Alignments for a candidate for bkdC in Haloglycomyces albus DSM 45210

GapMind for catabolism of small carbon sources

Alignments for a candidate for bkdC in Haloglycomyces albus DSM 45210

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_025274975.1 HALAL_RS0116060 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase

Query= curated2:P37942
         (424 letters)



>NCBI__GCF_000527155.1:WP_025274975.1
          Length = 562

 Score =  265 bits (678), Expect = 2e-75
 Identities = 175/442 (39%), Positives = 248/442 (56%), Gaps = 48/442 (10%)

Query: 6   MTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEG 65
           +T+P+LGESVTEGT+++WL A GD V   +P+ EV TDKV+ E+PS   GT+ ++   E 
Sbjct: 127 VTLPELGESVTEGTVTQWLKAVGDTVEADEPLLEVSTDKVDTEIPSPAAGTLQDIRVPED 186

Query: 66  QTLQVGEMICKIETEGANPAEQKQEQPAA------------------SEAAENPVAKSAG 107
           +T  VG+++  I T  A  A+  QE PA                   + AA  P A +A 
Sbjct: 187 ETANVGDVLAVIGTGAAPAADTPQESPAPQPAAPAEPKPEPSEKPEPAAAAPQPAAPAAP 246

Query: 108 AA-------DQPNKKRY-SPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQ 159
           A        ++P +  Y +P V +LA E+ +DL QVTGTG GGRI ++D+Q +I+     
Sbjct: 247 ATTPPAAPTNKPTEVSYVTPLVRKLANENDVDLSQVTGTGVGGRIRKQDVQEVID----- 301

Query: 160 EQNPEELKTAAPAPKSASKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPH 219
                  K++APAP SA    P E    P+   G  E  +T +R+  A  +  S      
Sbjct: 302 -----RQKSSAPAP-SAQPSAPVE----PSPLRGRVE-KMTRLRQVAAKALHDSLQSQAQ 350

Query: 220 AWTMMEVDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMN-SMWAGDK 278
             T++EVD+T ++  R + KD F    G  L+   F V A  +AL+++P +N SM   +K
Sbjct: 351 LTTVVEVDLTKVMNLRAAKKDEFLARHGVKLSPLPFMVVAAIEALQQYPIVNASMNMEEK 410

Query: 279 IIQKKDI-NISIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGG 337
            I   +  N+ +AV TE  L VPVIKNA +  I GIA+    LA+K R G LT DD+ GG
Sbjct: 411 TITYPEAENVGVAVDTEKGLIVPVIKNAGDLNIPGIARHTAELAEKARSGGLTPDDLSGG 470

Query: 338 TFTVNNTGSFGSVQSMGIINYPQAAILQVESIVKRPVVMDN----GMIAVRDMVNLCLSL 393
           TFTV NTGS G++    I+N PQ+AIL   ++VKRPV++D+     ++A R M+ L LS 
Sbjct: 471 TFTVTNTGSRGALFDTPIVNAPQSAILGTGALVKRPVIVDDPELGEVVAPRQMMYLALSY 530

Query: 394 DHRVLDGLVCGRFLGRVKQILE 415
           DHR++DG    RFL  VK  LE
Sbjct: 531 DHRLIDGADAARFLQSVKGRLE 552



 Score = 85.5 bits (210), Expect = 4e-21
 Identities = 60/192 (31%), Positives = 93/192 (48%), Gaps = 18/192 (9%)

Query: 6   MTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEG 65
           +TMP LGESVTEGT+++WL   GD V   +P+ EV TDKV+ EVPS   GT+ ++V  E 
Sbjct: 5   VTMPALGESVTEGTVTQWLKQEGDTVEVDEPLLEVSTDKVDTEVPSPVAGTLIKIVAAED 64

Query: 66  QTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPAVLRLA 125
             ++VG  +  +  E    A      PA + A E P  K       P     +PA     
Sbjct: 65  AEVEVGGELA-VVGEAGEAAGSPTPAPAEAPAEETPAEKPVEDTPAPVASAEAPA---SG 120

Query: 126 GEHGIDLDQVTGTGAGGRITRKDIQRLIETGG--------VQEQNPEELKTAAPAPKSAS 177
           G  G D   VT    G  +T   + + ++  G        + E + +++ T  P+P + +
Sbjct: 121 GGEGTD---VTLPELGESVTEGTVTQWLKAVGDTVEADEPLLEVSTDKVDTEIPSPAAGT 177

Query: 178 KPE---PKEETS 186
             +   P++ET+
Sbjct: 178 LQDIRVPEDETA 189


Lambda     K      H
   0.312    0.129    0.359 

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: 659
Number of extensions: 45
Number of successful extensions: 9
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: 424
Length of database: 562
Length adjustment: 34
Effective length of query: 390
Effective length of database: 528
Effective search space:   205920
Effective search space used:   205920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 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:

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
the source code
instructions for running GapMind on your computer

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