GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Rhodococcus qingshengii djl-6-2

Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_003940509.1 C1M55_RS23210 citrate synthase

Query= SwissProt::O34002
         (379 letters)



>NCBI__GCF_002893965.1:WP_003940509.1
          Length = 432

 Score =  213 bits (541), Expect = 1e-59
 Identities = 139/389 (35%), Positives = 211/389 (54%), Gaps = 26/389 (6%)

Query: 5   TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64
           T+  G     +  +AI+ ++ +   L YRGYP+++LA K +F +V+YLL   ELP D++L
Sbjct: 45  TLDPGFVNTASTSSAITYIDGEKGILRYRGYPIEQLAGKSTFIEVSYLLIYGELPTDAQL 104

Query: 65  KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQD-SSPEANLEK 123
           ++F +  R H  L E++K   D      HPM V  +AV+ L A +  + D   PE     
Sbjct: 105 ESFTDRIRRHTLLHEDLKRFFDGFPRNAHPMPVLSSAVNALSAYYQDSLDPEDPEQVELS 164

Query: 124 AMSLLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFGEEAA-----PEVVEAFN 178
            + LLA  P++ AY  ++  G+  + P   L+   NF+ MTFG  A      PEV +A +
Sbjct: 165 TIRLLAKLPTIAAYAYKKSVGQPFLYPDNSLNLVENFMRMTFGFPAEPYQGDPEVAKALD 224

Query: 179 VSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIGI 238
           + +IL+A+H  N ST T R++ S+ A+L ++V+  I AL GPLHGGAN+AV+   +EI  
Sbjct: 225 MLLILHADHEQNCSTSTVRMVGSSDANLFTSVSAGINALWGPLHGGANQAVLEMLDEI-- 282

Query: 239 RKDESLDEAATRSKAWMVDALAQKK---KVMGFGHRVYKNGDSRVPTMK-SALDAMIKHY 294
                  +A+  + A  V  +  K+   K+MGFGHRVY+N D R   ++ +A   + K  
Sbjct: 283 -------KASGSTAAEFVRKVKNKEDGVKLMGFGHRVYRNYDPRAALVRETAHTILAKLG 335

Query: 295 DRPEMLGLYNGL-EAAMEE----AKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAARITG 349
              E+L +   L EAA+ +     +++ PN+D+  G  Y  MGF   MFT LF   R+ G
Sbjct: 336 GDDELLNIAMQLEEAALTDDYFIERKLYPNVDFYTGLIYRAMGFPPRMFTVLFAMGRLPG 395

Query: 350 WTAHIMEQVADNA--LIRPLSEYNGPEQR 376
           W AH  E   D A  + RP   Y G  +R
Sbjct: 396 WIAHWREMHEDPATKIGRPRQIYTGYTER 424


Lambda     K      H
   0.316    0.130    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: 384
Number of extensions: 17
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: 379
Length of database: 432
Length adjustment: 31
Effective length of query: 348
Effective length of database: 401
Effective search space:   139548
Effective search space used:   139548
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: 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