GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadB in Klebsiella michiganensis M5al

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 BWI76_RS20455 BWI76_RS20455 multifunctional fatty acid oxidation complex subunit alpha

Query= CharProtDB::CH_003230
         (714 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS20455 BWI76_RS20455
           multifunctional fatty acid oxidation complex subunit
           alpha
          Length = 714

 Score = 1129 bits (2920), Expect = 0.0
 Identities = 566/707 (80%), Positives = 629/707 (88%), Gaps = 1/707 (0%)

Query: 1   MEMTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSA 60
           ME  SAFTL VR DNIAVITID PGEKMNTLKAEFAS+VR II+Q+R+NKELRG VF+SA
Sbjct: 1   METVSAFTLEVRPDNIAVITIDAPGEKMNTLKAEFASEVRGIIRQIRDNKELRGAVFISA 60

Query: 61  KPDNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELA 120
           KPDNFIAGADINMI  C +AQEAEALARQGQQ+MAEIH L I VIAAIHGACLGGGLELA
Sbjct: 61  KPDNFIAGADINMIARCHSAQEAEALARQGQQIMAEIHGLSIPVIAAIHGACLGGGLELA 120

Query: 121 LACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQAL 180
           LACHGRVC+DD KT LGLPEVQLGLLPGSGGTQRLPRLIGVS ALEMILTGKQLR +QAL
Sbjct: 121 LACHGRVCSDDDKTRLGLPEVQLGLLPGSGGTQRLPRLIGVSGALEMILTGKQLRPRQAL 180

Query: 181 KLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAGPLGRALLFKMVGKKTEHKT 240
           K GLVD+VV  +ILL+ AVELA K RP+SR +P RERILAGPLGR+LLF++V KKT HKT
Sbjct: 181 KAGLVDEVVAQTILLQTAVELALKGRPASRAVPARERILAGPLGRSLLFRLVAKKTHHKT 240

Query: 241 QGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDPG 300
           QGNYPATERIL+V+ETGLAQG SSGY  EARAFGELAMTPQSQALRSIFFASTD+KKD G
Sbjct: 241 QGNYPATERILQVMETGLAQGCSSGYAEEARAFGELAMTPQSQALRSIFFASTDLKKDRG 300

Query: 301 SDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEGKV 360
           +DA P  L SVGILGGGLMGGGIAYVTACK G+PVRIKDI P+GINHALKYSWD L+ +V
Sbjct: 301 ADAEPVALRSVGILGGGLMGGGIAYVTACKGGLPVRIKDIQPRGINHALKYSWDLLDKQV 360

Query: 361 RRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHTIF 420
           RRR+L+ASERD+Q+ LISG+ DY+GFAHRD++IEAVFE+L LKQ+MV+EVEQ+C   TIF
Sbjct: 361 RRRYLRASERDRQIGLISGSLDYQGFAHRDVVIEAVFEDLALKQKMVSEVEQHCRPETIF 420

Query: 421 ASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAKKQ 480
           ASNTSSLPIG+IAA A+RP++VIGLHFFSPV+KMPLVE+IPH GT  QTIAT VKLAK Q
Sbjct: 421 ASNTSSLPIGEIAAQASRPQRVIGLHFFSPVDKMPLVEVIPHIGTDRQTIATAVKLAKLQ 480

Query: 481 GKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDEVG 540
           GKTPIVV DKAGFYVNRILAPYINEA+R+L +GE VEHID ALVKFGFPVGPIQLLDEVG
Sbjct: 481 GKTPIVVADKAGFYVNRILAPYINEAMRLLMEGEPVEHIDNALVKFGFPVGPIQLLDEVG 540

Query: 541 IDTGTKIIPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQVDPA 600
           IDTGTKIIPVLEAA+GERFS PAN++SSILNDDRKGRKN RGFYLY  KGRKSKK+ DPA
Sbjct: 541 IDTGTKIIPVLEAAWGERFSPPANIISSILNDDRKGRKNNRGFYLYAAKGRKSKKRPDPA 600

Query: 601 IYPLIG-TQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPFL 659
           IY L+G +  Q R+S  QVAERCVM+MLNEA RC DE+V+RS RDGDIGAVFGIGFPPFL
Sbjct: 601 IYSLLGISSPQARLSEQQVAERCVMMMLNEAARCFDERVVRSARDGDIGAVFGIGFPPFL 660

Query: 660 GGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESFW 706
           GGPFRY+D+LGAGEV AI+QRLA QYG RFTPC+ L+ M  +G +FW
Sbjct: 661 GGPFRYMDTLGAGEVAAILQRLAAQYGPRFTPCDTLLHMAEQGATFW 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: 1328
Number of extensions: 33
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 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 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