Alignments for a candidate for ech in Klebsiella variicola At-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Klebsiella variicola At-22

Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate WP_012967492.1 KVAR_RS06705 fatty acid oxidation complex subunit alpha FadJ

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_000025465.1:WP_012967492.1
          Length = 714

 Score = 1098 bits (2840), Expect = 0.0
 Identities = 544/707 (76%), Positives = 618/707 (87%), Gaps = 1/707 (0%)

Query: 1   MEMTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSA 60
           M+  SAF L VR D IAVITID PGEKMNTLKAEF +QVR +I+Q+R++K +RGVVF+SA
Sbjct: 1   MDTVSAFKLEVRADKIAVITIDAPGEKMNTLKAEFGNQVRGLIRQVRDDKSVRGVVFISA 60

Query: 61  KPDNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELA 120
           K DNFIAGADINMI  C++AQEAEALARQGQQ+MAEIH L I VIAAIHGACLGGGLELA
Sbjct: 61  KADNFIAGADINMIARCRSAQEAEALARQGQQIMAEIHGLSIPVIAAIHGACLGGGLELA 120

Query: 121 LACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQAL 180
           LACHGR+C+DD KT LGLPEVQLGLLPGSGGTQRLPRLIGVSTAL+M+LTG+QLRA+QAL
Sbjct: 121 LACHGRICSDDEKTRLGLPEVQLGLLPGSGGTQRLPRLIGVSTALDMMLTGRQLRARQAL 180

Query: 181 KLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAGPLGRALLFKMVGKKTEHKT 240
           K GLVD+VVP +ILL+AAVELA K RP+SR +PVRER+LAGPLGR LLF  VGK+T+ KT
Sbjct: 181 KAGLVDEVVPQAILLQAAVELALKGRPASRDMPVRERVLAGPLGRHLLFHFVGKQTQRKT 240

Query: 241 QGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDPG 300
           QGNYPA +RIL+VVE GL  G SSGY  EARAFGELAMTPQSQALRSIFFASTD+KKD G
Sbjct: 241 QGNYPAVKRILQVVENGLTHGCSSGYAEEARAFGELAMTPQSQALRSIFFASTDLKKDRG 300

Query: 301 SDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEGKV 360
           ++A P PL S+ +LGGGLMGGGIAYVTACK G+PVRIKDI P+GINHALKYSW+ L  +V
Sbjct: 301 AEAEPGPLTSIAVLGGGLMGGGIAYVTACKGGLPVRIKDIQPRGINHALKYSWELLNKQV 360

Query: 361 RRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHTIF 420
           R+R L+ SERD+Q+A+ISG TDY+GFAHRD++IEAVFE+L LKQ+MV+EVEQ C   TIF
Sbjct: 361 RQRRLRPSERDRQMAMISGATDYQGFAHRDVVIEAVFEDLALKQRMVSEVEQYCGPQTIF 420

Query: 421 ASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAKKQ 480
           ASNTSSLPIGDIAA A RP +VIGLHFFSPVEKMPLVE+IPH GT  Q IAT V+LAK+Q
Sbjct: 421 ASNTSSLPIGDIAAQARRPGRVIGLHFFSPVEKMPLVEVIPHKGTDPQAIATVVQLAKRQ 480

Query: 481 GKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDEVG 540
           GKTPIVV DKAGFYVNRILAPYINEA+R+L +GE VE ID ALVKFGFPVGPIQLLDEVG
Sbjct: 481 GKTPIVVADKAGFYVNRILAPYINEAMRLLVEGEPVEEIDKALVKFGFPVGPIQLLDEVG 540

Query: 541 IDTGTKIIPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQVDPA 600
           IDTGTKIIPVLE A+GERFS PAN++ +IL DDRKGRKN RGFYLY  KGRKSKK+ DPA
Sbjct: 541 IDTGTKIIPVLERAFGERFSPPANIIDAILKDDRKGRKNNRGFYLYETKGRKSKKRPDPA 600

Query: 601 IYPLIG-TQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPFL 659
           +YPL+G  + Q R+SA QVAERCVM+MLNEA RC DEQ+IRS RDGDIGAVFGIGFPPFL
Sbjct: 601 VYPLLGIDRPQSRLSAQQVAERCVMMMLNEAARCFDEQIIRSARDGDIGAVFGIGFPPFL 660

Query: 660 GGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESFW 706
           GGPFRY+D++GAGEV AI+QRLA QYG RFTPC+ L+ M  +G +FW
Sbjct: 661 GGPFRYMDTIGAGEVAAILQRLAAQYGPRFTPCDTLLRMAEQGTTFW 707


Lambda     K      H
   0.319    0.137    0.393 

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: 1361
Number of extensions: 35
Number of successful extensions: 4
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: 714
Length of database: 714
Length adjustment: 39
Effective length of query: 675
Effective length of database: 675
Effective search space:   455625
Effective search space used:   455625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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)
SQLite3 databases

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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