Alignments for a candidate for pimF in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Escherichia coli BW25113

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 17892 b3846 fused 3-hydroxybutyryl-CoA epimerase/delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase/enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase (NCBI)

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



>FitnessBrowser__Keio:17892
          Length = 729

 Score =  347 bits (891), Expect = e-100
 Identities = 232/674 (34%), Positives = 359/674 (53%), Gaps = 39/674 (5%)

Query: 10  QDQVAIVTVDSP-PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEF 68
           +D +A +  D+P  VN L  A    + E +        ++ ++L      FI GADITEF
Sbjct: 14  EDGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQSDLKGLLLRSNKAAFIVGADITEF 73

Query: 69  GKPPQPPA---------LNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEA 119
                 P           N V   LE+ P PTIAA++G ALGGG E  L   +R+A  + 
Sbjct: 74  LSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCECVLATDYRLATPDL 133

Query: 120 KLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV--ENL 177
           ++GLPE KLG++PG GG+ R+PR +G + A+++I  G  +GA +ALK GLV+ VV  E L
Sbjct: 134 RIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDVGADQALKIGLVDGVVKAEKL 193

Query: 178 VAGAVAFAKKVL---AEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKA-RGLEAPF 233
           V GA A  ++ +    + +  R+ + +  KL+  +A  S FT A   + + A +   AP 
Sbjct: 194 VEGAKAVLRQAINGDLDWKAKRQPKLEPLKLSKIEATMS-FTIAKGMVAQTAGKHYPAPI 252

Query: 234 ACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAF----FAEREAAKVDGVPDG 289
                I AA     EE L  E + F+ L  +++++A    F    + + +A K+    D 
Sbjct: 253 TAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVKGKAKKL--TKDV 310

Query: 290 TKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARG 349
             P+   + A++GAG MGGGIA   A  G+PV + +  ++ L  G+    K       RG
Sbjct: 311 ETPK---QAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLLNKQLERG 367

Query: 350 GLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASN 409
            +     A  ++ I   +        D+++EAV E   VKK V    +   +   VLASN
Sbjct: 368 KIDGLKLAGVISTIHPTLDYAGFDRVDIVVEAVVENPKVKKAVLAETEQKVRQDTVLASN 427

Query: 410 TSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKV 469
           TS + I E+A   +RP++  GMHFF+P + M L EI+RG K++ + +   V+ A K+ K 
Sbjct: 428 TSTIPISELANALERPENFCGMHFFNPVHRMPLVEIIRGEKSSDETIAKVVAWASKMGKT 487

Query: 470 PVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTK-FGMPMGPFAMGDLAGLD 528
           P+VV  C GF  NR+L        +LL +GA  +++D V+ K FG PMGP  + D+ G+D
Sbjct: 488 PIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKIDKVMEKQFGWPMGPAYLLDVVGID 547

Query: 529 ----------IGWRSRKDRGIKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVE 578
                      G+  R  +  +  I DAL +A RFGQK G G+++Y++ S+   P  E +
Sbjct: 548 TAHHAQAVMAAGFPQRMQKDYRDAI-DALFDANRFGQKNGLGFWRYKEDSKG-KPKKEED 605

Query: 579 TLINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWP 638
             + D LA++   +RD ++EEI+ RM+ PM+NE  R LEE I A P++ D+  +YG G+P
Sbjct: 606 AAVEDLLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIATPAEADMALVYGLGFP 665

Query: 639 IYRGGPMHYADSVG 652
            + GG   + D++G
Sbjct: 666 PFHGGAFRWLDTLG 679


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: 1045
Number of extensions: 52
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: 729
Length adjustment: 39
Effective length of query: 660
Effective length of database: 690
Effective search space:   455400
Effective search space used:   455400
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:

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