GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Algoriphagus aquaeductus T4

Align Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; EC 2.3.1.168; Branched-chain alpha-keto acid dehydrogenase complex component E2; BCKAD-E2; BCKADE2; Dihydrolipoamide acetyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; Dihydrolipoamide branched chain transacylase; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (uncharacterized)
to candidate WP_111392718.1 CLV31_RS09795 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase

Query= curated2:P09062
         (423 letters)



>NCBI__GCF_003253485.1:WP_111392718.1
          Length = 505

 Score =  213 bits (543), Expect = 8e-60
 Identities = 140/427 (32%), Positives = 223/427 (52%), Gaps = 47/427 (11%)

Query: 8   MPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPGEV 67
           +P +GE I +V L  W  K GD +  D+++A+V +DKAT E+P+  +G +L    + G+V
Sbjct: 108 VPTVGESITEVTLANWIKKDGDFVTLDEIIAEVDSDKATFELPAEATG-ILRHVAKEGDV 166

Query: 68  MAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEPQKDVKPAAYQASASHEAAPI 127
           + +G  + +IEV       +   AK    PA P A+          ++  AS+S+ A   
Sbjct: 167 LEIGGLICKIEV------TEEAPAKTESAPAEPTAS----------SSSSASSSYAAGH- 209

Query: 128 VPRQPGDKPLASPAVRKRALDAGIELRYVHGSGPAGRILHED-LDAFMSKPQSAAGQ--- 183
                     ASPA  K   + GI    V GSG  GRI  ED L A  S P  AA +   
Sbjct: 210 ----------ASPAASKILAEKGISPESVSGSGKDGRITKEDALSAKKSAPAPAAEKPAP 259

Query: 184 ------TPNGYARRTDSEQVPVIGLRRKIAQRMQDAKRRVAHFSYVEEIDVTALEALR-- 235
                 +P       +  +  +  LR+ +++R+   K   A  +   E+++  +  LR  
Sbjct: 260 KVQESASPAAAPGSRNVRREKMSSLRKTVSRRLVAVKNETAMLTTFNEVNMKPIMDLRAK 319

Query: 236 --QQLNSKHGDSRGKLTLLPFLVRALVVALRDFPQINATYDDEAQIITRHGAVHVGIATQ 293
              Q   KHG   G    + F  +A+ VAL+++P +NA  D     I  +    + IA  
Sbjct: 320 FKDQFKEKHGVGLG---FMSFFTKAVCVALQEWPAVNAMIDGNE--IVYNDFCDISIAVS 374

Query: 294 GDNGLMVPVLRHAEAGSLWANAGEISRLANAARNNKASREELSGSTITLTSLGALGGIVS 353
              GL+VPV+R+AEA S      E+ RLA  AR+NK S EE++G T T+T+ G  G ++S
Sbjct: 375 APKGLVVPVIRNAEAMSFDQIEKEVVRLAGKARDNKLSIEEMTGGTFTITNGGVFGSMMS 434

Query: 354 TPVVNTPEVAIVGVNRMVERPVVIDGQIVVRKMMNLSSSFDHRVVDGMDAALFIQAVRGL 413
           TP++N P+ AI+G++ +VERP+ ++G++ +  MM ++ S+DHR++DG ++  F+  V+ L
Sbjct: 435 TPIINAPQSAILGMHNIVERPMAVNGEVKILPMMYVALSYDHRIIDGRESVSFLVRVKQL 494

Query: 414 LEQPACL 420
           LE P  L
Sbjct: 495 LEDPTRL 501



 Score = 60.8 bits (146), Expect = 9e-14
 Identities = 34/108 (31%), Positives = 62/108 (57%), Gaps = 3/108 (2%)

Query: 6   IKMPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPG 65
           +++P +GE I++V + +WF K GD +  D+V+ ++ +DKAT E P+  +G +L +  Q G
Sbjct: 5   MRVPTVGESISEVTVGQWFKKDGDQVQLDEVLCELESDKATFEFPAEAAG-ILRIKAQEG 63

Query: 66  EVMAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEPQKDVKP 113
           + + +G  +  IE E         ++KP   PAA  +A  E ++ + P
Sbjct: 64  DTVEIGGLICVIE-EADAASKPATESKP-PAPAAKASASGEVKEMIVP 109


Lambda     K      H
   0.316    0.133    0.376 

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: 457
Number of extensions: 13
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: 423
Length of database: 505
Length adjustment: 33
Effective length of query: 390
Effective length of database: 472
Effective search space:   184080
Effective search space used:   184080
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