Alignments for a candidate for pimF in Klebsiella michiganensis M5al

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_RS20455 BWI76_RS20455 multifunctional fatty acid oxidation complex subunit alpha

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



>FitnessBrowser__Koxy:BWI76_RS20455
          Length = 714

 Score =  339 bits (869), Expect = 3e-97
 Identities = 234/708 (33%), Positives = 354/708 (50%), Gaps = 45/708 (6%)

Query: 11  DQVAIVTVDSP--PVNALSAAVR---RGILENVNAAVADPAVQAIVLVCAGR-TFIAGAD 64
           D +A++T+D+P   +N L A      RGI+  +     +  ++  V + A    FIAGAD
Sbjct: 14  DNIAVITIDAPGEKMNTLKAEFASEVRGIIRQIRD---NKELRGAVFISAKPDNFIAGAD 70

Query: 65  ITEFGK---PPQPPAL----NDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVK 117
           I    +     +  AL      ++A +     P IAAIHG  LGGGLE+AL CH RV   
Sbjct: 71  INMIARCHSAQEAEALARQGQQIMAEIHGLSIPVIAAIHGACLGGGLELALACHGRVCSD 130

Query: 118 EAK--LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE 175
           + K  LGLPEV+LGLLPG+GGTQRLPR +G   A++MI+ G  +   +ALK GLV+EVV 
Sbjct: 131 DDKTRLGLPEVQLGLLPGSGGTQRLPRLIGVSGALEMILTGKQLRPRQALKAGLVDEVVA 190

Query: 176 NLVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMT--KKARGLEAPF 233
             +   +  A ++  + RP  R      ++ A    RS+    VA  T  K      A  
Sbjct: 191 QTIL--LQTAVELALKGRPASRAVPARERILAGPLGRSLLFRLVAKKTHHKTQGNYPATE 248

Query: 234 ACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPR 293
                +   +      G  +E   F +L ++ QS+A R  FFA  +  K  G     +P 
Sbjct: 249 RILQVMETGLAQGCSSGYAEEARAFGELAMTPQSQALRSIFFASTDLKKDRGAD--AEPV 306

Query: 294 PVSRVAIIGAGTMGGGIA-MSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLP 352
            +  V I+G G MGGGIA ++    G+PV + +     +   L       +    R  L 
Sbjct: 307 ALRSVGILGGGLMGGGIAYVTACKGGLPVRIKDIQPRGINHALKYSWDLLDKQVRRRYLR 366

Query: 353 PDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSY 412
                +++ LI+G +  +     D++IEAVFE +A+K+++ + V+ H +P  + ASNTS 
Sbjct: 367 ASERDRQIGLISGSLDYQGFAHRDVVIEAVFEDLALKQKMVSEVEQHCRPETIFASNTSS 426

Query: 413 LSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVV 472
           L I EIAA   RPQ V+G+HFFSP + M L E++    T    + TAV +AK   K P+V
Sbjct: 427 LPIGEIAAQASRPQRVIGLHFFSPVDKMPLVEVIPHIGTDRQTIATAVKLAKLQGKTPIV 486

Query: 473 VGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIG-- 530
           V    GF  NR+LA    ++ +LL EG   + +D  + KFG P+GP  + D  G+D G  
Sbjct: 487 VADKAGFYVNRILAPYINEAMRLLMEGEPVEHIDNALVKFGFPVGPIQLLDEVGIDTGTK 546

Query: 531 --------WRSRKDRGIKSEIADALCEAGRFGQKTGKGYYKYEQGSR--APMPDPEVETL 580
                   W  R      + I  ++    R G+K  +G+Y Y    R     PDP + +L
Sbjct: 547 IIPVLEAAWGERFSP--PANIISSILNDDRKGRKNNRGFYLYAAKGRKSKKRPDPAIYSL 604

Query: 581 INDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIY 640
           +      +   +  ++++++ ER V  M+NE AR  +E++     D D+  ++G G+P +
Sbjct: 605 LG-----ISSPQARLSEQQVAERCVMMMLNEAARCFDERVVRSARDGDIGAVFGIGFPPF 659

Query: 641 RGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688
            GGP  Y D++G   +A  L   A A   P   P   L  +A +G TF
Sbjct: 660 LGGPFRYMDTLGAGEVAAILQRLA-AQYGPRFTPCDTLLHMAEQGATF 706


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: 1017
Number of extensions: 56
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: 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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
the source code
instructions for running GapMind on your computer

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