GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Pseudomonas simiae WCS417

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate GFF4142 PS417_21215 3-hydroxyacyl-CoA dehydrogenase

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



>FitnessBrowser__WCS417:GFF4142
          Length = 715

 Score =  263 bits (673), Expect = 2e-74
 Identities = 213/717 (29%), Positives = 333/717 (46%), Gaps = 51/717 (7%)

Query: 10  QDQVAIVTVDSP--PVNALSAAVRRGI---LENVNAAVADPAVQAIVLVCAGRTFIAGAD 64
           QD + ++T+D P    N ++ A R  +   +E + A   D A   +V+  A +TF AG D
Sbjct: 11  QDGIVVLTLDMPGQSANTMNGAYREAMAAMVERLEAQKDDLA--GVVITSAKKTFFAGGD 68

Query: 65  ITEFGKPPQPPA---------LNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVA 115
           + E  K  +  A         L   +  LE   KP +AAI+G ALGGG E+ L CH+RVA
Sbjct: 69  LNELIKVDKAHAKDFYDSVRELKAQLRRLETLGKPVVAAINGAALGGGWEICLACHYRVA 128

Query: 116 V--KEAKLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEV 173
           +  K  +LGLPEV LGLLPG GG  R+ R +G E A+  ++ G  +   +AL+ GLV E+
Sbjct: 129 LDDKSVQLGLPEVTLGLLPGGGGVVRMVRMLGLEKALPYLLEGKKVRPQQALQAGLVNEL 188

Query: 174 V---ENLVAGAVAFAKKVLAEKRPL-RRLRDDDSKLAAAKADRSIFTNAVAAMTKKARG- 228
               + L+A + A+       K+P   +         ++     +   A + +  K +G 
Sbjct: 189 AADRDELLAKSRAWILANPDAKQPWDNKGYQIPGGTPSSPKVAQMLAIAPSILRSKTQGC 248

Query: 229 LEAP--FACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAF-FAEREAAKVDG 285
             AP    CA   GA +D  F+     E   F +LV    +K     F F   E      
Sbjct: 249 FPAPEKILCAAVEGAQVD--FDTAHLIETRYFTELVTGQVAKNMIGTFWFQLNEINAGSS 306

Query: 286 VPDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEAT 345
            P G  P    +V ++GAG MG GIA   A+AGI V L +      ++G        +  
Sbjct: 307 RPQGFAPYVTRKVGVLGAGMMGAGIAYVSASAGIEVVLKDINLAAAEKGKAHSAALLDKK 366

Query: 346 AARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAV 405
            +RG L  +     +A I      E++   DLIIEAVFE   +K +V  A  +     AV
Sbjct: 367 VSRGQLTAEQRETFLARIHPTATDEDLAGCDLIIEAVFEDRELKAKVSAAAQSVVGADAV 426

Query: 406 LASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKK 465
           +ASNTS L I  +A         +G+HFFSP + M L EI++GA+T+ + L        +
Sbjct: 427 IASNTSTLPISGLATAVPDQTRFIGLHFFSPVDKMPLVEIIKGARTSDETLARGFDFVLQ 486

Query: 466 IAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLA 525
           I K P+VV    GF  +R+    + +   +L EG     ++    K GMP+GP A+ D  
Sbjct: 487 IKKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGVAAPMIETEARKAGMPVGPLAVSDEV 546

Query: 526 GLD----IGWRSRKD-----RGIKSEIADALC-----EAGRFGQKTGKGYYKYEQGSRAP 571
            L     I  ++ KD     + + +  A A+      E  R G+  G G+Y Y  G    
Sbjct: 547 SLSLMNHIRQQTAKDLQAEGKAVPTHPATAVIDLLVNEYQRMGKAAGGGFYDYPSGGH-- 604

Query: 572 MPDPEVETLINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVW 631
                 + L  +  ++     + I+ +++ +R+++    E  R +EE +    +D +V  
Sbjct: 605 ------KYLWPELKSRFERPDQRISPQDVRDRLLFIQAIETVRCVEEGVLMSTADANVGS 658

Query: 632 LYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688
           ++G G+  + GG + + +  GL     R    A+   +  + PA LL + AA+G  F
Sbjct: 659 IFGIGFAPWSGGALQFINQYGLNDFIARARYLAEQYGERFMPPALLLEK-AAQGDVF 714


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: 1033
Number of extensions: 51
Number of successful extensions: 6
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: 715
Length adjustment: 39
Effective length of query: 660
Effective length of database: 676
Effective search space:   446160
Effective search space used:   446160
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: 55 (25.8 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