Aligments for a candidate for liuB in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS13985 BWI76_RS13985 urea
           carboxylase
          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.

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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 preprint 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

GapMind for catabolism of small carbon sources