GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cup4G11:RR42_RS17610
          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 (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