GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimF in Klebsiella michiganensis M5al

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate BWI76_RS01365 BWI76_RS01365 multifunctional fatty acid oxidation complex subunit alpha

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



>lcl|FitnessBrowser__Koxy:BWI76_RS01365 BWI76_RS01365
           multifunctional fatty acid oxidation complex subunit
           alpha
          Length = 729

 Score =  353 bits (905), Expect = e-101
 Identities = 233/674 (34%), Positives = 362/674 (53%), Gaps = 39/674 (5%)

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

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

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

Query: 178 VAGAVAFAKKVL---AEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKA-RGLEAPF 233
           + GAVA  ++ +    + +  R+ + +   L+  +A  S FT A   + + A +   AP 
Sbjct: 194 IDGAVAILRQAINGDLDWKAKRQPKLEPLHLSKIEAAMS-FTIAKGMVAQTAGKHYPAPL 252

Query: 234 ACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAF----FAEREAAKVDGVPDG 289
                I AA     EE L  E + F+ L  +++++A    F    + + +A K+    D 
Sbjct: 253 TAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVKAKAKKLTKDVDT 312

Query: 290 TKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARG 349
            K       A++GAG MGGGIA   A  G+PV + +  ++ L  G+    K       RG
Sbjct: 313 PK-----HAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLLNKQLERG 367

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

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

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

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

Query: 579 TLINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWP 638
           T+++  LA++   +RD +DEEI+ RM+ PM+NE  R LEE I A P++ D+  +YG G+P
Sbjct: 606 TVVDSLLAEVSQPKRDFSDEEIIARMMIPMVNEVVRCLEEGIIASPAEADMALVYGLGFP 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: 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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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