GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Echinicola vietnamensis KMM 6221, DSM 17526

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate Echvi_3057 Echvi_3057 citrate synthase I (hexameric type)

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



>FitnessBrowser__Cola:Echvi_3057
          Length = 428

 Score =  201 bits (510), Expect = 4e-56
 Identities = 129/389 (33%), Positives = 204/389 (52%), Gaps = 29/389 (7%)

Query: 11  GLRGQVAGQTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYT 70
           G +   + ++A++ +      L YRGY++ DLA  + F EV+YLL+YGELPTQ Q D + 
Sbjct: 45  GFKNTGSTKSAITFLDGEKGILRYRGYNIEDLAEKSNFLEVSYLLIYGELPTQEQYDQFA 104

Query: 71  GKLRQLRDLPQALKEVLERIPADAHPMDVMRT-GCSFLG----NLEPEQDFSQQHDKTDR 125
            ++     + + +K++L+  P+ AHPM V+ +  CS       +L+P +   +      R
Sbjct: 105 NEITYHTLVHEDIKKILDGFPSVAHPMGVLSSLICSLTAFYPTSLDPNRTDEEIKLSIVR 164

Query: 126 LLAAFPAIMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHGKKPSELHV-----KVMNVS 180
           L+A  P    + Y+ +  G       + +    +F+ ++      +  V     K ++  
Sbjct: 165 LMAKLPTFAAWAYK-NKMGHPANYPDNSLDYCSNFMKMMFALPAEKYEVDPIIAKALDKL 223

Query: 181 LILYAEHEFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQ 240
           LIL+A+HE N ST T R+  S+ + +++ I+A I +L GPLHGGAN++ +EM+E      
Sbjct: 224 LILHADHEQNCSTSTVRIVGSSQASIYASISAGINALWGPLHGGANQSVIEMLEAIKEDG 283

Query: 241 EAIEGTLGMLARKD---KIMGFGHAIYKDNDPRNEVIKGWSKKLADE------VGDTVLF 291
              +  L     K+   ++MGFGH +YK+ DPR ++I    KK AD+      V D VL 
Sbjct: 284 GDTKKYLDKAKDKNDPFRLMGFGHRVYKNFDPRAKII----KKAADDVLGKLGVNDPVLE 339

Query: 292 PVSE----AIDKTMWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFE 347
              E    A++   +  +KL+PN DFY    Y  +GIPT +FT +F   RL GW A   E
Sbjct: 340 IAKELEEAALNDQYFVDRKLYPNVDFYSGIIYRALGIPTDMFTVMFALGRLPGWIAQWKE 399

Query: 348 QRANNRII-RPSAEYTGVEQRKFVPIEQR 375
            R NN  I RP   YTG  +R +V +  R
Sbjct: 400 MRENNEPIGRPRQVYTGPNERSYVSMGDR 428


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: 373
Number of extensions: 16
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: 428
Length adjustment: 31
Effective length of query: 344
Effective length of database: 397
Effective search space:   136568
Effective search space used:   136568
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