GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Klebsiella michiganensis M5al

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate BWI76_RS13985 BWI76_RS13985 urea carboxylase

Query= reanno::pseudo6_N2E2:Pf6N2E2_2194
         (649 letters)



>FitnessBrowser__Koxy:BWI76_RS13985
          Length = 1201

 Score =  391 bits (1004), Expect = e-112
 Identities = 213/438 (48%), Positives = 285/438 (65%), Gaps = 7/438 (1%)

Query: 8   TLLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQI 67
           TLL+ANRG IACR++RT +AM +  VAV+S  D  + H R+AD  + LG   AA +YL  
Sbjct: 4   TLLIANRGAIACRILRTLRAMQVKGVAVYSEADLSSLHIRDADEALSLGDGPAAQTYLAT 63

Query: 68  DKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKALM 127
           +K+IAAA+ SGA+AIHPGYGFLSENA FA A E AGL F+GP    +   G K  A+AL 
Sbjct: 64  EKIIAAAQQSGARAIHPGYGFLSENAAFAEACEAAGLAFVGPTPRQLRVFGLKHTARALA 123

Query: 128 ETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALAS 187
           +  GVPL+ G    A   E  R AAE +GYPV+LK+TAGGGG GM+V  D  +L EA A+
Sbjct: 124 KAEGVPLLEGSELLADSDEACR-AAEAVGYPVMLKSTAGGGGIGMRVCRDARELTEAFAT 182

Query: 188 AQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAP 247
            QR  Q++F D+ + +EKY+ + RH+E+Q+F D  G+ + L  RDCS+QRR+QKV+EE P
Sbjct: 183 VQRLGQNNFSDAGVFLEKYIERARHLEVQIFGDGRGDVIALGVRDCSVQRRNQKVIEETP 242

Query: 248 APGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLDARG-EFFFMEMNTRLQVEHPVTEA 306
           AP L     QA+  AA+   +A+ Y  AGTVEF+ D+   +F+F+E+NTRLQVEH VTE 
Sbjct: 243 APNLPEGTAQALCAAAIALGKAVSYRSAGTVEFVYDSTARQFYFLEVNTRLQVEHGVTEQ 302

Query: 307 ITGLDLVAWQIRVAQGE--PLPITQAQVPLLGHAIEVRLYAEDPVNDFLPATGRL--ALY 362
           + G+DLV W I +A G+  PL +  A +   GHAI+ RLYAEDP   F P+ G L  A++
Sbjct: 303 VWGVDLVRWMIELAAGDLPPLDVLAAGLRPQGHAIQARLYAEDPGRQFQPSPGLLTEAIF 362

Query: 363 RESAKGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGLKT 422
              A G   R+D  VE G E+ PF+DPML K IAW  +R++A   L   L E  + G++T
Sbjct: 363 -PPADGAALRIDRWVEAGCEVPPFFDPMLAKTIAWRPSRDEAIAGLAQALAETRLYGVET 421

Query: 423 NIGFLRRIVAHPAFAAAE 440
           N  +L +I+    F   E
Sbjct: 422 NRLYLLQILGFAPFTEGE 439



 Score = 49.7 bits (117), Expect = 8e-10
 Identities = 27/69 (39%), Positives = 41/69 (59%)

Query: 581  GLAAPMNGSIVRVLVSVGQPVDAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSE 640
            G+ +P++G++ +V  + G  V AG  LVVLE+MKME  + AP  GVI+ ++ Q G  V  
Sbjct: 1130 GVESPISGNLWQVQTAAGSRVRAGDVLVVLESMKMEIPLLAPCDGVIQQVHVQPGSAVRA 1189

Query: 641  GSALVAFEE 649
            G  +    E
Sbjct: 1190 GQRVAVIIE 1198


Lambda     K      H
   0.319    0.134    0.389 

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: 1812
Number of extensions: 79
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 649
Length of database: 1201
Length adjustment: 43
Effective length of query: 606
Effective length of database: 1158
Effective search space:   701748
Effective search space used:   701748
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 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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