GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Rhodococcus qingshengii djl-6-2

Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate WP_050656086.1 C1M55_RS09265 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_002893965.1:WP_050656086.1
          Length = 679

 Score =  533 bits (1373), Expect = e-155
 Identities = 308/658 (46%), Positives = 404/658 (61%), Gaps = 22/658 (3%)

Query: 6   LTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYL 65
           + T+LVANRGEIA RV+RT + LG+ +VAV+S  D +ARH READ  V++G + A +SYL
Sbjct: 7   IDTVLVANRGEIAVRVIRTLRELGIRSVAVYSDADANARHVREADTAVNIGPAAARESYL 66

Query: 66  QIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKA 125
            IDK+I AAK++GAQ IHPGYGFLSEN+ F+ A  AAG+ FLGP   AI+ MG K  AK 
Sbjct: 67  VIDKVIDAAKSTGAQGIHPGYGFLSENSAFSAACAAAGIAFLGPSEHAIEVMGDKITAKN 126

Query: 126 LMETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEAL 185
            +    VP+VPG        E    A E IGYPVL+K +AGGGGKGM++VED + LAEAL
Sbjct: 127 SVAAFDVPVVPGIARPNLTDEELIAAAEDIGYPVLVKPSAGGGGKGMRLVEDPANLAEAL 186

Query: 186 ASAQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEE 245
            SA+REA SSFGD  + +E+++L+PRH+E+QV ADQHGN ++L ER+CS+QRRHQKV+EE
Sbjct: 187 RSARREAASSFGDDTLFLERFVLRPRHIEVQVLADQHGNVVHLGERECSLQRRHQKVIEE 246

Query: 246 APAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLL--DARGEFFFMEMNTRLQVEHPV 303
           AP+P L    R  +G AA  +A+++ Y GAGTVEF++  D   EFFFMEMNTRLQVEHPV
Sbjct: 247 APSPLLDQVTRDRIGAAACNTARSVDYTGAGTVEFIVSADKPDEFFFMEMNTRLQVEHPV 306

Query: 304 TEAITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYR 363
           TE +TGLDLV WQ+RVA GE L  +Q  + L GHAIE R+YAEDPG  FLP  GR+    
Sbjct: 307 TEMVTGLDLVEWQVRVAAGEKLAFSQSDITLTGHAIEARVYAEDPGRGFLPTGGRVVDLV 366

Query: 364 ESAAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKTN 423
           E  +G G RVDSG+  G  +   YDPML K+IA   DR  A  +L   L + A+ G+ TN
Sbjct: 367 E-PSGSGVRVDSGLLAGTVVGSDYDPMLSKVIAHAPDRAGALRKLDRALGDTAVLGVVTN 425

Query: 424 INFLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTTRAD 483
           I F R ++  P   A  LDTG + R  E  + A  D SDE   AAA     S+ +T+   
Sbjct: 426 IEFARFLLADPDVIAGNLDTGLLDRRVEDFVAA--DASDEVLIAAAAYRWLSRWTTSERF 483

Query: 484 DLSSPWGIGNGFRAGLPTEITLHLSCEEQDRALTL-------------GDADAHTAQLKG 530
           D   PW + +G+R G P   ++ LS   +   + +                 A +A L G
Sbjct: 484 D---PWDVPSGWRVGTPAPTSIRLSAGTRTAHVAIVGVPAAAKVEVEGSQPRAFSATLTG 540

Query: 531 EYLLTEHNGLRRQHRAIRRGDTLYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGS 590
             L    +G RR          L+L   G     E  +     E  H+    + +PM G+
Sbjct: 541 SELAVVIDGRRRTFVVAETDGGLWLAGGGTWHVREVAEVSVRGEDKHAGDAEIASPMPGA 600

Query: 591 IVRVLVEAGQTVEAGAQLVVLEAMKMEHSIRAPHAGIIKALYCQEGEMVSEGSALVEL 648
           ++ V VE G  V AG  LVV+EAMKMEHS+ +P  GI++ L  ++G+ V     L  +
Sbjct: 601 VIAVNVENGAAVSAGQPLVVVEAMKMEHSLTSPIDGIVEVL-VRQGDQVMVDQVLARV 657


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: 1039
Number of extensions: 43
Number of successful extensions: 6
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: 679
Length adjustment: 38
Effective length of query: 613
Effective length of database: 641
Effective search space:   392933
Effective search space used:   392933
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