Aligments for a candidate for pimF in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Aligments for a candidate for pimF in Cupriavidus basilensis 4G11

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate RR42_RS22630 RR42_RS22630 3-hydroxyacyl-CoA dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS22630
          Length = 696

 Score =  658 bits (1697), Expect = 0.0
 Identities = 355/692 (51%), Positives = 472/692 (68%), Gaps = 16/692 (2%)

Query: 10  QDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFG 69
           Q ++AI+ +D+PPVN L   VR G+ + +  A  D AV AIV++ AG+ F  GADI +F 
Sbjct: 9   QGRIAILLLDNPPVNGLGDTVRLGLFDGIAQATQDDAVAAIVILGAGKVFCGGADIRQFN 68

Query: 70  KPPQP--PALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVK 127
            P     P L  VIA +E S KP +AAIHG ALGGG+E+ALGCH+R+A  +A LGLPEV 
Sbjct: 69  APAASAQPTLRQVIARIEQSAKPVVAAIHGVALGGGMELALGCHYRIASADASLGLPEVN 128

Query: 128 LGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE-NLVAGAVAFAK 186
           LGL+PG GGTQRLPR +G   A+++I GG P+   +A+  G+ + +++ + +A A+AFA+
Sbjct: 129 LGLVPGGGGTQRLPRLIGVPAALELIQGGKPVRGDKAVALGMADALIDGDPLAAAMAFAE 188

Query: 187 KVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLP 246
           +V      L       ++   A A    F    AA++ KAR   A  A    + AA  LP
Sbjct: 189 RVAG----LPGAHPVIARRPCADAAGVDFAARSAAVSAKARNALAQRAAIACVQAATRLP 244

Query: 247 FEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTM 306
            + GL  ER  F +LV S +SKA R+ FFAEREA KV  +P G   R V+RV I+GAGTM
Sbjct: 245 IDAGLDDERARFDQLVASTESKALRHLFFAEREAPKVAALPAGASLRTVARVGILGAGTM 304

Query: 307 GGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGL 366
           G GIAM+FANAGI VTL+E  +  L RGL ++++N+E TAA+G L     A+RMA IT  
Sbjct: 305 GAGIAMAFANAGIAVTLLEQQQAALDRGLAMIRRNYEITAAKGKLTAQEIAQRMACITPT 364

Query: 367 VGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQ 426
           +    + DADL+IEAVFE MAVKK VF  +DA  KPGA+LA+NTS LSID IAA+T RPQ
Sbjct: 365 LADAALADADLVIEAVFEDMAVKKAVFARLDALCKPGAILATNTSRLSIDVIAASTSRPQ 424

Query: 427 DVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLA 486
           DV+G+HFFSPANVMKL E+V+G +TAP+ + T + +A+ I K+PV+V VC+GFVGNRML 
Sbjct: 425 DVIGLHFFSPANVMKLLEVVQGERTAPEVIATCMKMARAIGKIPVLVRVCEGFVGNRMLT 484

Query: 487 ARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIK------ 540
              +++  LL EGA PQQVD  +T+FGM MGP AM DLAG+DI W +RK           
Sbjct: 485 PYWREAGFLLEEGASPQQVDGALTRFGMAMGPLAMADLAGMDINWATRKRLAPTRPAHLR 544

Query: 541 -SEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEE 599
            S++AD +CE GRFGQKT  GYY+YE GSRAP+PDP V+ LI    A+ G++RR+++DEE
Sbjct: 545 YSKVADRICEQGRFGQKTNAGYYRYEAGSRAPLPDPAVDALIRACAAEAGIERREVSDEE 604

Query: 600 ILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAER 659
           I+ER +  + NEGARILEE IA R +DIDVV+++GYG+P +RGGPM +A+++GL    E+
Sbjct: 605 IVERCMLALANEGARILEEGIARRAADIDVVYVHGYGFPAWRGGPMFHAETIGLGRTLEK 664

Query: 660 LSAYAKATNDPSLEPAPLLARLAAEGK-TFAS 690
           + A   A +     PAPLL RL A+G+ TFA+
Sbjct: 665 IRA-LNAIHGEHWTPAPLLVRLVAQGRETFAA 695


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: 1160
Number of extensions: 50
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: 696
Length adjustment: 39
Effective length of query: 660
Effective length of database: 657
Effective search space:   433620
Effective search space used:   433620
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, or view the source code.

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