GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Dinoroseobacter shibae DFL-12

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate 3608406 Dshi_1806 citrate synthase I (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_6062
         (375 letters)



>FitnessBrowser__Dino:3608406
          Length = 430

 Score =  186 bits (471), Expect = 1e-51
 Identities = 129/373 (34%), Positives = 190/373 (50%), Gaps = 39/373 (10%)

Query: 32  LTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYTGKLRQLRDLPQALKEVLERIP 91
           L +RGY +  LA  + + EV YLLLYGELPT A+L+ +  ++     L + +        
Sbjct: 68  LLHRGYPIDQLAEKSHYLEVCYLLLYGELPTAAELEDFESRVTNHTMLHEQMMNFFRGFR 127

Query: 92  ADAHPMDVMRTGCSFLGNLEPEQDFSQQHDKTD------------RLLAAFPAIMCYWYR 139
            DAHPM VM      +G +     F   HD TD            RL+A  P I  + ++
Sbjct: 128 RDAHPMAVM------VGVVGAMSAF--YHDSTDIADPWQREVASIRLIAKMPTIAAWAFK 179

Query: 140 FSHQGQRIECVTDEVSIGGHFLHLLHGKKPSELHV------KVMNVSLILYAEHEFNAST 193
           +S  GQ      +++    +FL +     P+E +V      + M+    L+A+HE NAST
Sbjct: 180 YSI-GQPFVYPRNDLDYASNFLRMCFAV-PTEDYVVDPILSRAMDRIFTLHADHEQNAST 237

Query: 194 FTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQEAIEGTLGMLARK 253
            T R+ +S+ ++ F+CI A I  L GP HGGAN+A +EM++   S     E       + 
Sbjct: 238 STVRLASSSGANPFACIAAGIACLWGPAHGGANQACLEMLQEIGSVDRIPEYIARAKDKD 297

Query: 254 D--KIMGFGHAIYKDNDPRNEVIKGWSKKLADEVG---DTVLFPVSE----AIDKTMWEQ 304
           D  ++MGFGH +YK+ DPR +V+K  + ++ + +G   + +L    E    A+    +  
Sbjct: 298 DPFRLMGFGHRVYKNFDPRAKVMKQSADEVLELLGVENNPILQVAKELEAAALADPYFAD 357

Query: 305 KKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQ--RANNRIIRPSAEYT 362
           KKLFPN DFY       MG PT +FTPIF  SR  GW +   EQ    N +I RP   Y 
Sbjct: 358 KKLFPNVDFYSGIILEAMGFPTAMFTPIFAVSRTVGWISQWKEQLEDPNLKIGRPRQLYQ 417

Query: 363 GVEQRKFVPIEQR 375
           GV  R +V +E+R
Sbjct: 418 GVTLRDYVDVEKR 430


Lambda     K      H
   0.321    0.135    0.406 

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: 407
Number of extensions: 34
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: 375
Length of database: 430
Length adjustment: 31
Effective length of query: 344
Effective length of database: 399
Effective search space:   137256
Effective search space used:   137256
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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