Alignments for a candidate for liuB in Sphingomonas histidinilytica UM2

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Sphingomonas histidinilytica UM2

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_079649074.1 B5X82_RS15605 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_900167915.1:WP_079649074.1
          Length = 660

 Score =  525 bits (1351), Expect = e-153
 Identities = 313/674 (46%), Positives = 401/674 (59%), Gaps = 37/674 (5%)

Query: 1   MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60
           MF K+LIANRGEIACR+I+TARR+GI+TVAVYSDAD  A HV +ADEA+ IG +PA+ESY
Sbjct: 1   MFKKILIANRGEIACRVIKTARRMGIKTVAVYSDADARAPHVEMADEAVHIGASPASESY 60

Query: 61  LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120
           L +  I+QA +  GA+A+HPGYGFLSE   FAEA+A A + F+GPP  AI AMG K  +K
Sbjct: 61  LVADKIIQACKDTGAEAVHPGYGFLSERTSFAEALAAANIAFIGPPANAIAAMGDKIESK 120

Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180
            L +++GV VVPGY GE  D       A +IGYPV++KA AGGGGKGMR    ++D    
Sbjct: 121 KLAKQAGVNVVPGYVGEIDDTDHAVRIANDIGYPVMMKASAGGGGKGMRLAYSEKDVREN 180

Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240
            E+ +RE  ++FGD  V +E+++  PRHIE+QV GD+HGNIV+L ER+CS+QRRHQKV+E
Sbjct: 181 FESVKREGLNSFGDDRVFIEKFIESPRHIEIQVLGDKHGNIVYLNERECSIQRRHQKVVE 240

Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFI---ADVTNGLWPDHFYFMEMNTR 297
           EAP+P ++ E+R+AMG+  V  A+A+GY  AGTVE I   AD T       FYF+EMNTR
Sbjct: 241 EAPSPFVSPEMRKAMGEQCVALARAVGYHSAGTVELIVSGADTTG----QGFYFLEMNTR 296

Query: 298 LQVEHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPAT 357
           LQVEHPVTE ITG+DLVE  +RVA GE L   QAD+ +NGWA E R+YAEDP RGFLP+T
Sbjct: 297 LQVEHPVTECITGLDLVEQMIRVAYGEKLAFTQADVKINGWAVENRVYAEDPYRGFLPST 356

Query: 358 GRLTELSFPEGTS--RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECR 415
           GRL     P      RVD GV +G  I+ +YDP+IAKLI  G+ R AA+ R   AL    
Sbjct: 357 GRLVRYRPPAEVDNVRVDDGVYEGSEISMFYDPMIAKLITWGETREAAIDRQIAALDRFE 416

Query: 416 IGGTVTNRDFLIRLTEEHDFRSGHPDTGLIDREI-ERLTAPVAPGDEALALAAIFST-GA 473
           I G   N DFL  L +   FRSG+  TG I  E  E  T   A     L LAA+     +
Sbjct: 417 IDGIGHNVDFLSALMQHPRFRSGNITTGFIAEEFPEGFTGAAADARLGLHLAAVAGVLAS 476

Query: 474 LDPNRSTD-------PWSSLGSWQIWGD-AHRMVVI----EHADVRATVTLASRGRDQFA 521
           +D  R+         P     SW +  D   R + I       D    V  A     Q  
Sbjct: 477 IDAARAAQIDGRLNGPADPSTSWVVTLDKVERQIEILGDAVSVDGTPVVVDAPYAPGQKL 536

Query: 522 VRAGASTLPVLV-LDRFEGGARLEVAGQKRLIRFSRDREALTLFHGGRNLVFHVPDGLTG 580
           V A     P+ + ++R   G R    G    +R    R A    H    ++  +P  ++ 
Sbjct: 537 VEALIDGEPLSIRVERKRTGWRFTTRGASHELRVLTPRVAALSHH----MIEKIPPDMS- 591

Query: 581 GQSSEIADDELVAPMPGLVKLVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIANVH 640
                     L+ PMPGLV  + V  G  V  GQ L V+EAMKME  L A + GT+  V 
Sbjct: 592 --------RFLLCPMPGLVTAIHVAEGAKVEAGQPLAVVEAMKMENILRAEKAGTVKAVA 643

Query: 641 VAEGAQVSEGTVLV 654
              G  ++   V++
Sbjct: 644 AKAGDSLAVDAVIL 657


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: 1098
Number of extensions: 48
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 662
Length of database: 660
Length adjustment: 38
Effective length of query: 624
Effective length of database: 622
Effective search space:   388128
Effective search space used:   388128
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 24 2021. The underlying query database was built on Sep 17 2021.

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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