Alignments for a candidate for pimF in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Sphingomonas koreensis DSMZ 15582

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate Ga0059261_2827 Ga0059261_2827 3-hydroxyacyl-CoA dehydrogenase

Query= metacyc::MONOMER-20678
         (699 letters)



>FitnessBrowser__Korea:Ga0059261_2827
          Length = 683

 Score =  597 bits (1538), Expect = e-175
 Identities = 320/692 (46%), Positives = 445/692 (64%), Gaps = 17/692 (2%)

Query: 1   MSEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFI 60
           ++E  +   +D VAIVT+D PPVNA+S A+  G+ + + AA++D A +AIVL+CAGRTFI
Sbjct: 4   INEGTSLTVEDGVAIVTLDFPPVNAMSPALMDGLYDALMAALSDDAAKAIVLICAGRTFI 63

Query: 61  AGADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK 120
           AGAD+   GK         +  ++ENSPKPT+AA+HGTALGGG+E AL  H+R+AV  A+
Sbjct: 64  AGADLKSLGKVQPKVDFFALQDSIENSPKPTVAALHGTALGGGMETALTFHYRIAVPSAR 123

Query: 121 LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVEN--LV 178
           +GLPEV LGLLPG GGTQRLPR  G E A+ +++ G  +GA EAL  GL++ +     L 
Sbjct: 124 MGLPEVNLGLLPGGGGTQRLPRITGAEAALDLLISGRQVGAKEALTIGLIDRLAAEGALR 183

Query: 179 AGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADA 238
             A+AFAK+++    P +R+RD ++K+AA + D ++F     +  K+  GL+AP A    
Sbjct: 184 EDAIAFAKELVDAGEPPKRIRDCEAKVAADRKDANLFERFRTSHAKQLNGLDAPQAIVRC 243

Query: 239 IGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRV 298
           + AA+  P+E+GL  ER  F  L+   QS A R+ F AER A K+ G+       PV++V
Sbjct: 244 VEAAVAGPWEKGLAIERTEFQTLLAGPQSAALRHVFMAERAAQKIPGLRADLPLIPVTKV 303

Query: 299 AIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAK 358
            I+GAGTMG GIAM+F  AG  VT++ET +  L RG+  +    ++   RG L  D    
Sbjct: 304 GIVGAGTMGSGIAMAFLAAGFAVTVVETQQAALDRGVAHITATLQSRVERGKLAADKAEA 363

Query: 359 RMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEI 418
           ++A +T  + L  + DADL++EA+FE +A K+ +F  + A  +P  +LA+NTS+L +D I
Sbjct: 364 QIAALTPTLDLSALADADLVVEAIFENLAAKQALFGTLSAIVRPDTILATNTSFLDVDAI 423

Query: 419 AATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDG 478
           AA    P+ VLGMHFFSPANVM+L E+VR AKT+   L + +++AKK+ K  VV GVC G
Sbjct: 424 AAGAAGPERVLGMHFFSPANVMRLLEVVRAAKTSEAVLASVMALAKKLGKAAVVSGVCFG 483

Query: 479 FVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRG 538
           F+GNRMLAAR   ++ ++  G LP  +D ++T FG PMGPFAM DLAGLDIGW    D  
Sbjct: 484 FIGNRMLAARQVHADAMVLAGVLPWNIDRILTGFGFPMGPFAMLDLAGLDIGWEGDTD-- 541

Query: 539 IKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDE 598
               +   L  AGR GQK+G GYY YE  ++ P P      +I   LA +      ++D 
Sbjct: 542 ---SVKSRLVAAGRKGQKSGAGYYDYE--NKTPSPSQTALDVIAG-LASVAPGSVTLSDR 595

Query: 599 EILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAE 658
           EIL+R++ PMINEGA+ILEE IA R SDID+VW+ GYGWP   GGPM +AD++GL  + +
Sbjct: 596 EILDRLLLPMINEGAKILEEGIALRGSDIDLVWITGYGWPAQTGGPMFHADAIGLTRVVD 655

Query: 659 RLSAYAKATNDPSLEPAPLLARLAAEGKTFAS 690
            L           +EPA LL +LA+EG + A+
Sbjct: 656 GL-------RHMGVEPAALLLKLASEGGSLAA 680


Lambda     K      H
   0.317    0.134    0.383 

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: 1111
Number of extensions: 43
Number of successful extensions: 5
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: 699
Length of database: 683
Length adjustment: 39
Effective length of query: 660
Effective length of database: 644
Effective search space:   425040
Effective search space used:   425040
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 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:

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 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