GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Sulfurihydrogenibium subterraneum DSM 15120

Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; CS; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_028950703.1 Q385_RS0105475 citrate/2-methylcitrate synthase

Query= SwissProt::H8F0D7
         (393 letters)



>NCBI__GCF_000619805.1:WP_028950703.1
          Length = 375

 Score =  231 bits (588), Expect = 3e-65
 Identities = 128/361 (35%), Positives = 199/361 (55%), Gaps = 5/361 (1%)

Query: 28  IKKGLAGVVVDTTAISKVVPQTNSLTYRGYPVQDLAARCSFEQVAFLLWRGELPTDAELA 87
           + +GLAG+ V  ++IS V  +   L YRG P+Q+L    +F +V++LL  G++P + EL 
Sbjct: 3   VYEGLAGIPVVKSSISYVDGENGILEYRGIPIQELVENSNFLEVSYLLIFGKIPDEKELL 62

Query: 88  LFSQRERASRRVDRSMLSLLAKLPDNCHPMDVVRTAISYLGAEDPDEDDAAANRA--KAM 145
            F    + + +    +L +L  LP N HPM ++++ I     +D D D         + +
Sbjct: 63  KFELDIKENLKYSERILDILKSLPKNLHPMKILQSLIPVFAFDDIDTDIMKEENKYRQTV 122

Query: 146 RMMAVLPTIVAIDMRRRRGLPPIAPHSGLGYAQNFLHMCFGEVPETAVVSAFEQSMILYA 205
           R+MA++P ++A   R + G   + P+    Y +NFL+M  G+  E       ++++IL+A
Sbjct: 123 RIMAIVPVVIAFSKRLKEGKEIVFPNKNFYYTENFLYMLKGKPVEKIYWQTLDKTLILHA 182

Query: 206 EHGFNASTFAARVVTSTQSDIYSAVTGAIGALKGRLHGGANEAVMHDMIEI-GDPANARE 264
           EH  NASTF A VV ST +D+Y+ V+ A+G+L GRLHGGANE V   +  +  D    RE
Sbjct: 183 EHTINASTFTAMVVVSTLADLYACVSSAVGSLSGRLHGGANEEVYKMLSSLPNDEKIIRE 242

Query: 265 WLRAKLARKEKIMGFGHRVYRHGDSRVPTMKRALERVGTVRDGQ--RWLDIYQVLAAEMA 322
           +++ KL  K+KIMGFGHR+Y+  D R   MK  LE++   +        +I++ +A E  
Sbjct: 243 YIKEKLKNKDKIMGFGHRIYKTYDPRAKIMKYLLEKLQKEKSTPLLEKAEIFEKIALEYL 302

Query: 323 SATGILPNLDFPTGPAYYLMGFDIASFTPIFVMSRITGWTAHIMEQATANALIRPLSAYC 382
               I  N+DF +G  Y  M      +T IF M+R+ GW +H +E    N L RP   Y 
Sbjct: 303 EEKKIYTNIDFYSGVLYSQMEIPSDFYTTIFAMARVPGWISHCIEYVRNNKLFRPTQVYD 362

Query: 383 G 383
           G
Sbjct: 363 G 363


Lambda     K      H
   0.321    0.134    0.397 

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: 301
Number of extensions: 23
Number of successful extensions: 4
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: 393
Length of database: 375
Length adjustment: 30
Effective length of query: 363
Effective length of database: 345
Effective search space:   125235
Effective search space used:   125235
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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