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_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:

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:

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:

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:

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