Aligments for a candidate for pimF in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments for a candidate for pimF in Escherichia coli BW25113

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 16447 b2341 fused enoyl-CoA hydratase and epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase (NCBI)

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



>lcl|FitnessBrowser__Keio:16447 b2341 fused enoyl-CoA hydratase and
           epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase
           (NCBI)
          Length = 714

 Score =  343 bits (879), Expect = 2e-98
 Identities = 238/707 (33%), Positives = 357/707 (50%), Gaps = 36/707 (5%)

Query: 11  DQVAIVTVDSP--PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGR-TFIAGADITE 67
           D +A++T+D P   +N L A     +   +     +  ++ +V V A    FIAGADI  
Sbjct: 14  DNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFIAGADINM 73

Query: 68  FGK---PPQPPAL----NDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK 120
            G      +  AL      ++A +   P   IAAIHG  LGGGLE+AL CH RV   + K
Sbjct: 74  IGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGRVCTDDPK 133

Query: 121 --LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVEN-- 176
             LGLPEV+LGLLPG+GGTQRLPR +G   A++MI+ G  + A +ALK GLV++VV +  
Sbjct: 134 TVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVDDVVPHSI 193

Query: 177 LVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTK-KARG-LEAPFA 234
           L+  AV  AKK     RPL  +R+   ++ A    R++    V   T+ K +G   A   
Sbjct: 194 LLEAAVELAKKERPSSRPLP-VRE---RILAGPLGRALLFKMVGKKTEHKTQGNYPATER 249

Query: 235 CADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRP 294
             + +   +      G   E   F +L ++ QS+A R  FFA  +  K  G      P P
Sbjct: 250 ILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDPG--SDAPPAP 307

Query: 295 VSRVAIIGAGTMGGGIA-MSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPP 353
           ++ V I+G G MGGGIA ++   AGIPV + +   + +   L       E    R  L  
Sbjct: 308 LNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEGKVRRRHLKA 367

Query: 354 DAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYL 413
               K++ALI+G          DLIIEAVFE + +K+++   V+ +     + ASNTS L
Sbjct: 368 SERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHTIFASNTSSL 427

Query: 414 SIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVV 473
            I +IAA   RP+ V+G+HFFSP   M L EI+  A T+   + T V +AKK  K P+VV
Sbjct: 428 PIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAKKQGKTPIVV 487

Query: 474 GVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWR- 532
               GF  NR+LA    ++ ++L +G   + +DA + KFG P+GP  + D  G+D G + 
Sbjct: 488 RDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDEVGIDTGTKI 547

Query: 533 ------SRKDR-GIKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTL 585
                 +  +R    + +  ++    R G+K G+G+Y Y  G +      +V+  I   +
Sbjct: 548 IPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLY--GQKGRKSKKQVDPAIYPLI 605

Query: 586 AKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPM 645
              G  R  I+  ++ ER V  M+NE  R ++E++     D D+  ++G G+P + GGP 
Sbjct: 606 GTQGQGR--ISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPFLGGPF 663

Query: 646 HYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTFASLT 692
            Y DS+G   +   +   A         P   L  + A G++F   T
Sbjct: 664 RYIDSLGAGEVVAIMQRLATQYGS-RFTPCERLVEMGARGESFWKTT 709


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: 1044
Number of extensions: 52
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: 714
Length adjustment: 39
Effective length of query: 660
Effective length of database: 675
Effective search space:   445500
Effective search space used:   445500
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