GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Pseudovibrio axinellae Ad2

Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate WP_068006658.1 PsAD2_RS13240 biotin/lipoyl-binding protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_3984
         (651 letters)



>NCBI__GCF_001623255.1:WP_068006658.1
          Length = 629

 Score =  528 bits (1361), Expect = e-154
 Identities = 298/646 (46%), Positives = 405/646 (62%), Gaps = 28/646 (4%)

Query: 8   TLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQI 67
           ++LVANRGEIA RV RTA+  G  ++AV+S  D  A H  +AD+   +GG+  A+SYL I
Sbjct: 4   SVLVANRGEIARRVFRTARQKGYRSIAVYSEADATAPHVGDADVAACIGGATPAESYLNI 63

Query: 68  DKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKALM 127
           + ++ AA+ +GAQA+HPGYGFL+ENA FA+A +AAGL+F+GPPA AI+ MGSK  +K  M
Sbjct: 64  EAVLEAARKTGAQAVHPGYGFLAENADFAKACDAAGLVFVGPPAQAIELMGSKRLSKLRM 123

Query: 128 ETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALAS 187
             AGVP VPGY G  Q  E       RIG P+++KA+AGGGG+G+++VE++  L + LA+
Sbjct: 124 IEAGVPCVPGYSGADQSTEVLAAEAARIGVPLMIKASAGGGGRGLRLVENLEGLEDKLAA 183

Query: 188 AQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAP 247
           A  EA+ +FG+  +++EK ++ PRHVEIQ+FAD HGN ++L ERDCS+QRRHQKV+EEAP
Sbjct: 184 AASEAVGAFGNGELILEKAVINPRHVEIQIFADNHGNVVHLGERDCSVQRRHQKVIEEAP 243

Query: 248 APGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAI 307
            P ++PE+R AMG+AAV +A+AIGY GAGTVEFLL A G F+FMEMNTRLQVEHPVTE I
Sbjct: 244 GPSVTPEIRDAMGQAAVEAARAIGYRGAGTVEFLLAADGSFYFMEMNTRLQVEHPVTEEI 303

Query: 308 TGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYRESAA 367
           TG DLVAWQ+ VA G+ LP+ Q+ +   GHA+E+RLYAED    FLP TG++  +     
Sbjct: 304 TGQDLVAWQLDVAAGKPLPLAQEDISFSGHAMELRLYAEDADAGFLPQTGQVVAWN---- 359

Query: 368 GP--GRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKTNIN 425
           GP    RVDS +E+G  IS +YDPM+ KLIA G DRE+AR +LL  LD+  + GL  N +
Sbjct: 360 GPELALRVDSAIEQGSVISSYYDPMIAKLIAHGADREEARRKLLRGLDQLVLQGLVHNGS 419

Query: 426 FLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTTRADDL 485
           FL+ ++    FAA E  T F+   +E    A   + +     A   FA+++  T      
Sbjct: 420 FLKSVLLDDVFAAGEATTAFL-NDRELGSVAADSVRELMRDLAVHLFARNKGQTRWTTAT 478

Query: 486 SSPWGIGNGFRAGLPTEITLHLSCEEQDRALTLGDADAHTAQLKGEYLLTEHNGLRRQHR 545
             P  I     +  P E    L   EQD    LG             L+   +G+RR   
Sbjct: 479 PLPVKIKLDGESVTPRE---DLQILEQD---DLGK------------LVFYVDGVRRS-A 519

Query: 546 AIRRGDT--LYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQTVE 603
            + +G     ++  DG+ +  E     +    + +    + APM G++V +  E G  V 
Sbjct: 520 FVSKGPEGGFWISLDGQTQFFEEQSLSTRKTDNSATSSSVIAPMPGAVVALKTEQGAQVS 579

Query: 604 AGAQLVVLEAMKMEHSIRAPHAGIIKALYCQEGEMVSEGSALVELE 649
            G  L+VLEAMKM+H + AP  GI+  L  QEG  V+    LV LE
Sbjct: 580 KGDVLLVLEAMKMQHELTAPRDGIVAELGTQEGAQVNSRDVLVRLE 625


Lambda     K      H
   0.318    0.134    0.386 

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: 930
Number of extensions: 29
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: 651
Length of database: 629
Length adjustment: 38
Effective length of query: 613
Effective length of database: 591
Effective search space:   362283
Effective search space used:   362283
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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