GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS01365
          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 (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