Alignments for a candidate for pimF in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Cupriavidus basilensis 4G11

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate RR42_RS11095 RR42_RS11095 3-hydroxyacyl-CoA dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS11095
          Length = 693

 Score =  696 bits (1797), Expect = 0.0
 Identities = 365/688 (53%), Positives = 482/688 (70%), Gaps = 13/688 (1%)

Query: 10  QDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFG 69
           QD VA++T+D+PPVN L  + R GI+E +  A+ D AV+AIV+  AG+ F  GADI EF 
Sbjct: 8   QDGVAVITLDNPPVNGLGLSTRLGIVEGMTRALDDAAVKAIVITGAGKAFSGGADIREFN 67

Query: 70  KPP--QPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVK 127
            P   Q P L+ VI  +E S KP +AAIH  A+GGGLE+ALGC++RVA K A++ LPEVK
Sbjct: 68  TPKATQEPTLHSVIKVVEGSSKPVVAAIHSVAMGGGLELALGCNYRVASKGAQIALPEVK 127

Query: 128 LGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE-NLVAGAVAFAK 186
           LGLLPGAGGTQRLPR +G E A+ MIV G+ I + +     L +E+V+ +++  AVAFAK
Sbjct: 128 LGLLPGAGGTQRLPRVIGLEAALNMIVSGNAIPSEKFAGTKLFDEIVDGDVLPAAVAFAK 187

Query: 187 KVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLP 246
              A   P  ++RD   K   A+   +   N VAA+   A+   AP  C DA+ A++  P
Sbjct: 188 TAAANPGPYPKVRDLKVKHENAEGFIAFSRNTVAAV---AKNFPAPLKCVDAVAASLK-P 243

Query: 247 FEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTM 306
           FE GLK EREGFM L+ + +S+A R+AFF ER A+K+  VP+GT  R + RVA+IGAGTM
Sbjct: 244 FEAGLKAEREGFMYLITTPESRALRHAFFGERAASKIPDVPEGTATRKIERVAVIGAGTM 303

Query: 307 GGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGL 366
           GGGI M+F NAG+PV ++ET +E L RG+  ++KN+E +A +G L  +   +RM L+T  
Sbjct: 304 GGGITMNFLNAGVPVIMLETKQEALDRGVATIRKNYENSAKKGKLTQEKVEQRMGLLTTT 363

Query: 367 VGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQ 426
           +  + +KDAD++IEAVFE M VK+ VF  +D   K GA+LASNTS L +++IA+ TKRPQ
Sbjct: 364 LSYDEIKDADMVIEAVFEEMGVKEIVFKKLDEVMKQGAILASNTSTLDVNKIASFTKRPQ 423

Query: 427 DVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLA 486
           DV+GMHFFSPANVMKL E+VRG KT  D L T + +AKKI K  VV GVCDGF+GNRM+ 
Sbjct: 424 DVVGMHFFSPANVMKLLEVVRGEKTGKDVLATVMQLAKKIKKTAVVSGVCDGFIGNRMIE 483

Query: 487 ARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIK------ 540
             S+Q+  LL EGALP+QVD  + KFG  MGPF MGDLAG DIGW  RK R I       
Sbjct: 484 QYSRQAGYLLDEGALPEQVDKAIEKFGFAMGPFRMGDLAGNDIGWAIRKRRAIDKPEIQY 543

Query: 541 SEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEI 600
           S+ AD LCE GR+GQKTG G+Y Y+ G R P P+ +V  +I      LG+ RR I+DEEI
Sbjct: 544 SKTADLLCELGRYGQKTGAGWYDYKAGDRKPYPNQQVNDMIVQHSKDLGITRRKISDEEI 603

Query: 601 LERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERL 660
           +ER+V+ ++NEGA+ILEE IA++ SDID+V+L GYG+P++RGGPM YAD VGL ++A+ +
Sbjct: 604 VERLVFALVNEGAKILEEGIASKASDIDMVYLTGYGFPLFRGGPMLYADQVGLFNVAQSM 663

Query: 661 SAYAKATNDPSLEPAPLLARLAAEGKTF 688
           + YAK  +  + + APLL +LAAEGK F
Sbjct: 664 ARYAKGYHGEAWQAAPLLVKLAAEGKGF 691


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: 1119
Number of extensions: 49
Number of successful extensions: 8
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: 693
Length adjustment: 39
Effective length of query: 660
Effective length of database: 654
Effective search space:   431640
Effective search space used:   431640
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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