLI +G  R AA+  ++ AL E  I G
Sbjct: 357 TRYQPPAESAHVRVDTGVYEGGEISMFYDPMIAKLITYGPTRDAAIAHMRQALDEYYIRG 416

Query: 419 TVTNRDFLIRLTEEHDFRSGHPDTGLIDREIER-LTAPVAPGDEALALAAIFSTGALDPN 477
              N  FL  L  +  F  G   T  I  E      A   P D+   L A+    A   N
Sbjct: 417 LSHNIPFLASLFSKERFVKGALTTNFIAEEYANGFHANDLPADDPTVLIAV----AAAAN 472

Query: 478 RSTDPWSSLGSWQIWGDAHR-----MVVIEHADVRATVTLASRGRDQFAVRAGASTLPVL 532
           R      +  S Q  G   +     +VV+       TV  A  G   +AV  G  T+ V 
Sbjct: 473 RRIHERDTRISGQFPGHEMKAGDEWVVVMSGQYHDITVRPAENG---YAVALGGETVDVR 529

Query: 533 VLDRF-EGGARLEVAGQKRLIRFSRDREALTLFHGGRNLVFHV-------PDGLTGGQSS 584
              +  E   R  V G+   ++  R    L L H G  +   V        + L   ++ 
Sbjct: 530 TDWQIGEPLFRANVDGRAVAVQIERVGSGLRLAHAGSRVDVLVLTPHAAKMNKLMPFKAP 589

Query: 585 EIADDELVAPMPGLVKLVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIANVHVAEG 644
                 L++PMPGL+  + V AG  V  G+ L V+EAMKME  L A R+ T+A  H A G
Sbjct: 590 PDMSKYLLSPMPGLLVKLLVEAGQEVKAGEPLAVVEAMKMENILKAERDATVAKTHAASG 649


Lambda     K      H
   0.319    0.135    0.394 

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: 1102
Number of extensions: 60
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: 662
Length of database: 663
Length adjustment: 38
Effective length of query: 624
Effective length of database: 625
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 (21.8 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