GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pta in Cupriavidus basilensis 4G11

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate RR42_RS17610 RR42_RS17610 malate dehydrogenase

Query= SwissProt::P77844
         (329 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS17610 RR42_RS17610 malate
           dehydrogenase
          Length = 774

 Score =  171 bits (433), Expect = 6e-47
 Identities = 102/317 (32%), Positives = 174/317 (54%), Gaps = 7/317 (2%)

Query: 17  EHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGLHLNTAY---LVN 73
           E   IV  EG+++R+L A   ++D+ + +  ++G P  I  R    GL L       +VN
Sbjct: 459 EKKRIVFAEGEEERVLRAVQVIVDEKLANPILVGRPAVIAHRIERFGLRLRGGIDFTVVN 518

Query: 74  PLTDPRLEEFAEQFAELRKSKSVTIDEAR-EIMKDISYFGTMMVHNGDADGMVSGAANTT 132
           P  D R  +++E + ++   + +T   A+ E+ +  +  G M+V  G+ADGM+ G  +TT
Sbjct: 519 PEHDARFRDYSEAYFKMMARQGITQQYAKLEMRRRTTLIGAMLVKQGEADGMICGTVSTT 578

Query: 133 AHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQLGEIAVVSAKTA 192
           A  ++   Q++    E  V +++  +VL GR     D  VN +PTA QL EI +++A+  
Sbjct: 579 AAHLRYIDQVLGGSSE--VYAAMNGLVLPGRQIFLVDTHVNIDPTAGQLAEITLMAAEEL 636

Query: 193 AQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPLQFDAAVDPGVAR 252
            +FGI P+VA++S+S   +       +  + LA  R   P+L VDG +  D A+DP +  
Sbjct: 637 KRFGIVPKVALMSHSNFGTSEAPSAQKMRETLAILRERAPDLEVDGEMHGDCALDPKLRD 696

Query: 253 KKMPDSDVAGQANVFIFPDLEAGNIGYKTAQ-RTGHALAVGPILQGLNKPVNDLSRGATV 311
             +PD  + G+AN+ + P+++A NI Y   +   G+ +A+GPIL G+  PV+ L+  ATV
Sbjct: 697 TLVPDGTLKGEANLLVCPNIDAANIAYNLLKVAAGNNVAIGPILLGVKAPVHILTPSATV 756

Query: 312 PDIVNTVAITAIQAGGR 328
             IVN  ++  + A  +
Sbjct: 757 RRIVNMTSLVVVDAAAK 773


Lambda     K      H
   0.318    0.134    0.386 

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: 598
Number of extensions: 39
Number of successful extensions: 4
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: 329
Length of database: 774
Length adjustment: 34
Effective length of query: 295
Effective length of database: 740
Effective search space:   218300
Effective search space used:   218300
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 (21.7 bits)
S2: 52 (24.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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