Alignments for a candidate for liuB in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Sphingomonas koreensis DSMZ 15582

Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate Ga0059261_3993 Ga0059261_3993 Acetyl/propionyl-CoA carboxylase, alpha subunit

Query= reanno::pseudo1_N1B4:Pf1N1B4_3984
         (651 letters)



>FitnessBrowser__Korea:Ga0059261_3993
          Length = 669

 Score =  525 bits (1353), Expect = e-153
 Identities = 319/679 (46%), Positives = 405/679 (59%), Gaps = 52/679 (7%)

Query: 9   LLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68
           +LVANRGEIACRV RTAK +G+ TVAV+S  D  A H   AD  V LG + AA+SYL+ +
Sbjct: 5   ILVANRGEIACRVFRTAKRMGIATVAVYSDADARAPHVLMADEAVRLGPAPAAESYLKAE 64

Query: 69  KLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKALME 128
            ++AAAKA+GA AIHPGYGFLSE   FARA   AG+ F+GPP  AI AMG K  +K L +
Sbjct: 65  LILAAAKATGADAIHPGYGFLSERESFARACAEAGIAFVGPPPGAIAAMGDKIESKKLAK 124

Query: 129 TAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188
            AGV +VPG+ G   D E        IGYPV++KA+AGGGGKGM++      + E   + 
Sbjct: 125 EAGVNVVPGFVGVIDDTEHAVKIAAEIGYPVMMKASAGGGGKGMRLAYSEQDVREGFEAT 184

Query: 189 QREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248
           +RE L+SFGD R+ +EK++  PRH+EIQV  DQHGN +YL ER+CSIQRRHQKVVEEAP+
Sbjct: 185 KREGLASFGDDRVFIEKFIESPRHIEIQVLGDQHGNIVYLGERECSIQRRHQKVVEEAPS 244

Query: 249 PGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLL---DARGE-FFFMEMNTRLQVEHPVT 304
           P ++PE+RR MGE AV  ++A+GY  AGTVE ++   D  GE F+F+EMNTRLQVEHPVT
Sbjct: 245 PFVTPEMRRKMGEQAVALSRAVGYYSAGTVELIVSGADTSGEGFYFLEMNTRLQVEHPVT 304

Query: 305 EAITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYRE 364
           EA+TGLDLV   IRVA GE L   QD V L G AIE R+YAEDP   FLP+TGRL  YR 
Sbjct: 305 EAVTGLDLVEQMIRVAAGETLAFGQDDVKLTGWAIENRIYAEDPYRSFLPSTGRLVRYRP 364

Query: 365 SAA---------GPGR-RVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDE 414
            AA         G G  RVD GV EG E+S FYDPM+ KLI WG+ R+ A    ++ LD 
Sbjct: 365 PAAQDTPYGEVGGEGYVRVDDGVAEGGEVSMFYDPMIAKLITWGQTRDAAADLQVAALDR 424

Query: 415 FAIGGLKTNINFLRRIIGHPAFAAAELDTGFI-PRYQEQLLPAPSDLSDEFWQAAAQAFA 473
           F + GL  NI+FL  ++ HP F + EL TGFI   Y E    AP+D +    + A  A  
Sbjct: 425 FELEGLGNNIDFLSALMQHPRFRSGELTTGFIAEEYPEGFAGAPAD-AMLTRRLATIAAV 483

Query: 474 QSQSSTTRADDLSSPWGIGNGFRAGLPT---EITLHLSCEEQDRALTLGDADAHTAQLKG 530
            S   + RA  +S   G        +P    +  +HL+    +  ++LGD     A + G
Sbjct: 484 LSWRQSERASMISGQLG-------AMPVAKRDWVVHLAAIAHE--VSLGDG----AIVDG 530

Query: 531 EYLLTEHNGLRRQHRAIRRGDT-------------LYLQWDGELRRIESYDPISAVEASH 577
           E +            A+ RGD                L   G   R+E Y P  A  A H
Sbjct: 531 ELVEGSVEWAPGDRIAVARGDDGELAVRVAKTRTGWVLTTRGAAHRVEVYRPRVAELAKH 590

Query: 578 -------SHQGGLTAPMNGSIVRVLVEAGQTVEAGAQLVVLEAMKMEHSIRAPHAGIIKA 630
                       L APM G + RV V  G  VEAG  L V+EAMKME+ +RA   G++KA
Sbjct: 591 MIEKIPPDMSRFLLAPMPGLLTRVEVAVGDKVEAGQPLAVVEAMKMENILRAEKTGVVKA 650

Query: 631 LYCQEGEMVSEGSALVELE 649
           +    GE ++  +A++E E
Sbjct: 651 VNFGAGESLAVDAAILEFE 669


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: 1093
Number of extensions: 46
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: 651
Length of database: 669
Length adjustment: 38
Effective length of query: 613
Effective length of database: 631
Effective search space:   386803
Effective search space used:   386803
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 Apr 09 2024. 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources