GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Klebsiella michiganensis M5al

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate BWI76_RS01360 BWI76_RS01360 acetyl-CoA C-acyltransferase FadA

Query= metacyc::MONOMER-3207
         (400 letters)



>FitnessBrowser__Koxy:BWI76_RS01360
          Length = 387

 Score =  299 bits (766), Expect = 8e-86
 Identities = 175/405 (43%), Positives = 242/405 (59%), Gaps = 23/405 (5%)

Query: 1   MRDVFICDAIRTPIGRF-GGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQ 59
           M  V I DA+RTP+GR  GGA   VRADDL+A  +++L+  NP+++   +D++++GC  Q
Sbjct: 1   MEQVVIVDAVRTPMGRSKGGAFRHVRADDLSAHLMRSLLSRNPSLEASAIDDIYWGCVQQ 60

Query: 60  AGEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVES 119
             E   N+AR A LLA +P S+P  T+NRLC S M A+  A R I +G+  + + GGVE 
Sbjct: 61  TLEQGFNIARNAALLAEIPHSVPATTVNRLCGSSMQALHDAARMIMTGDASVCLIGGVEH 120

Query: 120 MSRAPFVMG-KAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSR 178
           M   P   G     G SRN+      +G                   TA+ +A  + +SR
Sbjct: 121 MGHVPMSHGVDFHPGLSRNVAKAAGMMGL------------------TAEMLARLHGISR 162

Query: 179 ADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE-TIVERDEHLRPETTLEALTKL 237
             QD FA RS  +A AA  +G F  EI+P       G       DE +RPETT+EAL  L
Sbjct: 163 EMQDQFAARSHARAWAATQSGAFKTEIIPTGGHDADGVLKSYSYDEVIRPETTVEALAAL 222

Query: 238 KPVNGP-DKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGI 296
           +P   P   TVTAG +S ++DGAAA++L S    ++ GL PRARV  MA  G  P +MG 
Sbjct: 223 RPAFDPVTGTVTAGTSSALSDGAAAMLLMSESRARELGLKPRARVRSMAVVGCDPSIMGY 282

Query: 297 GPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQ-VNPNGGAIALG 355
           GPVPA +   ++ G++ SD DV E+NEAFA+Q L  +++LG+ +   + +N NGGAIALG
Sbjct: 283 GPVPASKLALKKAGLSASDIDVFEMNEAFAAQILPCIKDLGLMEQIDEKINLNGGAIALG 342

Query: 356 HPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           HPLG SGAR+  T ++Q+E+   + GLATMC+G+GQG+A   ERV
Sbjct: 343 HPLGCSGARISTTLINQMERKDAQFGLATMCIGLGQGIATVFERV 387


Lambda     K      H
   0.318    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: 385
Number of extensions: 18
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: 400
Length of database: 387
Length adjustment: 31
Effective length of query: 369
Effective length of database: 356
Effective search space:   131364
Effective search space used:   131364
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: 50 (23.9 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