GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Psychromonas ingrahamii 37

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_011770893.1 PING_RS13510 citrate synthase

Query= BRENDA::Q9I5E3
         (375 letters)



>NCBI__GCF_000015285.1:WP_011770893.1
          Length = 436

 Score =  187 bits (474), Expect = 6e-52
 Identities = 115/368 (31%), Positives = 192/368 (52%), Gaps = 21/368 (5%)

Query: 26  GQEGAGLTYRGYDVRDLAAAAIFEEVAYLLLYGELPNKQQLDAYLKKLQGQRDLPQALKE 85
           G++G  L YRGY +  LA  + + E AYL+L GELPN+ QL+ + K +     + + +K+
Sbjct: 72  GEKGI-LRYRGYPIEQLAEKSTYLETAYLILNGELPNQTQLNGWHKDIMAHTFIHENIKK 130

Query: 86  VLERIPKDAHPMDVMRTGASVLGTLEPELSFDQQRDVADR----LLAAFPAIMTYWYRFT 141
           +++    DAHPM  +    + L T  P+      +   DR    L+A  P +  + YR +
Sbjct: 131 LIDSFHYDAHPMGTLVGTVAALSTFYPDAKNIHDQACRDRQIWRLIAKMPTLAAFSYRHS 190

Query: 142 HEGQRIDCNSDEPTIGGHFLALLHGK-----KPSELHVKVMNVSLILYAEHEFNASTFTA 196
                +  +     IG +F+++L  K     +P+ +  K +NV  IL+A+HE N  T   
Sbjct: 191 IGLPYVYPDQSLSYIG-NFMSMLWKKSELQYQPNPILEKAINVLFILHADHEQNCGTSVM 249

Query: 197 RVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIERFSSPQEATAELLKMLERKD-- 254
           R  AS  SD +S  + AI +L GPLHGGANEA + ++    S  +   E +K ++  +  
Sbjct: 250 RAVASAYSDPFSATSSAIAALYGPLHGGANEAVLHMLAEIGS-VDRVPEFIKTVKSGEVS 308

Query: 255 KIMGFGHAIYKDSDPRNEVIKGWSKQLADEVGDKVLFAVSEAIDKTMWE-----QKKLFP 309
           ++MGFGH +YK+ DPR ++ K  + ++    G   L A++  +++   +      + L+P
Sbjct: 309 RLMGFGHRVYKEYDPRAKICKTLANEVFSVTGVNPLLAIALELERVALQDDYFISRHLYP 368

Query: 310 NADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTA--HVFEQRANNRIIRPSAEYTGVEQR 367
           N DFY    Y  MG P  +F  +F  +R +GW A    F    +++I RP   Y G E R
Sbjct: 369 NVDFYSGLIYQAMGFPVGMFPVLFAIARNTGWLAQWQEFLVDPDHKIARPRQIYCGSEVR 428

Query: 368 AFVPLEQR 375
            ++ +++R
Sbjct: 429 DYIAVDKR 436


Lambda     K      H
   0.319    0.134    0.396 

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: 367
Number of extensions: 14
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 375
Length of database: 436
Length adjustment: 31
Effective length of query: 344
Effective length of database: 405
Effective search space:   139320
Effective search space used:   139320
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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