GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Haloterrigena daqingensis JX313

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate WP_076582964.1 BB347_RS13025 2-oxo acid dehydrogenase subunit E2

Query= reanno::Marino:GFF1672
         (378 letters)



>NCBI__GCF_001971705.1:WP_076582964.1
          Length = 541

 Score =  196 bits (499), Expect = 1e-54
 Identities = 118/341 (34%), Positives = 190/341 (55%), Gaps = 14/341 (4%)

Query: 46  EEARTKPEPA-AQLSTATASP---VAAASRQRIPASPAVRRLVREHELNLSDIQG-SGKD 100
           + A T+  P  + +S AT++P   +  A R++  A+PA RR+  E  +N+  +     +D
Sbjct: 203 DRAGTEATPTTSSVSGATSAPSTDLEDADREQTLAAPATRRIAEEEGVNIDAVPAVEERD 262

Query: 101 GR-VLKADVLAYIEEGPKQAQNQAPADDAQTATTRSARRAPAADQEA-RVEPIRGIKAAM 158
           G+  +  D +    E  +Q    A ++  +      A     +D E  R EP  G++   
Sbjct: 263 GQPFVTPDAVREYAEAKRQG---AESEGLEAGGAADATGVDFSDGERERREPFAGVRKRT 319

Query: 159 AKSMVKSATTIPHFIYSEDIDVTDLLKLREQLKPEAEARGSRLTLMPFFMKAMALAVQEF 218
           A +MV+S  T PH  + +++DVT L++ RE LKP A  RG RLT MPF +KA+  A++E+
Sbjct: 320 ADAMVESKFTAPHVTHHDEVDVTALVEAREDLKPRAADRGIRLTYMPFIVKAVVAALKEY 379

Query: 219 PVLNSQLNDDVTEIHYLPQCNIGMAVDGKAGLTVPNIKGVESLSLLGIADEVARLTEAAR 278
           P +N+ ++DD  EI Y    N+G+A    AGL VP ++  +   LL +A  +  L + AR
Sbjct: 380 PEMNAVIDDDAEEIVYRDYYNVGIATATDAGLLVPVVENADQQGLLALASSMNELVQKAR 439

Query: 279 SGRVSQEDLKGGTITISNIGALGGTYTAPIINAPEVAIVALGRTQKLPRFDANGQVVE-- 336
              VS  +L+G T T++N+G +GG Y  PI+N PE  I+A+G  ++ PR   + +  E  
Sbjct: 440 ERTVSPTELQGSTFTVTNVGGIGGEYATPILNYPEAGILAVGEIKRKPRVVTDEEGTETI 499

Query: 337 --RAIMTVSWAGDHRIIDGGTIARFCNRWKGYLESPQTMLL 375
             R+++T+S + DHR+IDG   A+F N     LE+P  +LL
Sbjct: 500 EPRSVLTLSLSFDHRLIDGAIGAQFMNTVMESLENPHLLLL 540



 Score = 57.4 bits (137), Expect = 9e-13
 Identities = 56/204 (27%), Positives = 86/204 (42%), Gaps = 36/204 (17%)

Query: 2   TDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPL--FAFIPRDREEPE------EARTKPE 53
           TDKA+VE+ +P  G V++L++ +  +  V      FA    D E  E       A  + E
Sbjct: 41  TDKALVEVPSPVDGTVSELHYAEGDVIPVGNVFVTFALEGEDAETAEPDSGSASADEETE 100

Query: 54  PAAQLSTA-------TASPVAAAS--------RQRIPASPAVRRLVREHELNLSDIQGSG 98
           P     +A         SP A  +        + R+   P +RR  RE  L+LS ++GSG
Sbjct: 101 PTTDAESAPTDEESEAGSPGAIGADTEETGTPQDRVFVPPRLRRKAREDGLDLSSVRGSG 160

Query: 99  KDGRVLKADVLAYIEEGPKQAQNQAPADDAQTATTRSARRAPAADQEARVEPIRGIKAAM 158
             GR+  AD+         +A + A     +T  + S+    A D    V+   G +A  
Sbjct: 161 PGGRITAADI---------RAASAADDGGQETPDSGSSDTETAGDSSDTVDDRAGTEATP 211

Query: 159 AKSMVKSATTIPHFIYSEDIDVTD 182
             S V  AT+ P    S D++  D
Sbjct: 212 TTSSVSGATSAP----STDLEDAD 231


Lambda     K      H
   0.316    0.131    0.367 

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: 452
Number of extensions: 16
Number of successful extensions: 5
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: 378
Length of database: 541
Length adjustment: 33
Effective length of query: 345
Effective length of database: 508
Effective search space:   175260
Effective search space used:   175260
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 (21.6 bits)
S2: 51 (24.3 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