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 methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate Ga0059261_4056 Ga0059261_4056 Acetyl/propionyl-CoA carboxylase, alpha subunit

Query= BRENDA::Q9I299
         (655 letters)



>FitnessBrowser__Korea:Ga0059261_4056
          Length = 626

 Score =  563 bits (1451), Expect = e-165
 Identities = 328/653 (50%), Positives = 420/653 (64%), Gaps = 34/653 (5%)

Query: 8   IQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYL 67
           I  LL+ANRGEIACR++R+AR LGI +VAV+SD D HA HV EAD AV +GG++  +SYL
Sbjct: 2   INSLLIANRGEIACRIIRTARKLGIRTVAVYSDADAHALHVREADQAVHIGGSQARESYL 61

Query: 68  RGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKA 127
            G+R+IAAA  +GA+AIHPGYGFLSENADFA A   AGL+++GP   +I AMG K AAK 
Sbjct: 62  VGERVIAAAKETGAEAIHPGYGFLSENADFAEAVVAAGLIWVGPNPDSIRAMGLKDAAKK 121

Query: 128 LMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEAL 187
           LM++A VP+ PGY GE Q L+  +REA +IGYPVL+KA AGGGGKGM+ V+   + A+AL
Sbjct: 122 LMQDARVPVTPGYLGEDQSLDRLQREADKIGYPVLIKAVAGGGGKGMRRVDVAEDFADAL 181

Query: 188 SSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEE 247
           +S QREA ++FGD R+L+EKY+L PRH+E+QVF D HG+ ++L ERDCS+QRRHQKV+EE
Sbjct: 182 ASCQREAASSFGDDRVLIEKYILAPRHIEVQVFGDSHGNIVHLFERDCSMQRRHQKVIEE 241

Query: 248 APAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLD-----ERGQFFFMEMNTRLQVE 302
           APAPG+    R A+ EAAV+AA+A+ YVGAGT+EF+ D        + +FMEMNTRLQVE
Sbjct: 242 APAPGMDKSARFAVCEAAVKAARAVNYVGAGTIEFIADASQGLHADRIWFMEMNTRLQVE 301

Query: 303 HPVTEAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLM 362
           HPVTEAITG+DLV WQ+RVA GE LPL QE++ ++GHAIE RLYAEDP   FLP++G+L 
Sbjct: 302 HPVTEAITGVDLVEWQLRVASGEPLPLRQEEIAISGHAIEARLYAEDPARGFLPSTGKL- 360

Query: 363 LYREAAAGP-GRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGG 421
              E    P   RVD+GV  G  +SPFYDPM+AKLI   +TREEA   L + L+  +V  
Sbjct: 361 ---EVLDFPVNARVDTGVEAGSVISPFYDPMIAKLIVHSDTREEAIALLRSELSYLTVWP 417

Query: 422 LRTNLAFLRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAEAWLQSEPGH 481
           +RTN  FL R+LG   F  A+LDTG I R  + L   P  LP       A  WL+++   
Sbjct: 418 VRTNAGFLFRLLGDGDFVRAQLDTGLIERRGEVLTIDP--LPTAADLTRATYWLETD--- 472

Query: 482 RRDDDPHSPWSRNDGWRSALARESDLMLRCRDERRCVRLRHASPSQYRLDGDDLVSRVDG 541
               D  S     +G+R   +  +   L    ER            +  D  D+ S   G
Sbjct: 473 -IPSDTLSMAHGLEGFRLNRSPVTQRALAVNGER----------IVFTADHGDIASHFYG 521

Query: 542 VTRRSAALRRGRQLFLEWEGELLAIEAVDPIAEAEAAHAHQGGLSAPMNGSIVRVLVEPG 601
             R  AAL       L   G    + A D    A  A A  G + APM G IV V V  G
Sbjct: 522 HERDGAAL-------LVHGGATFRVTA-DRTDGAAGAAAGDGSILAPMPGRIVSVEVAEG 573

Query: 602 QTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEGTPLVELDENQ 654
           Q V AG  L+VLEAMKME ++ AP  G ++ L    G  V+    LV++ + +
Sbjct: 574 QAVIAGQKLLVLEAMKMEQALTAPFDGTIETLNAVAGAQVQVDALLVKVAKGE 626


Lambda     K      H
   0.319    0.135    0.397 

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: 960
Number of extensions: 38
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: 655
Length of database: 626
Length adjustment: 38
Effective length of query: 617
Effective length of database: 588
Effective search space:   362796
Effective search space used:   362796
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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