GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Haloterrigena daqingensis JX313

Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; CS; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_076581092.1 BB347_RS10075 citrate synthase

Query= SwissProt::H8F0D7
         (393 letters)



>NCBI__GCF_001971705.1:WP_076581092.1
          Length = 382

 Score =  271 bits (692), Expect = 3e-77
 Identities = 155/372 (41%), Positives = 209/372 (56%), Gaps = 12/372 (3%)

Query: 27  DIKKGLAGVVVDTTAISKVVPQTNSLTYRGYPVQDLAARCSFEQVAFLLWRGELPTDAEL 86
           D+KKGL GV+V  + +S +      L YRGY +++LA   S+E+V +LLW GELP   EL
Sbjct: 4   DLKKGLEGVLVAESGLSSIDGDAGRLIYRGYSIEELARGASYEEVLYLLWHGELPGADEL 63

Query: 87  ALFSQRERASRRVDRSMLSLLAKLPD-NCHPMDVVRTAISYLGAEDPDED----DAAANR 141
             F+      R V   +L  + +L   +  PM  +RTA+S L A +P+ D    D  A  
Sbjct: 64  ESFTAAINEERDVSEDVLETMERLATADEQPMAALRTAVSMLSASEPETDADPEDLEATL 123

Query: 142 AKAMRMMAVLPTIVAIDMRRRRGLPPIAPHSGLGYAQNFLHMCFGEVPETAVVSAFEQSM 201
            K  R+ A +PT +A   R R    P+ PH  LG A NFL+M  GE P       F+Q++
Sbjct: 124 RKGRRITAKIPTALAAFERYRLDEEPVDPHPELGLAANFLYMLTGEEPSDIHAETFDQAL 183

Query: 202 ILYAEHGFNASTFAARVVTSTQSDIYSAVTGAIGALKGRLHGGANEAVMHDMIEIGD-PA 260
           IL+A+HG NASTF + V+ ST +DIYSAVTG + AL G LHGGAN+ VM  + EI +   
Sbjct: 184 ILHADHGLNASTFTSMVIGSTMADIYSAVTGGVSALSGPLHGGANQDVMEVLFEIDESDL 243

Query: 261 NAREWLRAKLARKEKIMGFGHRVYRHGDSRVPTMKRALERVGTVRDGQRWLD----IYQV 316
           + REW+        +I GFGHRVY   D R   ++   + +    D  +W D    I Q 
Sbjct: 244 DHREWVEQANEAGRRIPGFGHRVYNVKDPRAEILQERSKELANEGD-SKWYDYTTTIEQY 302

Query: 317 LAAEMASA-TGILPNLDFPTGPAYYLMGFDIASFTPIFVMSRITGWTAHIMEQATANALI 375
           L+ E   A  GI PN+DF +G  YY +G  I  +TPIF MSR+ GW  H++E    N LI
Sbjct: 303 LSEEQGLAEKGIAPNVDFYSGSVYYQLGIPIDMYTPIFAMSRVGGWVGHVLEYQEDNRLI 362

Query: 376 RPLSAYCGHEQR 387
           RPLS Y G E +
Sbjct: 363 RPLSRYTGPEDQ 374


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: 378
Number of extensions: 23
Number of successful extensions: 5
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: 382
Length adjustment: 30
Effective length of query: 363
Effective length of database: 352
Effective search space:   127776
Effective search space used:   127776
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 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