Alignments for a candidate for liuB in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Dinoroseobacter shibae DFL-12

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 3607987 Dshi_1395 acetyl-CoA carboxylase, biotin carboxylase (RefSeq)

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



>FitnessBrowser__Dino:3607987
          Length = 448

 Score =  399 bits (1025), Expect = e-115
 Identities = 210/432 (48%), Positives = 278/432 (64%), Gaps = 3/432 (0%)

Query: 9   LLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68
           +L+ANRGEIA RV+R  + +G+ +VAVHS  D DA H R AD  V +G   +  SYL I 
Sbjct: 5   ILIANRGEIALRVIRACRELGIQSVAVHSTADTDAMHVRMADEAVCIGPPPSPQSYLSIP 64

Query: 69  KLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKALME 128
            +I+A + +GA+AIHPGYGFLSENA F + +++ GL F+GP A  I  MG K  AK  M+
Sbjct: 65  AIISACEITGAEAIHPGYGFLSENANFVQIVQDHGLTFIGPTAEHIRVMGDKITAKETMK 124

Query: 129 TAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188
             GVP VPG  G   DLET R  A  IGYPV++KATAGGGG+GMK+ +    L EA  +A
Sbjct: 125 NLGVPCVPGSDGGVPDLETARRVAGEIGYPVIVKATAGGGGRGMKLAKTAEDLDEAFQTA 184

Query: 189 QREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248
           + E +++FG+  + +EKYL  PRH+E+QVF D  G  ++L ERDCS+QRRHQKV EEAP+
Sbjct: 185 RSEGKAAFGNPDVYLEKYLSTPRHIEVQVFGDGKGGAVHLGERDCSLQRRHQKVFEEAPS 244

Query: 249 PGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 308
           P + A+ R  +G+    A   I Y GAGT+EFL +  GEF+F+EMNTRLQVEHPVTEAI 
Sbjct: 245 PVIDAETRARIGKTCAEAVARIDYAGAGTIEFLYE-NGEFYFIEMNTRLQVEHPVTEAIF 303

Query: 309 GLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPVNDFLPATGRLALYRESAKG 368
           G+DLV  QIRVA G P+   Q  + + GHAIEVR+ AE  V  F P  G +  +  +  G
Sbjct: 304 GVDLVKEQIRVAAGYPMTFKQENLQVRGHAIEVRINAE-KVPAFTPCPGMVTTF-HTPGG 361

Query: 369 PGRRVDSGVEEGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGLKTNIGFLR 428
            G R+DS +  G  I P+YD ++GKLI   ++R  A  RL   L E  + G+ T +    
Sbjct: 362 LGVRMDSALYGGYSIPPYYDSLIGKLIVLAQDRPAALARLNRALGELIVDGIDTTVPLFH 421

Query: 429 RIVAHPAFAAAE 440
            ++A  A    +
Sbjct: 422 ALLAEEAIQTGD 433


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: 739
Number of extensions: 34
Number of successful extensions: 3
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: 649
Length of database: 448
Length adjustment: 35
Effective length of query: 614
Effective length of database: 413
Effective search space:   253582
Effective search space used:   253582
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: 52 (24.6 bits)

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

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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 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

GapMind for catabolism of small carbon sources