GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Pseudomonas fluorescens FW300-N1B4

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate Pf1N1B4_1787 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1787
          Length = 408

 Score =  354 bits (908), Expect = e-102
 Identities = 188/405 (46%), Positives = 258/405 (63%), Gaps = 6/405 (1%)

Query: 292 PRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGL 351
           P  + R A+IGAGTMG GI M  ANAG+PV  ++   + L++ L  + + +     +G +
Sbjct: 5   PFDIQRAAVIGAGTMGRGIVMCLANAGVPVQWVDNNPQMLEQALTSVAETYAHNVRQGRI 64

Query: 352 PPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTS 411
                  R+A +T       ++D DL+IEAV+E + +K+++F  +D   KP A+LASNTS
Sbjct: 65  VQAEADARIARVTAAADYAAIRDVDLVIEAVYENLELKQKIFRELDGLLKPEAILASNTS 124

Query: 412 YLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPV 471
            L ID IAA T+RPQ VLG+HFFSPA++MKL EIVRGA+T P  L  A+ + K++ KV V
Sbjct: 125 ALDIDAIAAATRRPQQVLGLHFFSPAHIMKLLEIVRGAQTEPAVLDAALELGKRMGKVSV 184

Query: 472 VVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGW 531
           V G C GF+GNRML     ++ K+L EGALP QVDA +  FG  MGPF M D+ G+D+ W
Sbjct: 185 VSGNCHGFIGNRMLHPYVLEARKMLLEGALPYQVDAALQGFGFAMGPFRMYDVVGIDLEW 244

Query: 532 RSRKDRG-----IKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLA 586
           R+R+  G      + ++ + LCE GRFGQK+G GYY YE GSR    D EV+ L+ +   
Sbjct: 245 RARELAGKGQDAPEVQVDNRLCELGRFGQKSGDGYYHYEPGSRQAEHDLEVDALVLEVSE 304

Query: 587 KLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMH 646
            LG +RR+I  EE+LER +  ++NEGA+IL+E IAA   DID+V+L GYG+P  +GGPM 
Sbjct: 305 GLGFQRREIGPEEVLERCLLALVNEGAKILQEGIAASAHDIDLVYLNGYGFPADKGGPMA 364

Query: 647 YADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTFASL 691
           +AD  GL+ I  RL        D    PA L+  L AEG+ FA +
Sbjct: 365 WADQQGLEDIHLRLLQLETKQGD-HWAPARLIGELVAEGRGFADV 408


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: 611
Number of extensions: 26
Number of successful extensions: 2
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: 408
Length adjustment: 35
Effective length of query: 664
Effective length of database: 373
Effective search space:   247672
Effective search space used:   247672
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: 52 (24.6 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