GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Herbaspirillum seropedicae SmR1

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate HSERO_RS16825 HSERO_RS16825 NADP-dependent malic enzyme oxidoreductase

Query= SwissProt::P77844
         (329 letters)



>FitnessBrowser__HerbieS:HSERO_RS16825
          Length = 770

 Score =  182 bits (462), Expect = 2e-50
 Identities = 107/321 (33%), Positives = 177/321 (55%), Gaps = 9/321 (2%)

Query: 12  KRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGLHLNTAY- 70
           K+A      IV  EG+++R+L A   ++D+++    ++G P  +++R  + GL L     
Sbjct: 448 KKAAEAKKRIVYAEGEEERVLRAVQVIVDENLAKPILVGRPEVLEQRIQKFGLRLRAGTD 507

Query: 71  --LVNPLTDPRLEEFAEQFAELRKSKSVTIDEAR-EIMKDISYFGTMMVHNGDADGMVSG 127
             ++NP  D R  ++ + F E+ + K VT   A+ E+ +  +  G+M +H GDADGM+ G
Sbjct: 508 FEVINPNFDNRYRDYWQTFLEMSRRKGVTEQYAKLEMRRRHTLIGSMAIHKGDADGMICG 567

Query: 128 AANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQLGEIAVV 187
              TT   +    Q++      +V +++  ++L  R     D  VN NP A +L EI ++
Sbjct: 568 TYGTTQLHLHYIDQVLGKREGVNVYAAMNAVILPNRQLVMVDTHVNENPNARELAEITML 627

Query: 188 SAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPLQFDAAVD 247
           +A+   +FG+ PR A+LS+S   S       +  +ALA  R + PEL VDG +  D A+D
Sbjct: 628 AAEEMRRFGLHPRAALLSHSNFGSSNSESARKMREALAILREIAPELEVDGEMHGDTALD 687

Query: 248 PGVARKKMPDSDVAGQANVFIFPDLEAGNIGY---KTAQRTGHALAVGPILQGLNKPVND 304
             +    +PDS + G AN+ + P+++A NI Y   KTA  +G+ +A+GPIL G  KPV+ 
Sbjct: 688 SKLLNAVIPDSPLKGDANLLVMPNIDAANIAYNLLKTA--SGNGVAIGPILLGCAKPVHI 745

Query: 305 LSRGATVPDIVNTVAITAIQA 325
           L+  ATV  I+N  A+  + A
Sbjct: 746 LTPSATVRRIINMTALCVMDA 766


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: 591
Number of extensions: 26
Number of successful extensions: 3
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: 770
Length adjustment: 34
Effective length of query: 295
Effective length of database: 736
Effective search space:   217120
Effective search space used:   217120
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