GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Pedobacter sp. GW460-11-11-14-LB5

Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate CA265_RS08845 CA265_RS08845 citrate (Si)-synthase

Query= SwissProt::O34002
         (379 letters)



>FitnessBrowser__Pedo557:CA265_RS08845
          Length = 429

 Score =  194 bits (493), Expect = 4e-54
 Identities = 128/389 (32%), Positives = 201/389 (51%), Gaps = 24/389 (6%)

Query: 5   TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64
           T+  G     +  + I+ ++ +   L YRGY ++ELAAK SF +V YL+   +LP  ++L
Sbjct: 41  TLDTGFKNTGSTKSKITFLDGEKGILKYRGYSIEELAAKSSFLEVIYLIIYGDLPTQAQL 100

Query: 65  KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQDSSPEANLEKA 124
           +        H  + E++K   D   +  HPM    + +  L   +      +  A  +  
Sbjct: 101 EGLQAEISKHTLIHEDMKKFFDGYPSRSHPMGQLGSLIFSLSTFYPECLKPNQTAEEQDL 160

Query: 125 --MSLLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFGE-----EAAPEVVEAF 177
             + LLA FP++V++  ++  G  LI P+   DY  NFLWMTFG+     +  P VV A 
Sbjct: 161 TIIKLLAKFPTIVSFVYKKSLGHPLIYPKNKYDYVTNFLWMTFGQRTEDYDVNPIVVNAM 220

Query: 178 NVSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIG 237
           N  +IL+A+H  N S  T R++ S+  +L++++   I AL GPLHGGAN+AV+   E I 
Sbjct: 221 NKLLILHADHEQNCSASTVRIVGSSDCNLYASIAAGIAALWGPLHGGANQAVIDMLELI- 279

Query: 238 IRKDESLDEAATRSKAWMVDALAQKK--KVMGFGHRVYKNGDSRVPTMKSALDAMIKH-- 293
             K +  D     ++ W+  A  +    ++MGFGHRVYKN D R   +K A D ++++  
Sbjct: 280 --KADGGD-----TEKWIAKAKDKNDPFRMMGFGHRVYKNFDPRAKIIKKACDDILENLG 332

Query: 294 YDRPEMLGLYNGLEAAMEEA----KQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAARITG 349
            D P +       EAA+ +     +++ PN+D+ +G  Y  +GF +EMFT LF   R+ G
Sbjct: 333 IDDPILEIAKKLEEAALTDQYFIDRKLYPNVDFYSGIIYRALGFPSEMFTVLFALGRLPG 392

Query: 350 WTAHIMEQVADNALI-RPLSEYNGPEQRQ 377
           W A   E   +   I RP   Y G   R+
Sbjct: 393 WIAQWKEMHENKEPIGRPRQIYVGETDRE 421


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: 357
Number of extensions: 13
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: 429
Length adjustment: 31
Effective length of query: 348
Effective length of database: 398
Effective search space:   138504
Effective search space used:   138504
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 17 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