GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Paraburkholderia bryophila 376MFSha3.1

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate H281DRAFT_06308 H281DRAFT_06308 malate dehydrogenase (oxaloacetate-decarboxylating)(NADP+)

Query= SwissProt::P77844
         (329 letters)



>FitnessBrowser__Burk376:H281DRAFT_06308
          Length = 779

 Score =  178 bits (451), Expect = 5e-49
 Identities = 107/318 (33%), Positives = 174/318 (54%), Gaps = 9/318 (2%)

Query: 10  LLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGLHLNTA 69
           L +    E   IV  EG+++R+L A   ++D+ +    ++G P  I++R    GL L   
Sbjct: 455 LARGVEPEKKRIVFAEGEEERVLRAMQIIVDEKLAKPILIGRPAVIEQRIARYGLRLVAG 514

Query: 70  Y---LVNPLTDPRLEEFAEQFAELRKSKSVTIDEAR-EIMKDISYFGTMMVHNGDADGMV 125
               +VN   D R  +F +++ ++   K +T   A+ E+ +  +  G M+V  G+ADGM+
Sbjct: 515 QDYTVVNTDHDERYRDFWQEYYKMMSRKGITAQMAKLEMRRRTTLIGAMLVRKGEADGMI 574

Query: 126 SGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQLGEIA 185
            G  +TT   +    Q+I      +V +++  +VL  R     D  VN +PT EQL EI 
Sbjct: 575 CGTISTTHRHLHFIDQVIGKREGCAVYAAMNALVLPNRQIFLVDTHVNVDPTPEQLAEIT 634

Query: 186 VVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPLQFDAA 245
           +++A+   +FGI+P+VA++S+S   S       +  D LA  +   PEL VDG +  D A
Sbjct: 635 IMAAEEVRRFGIEPKVALVSHSNFGSSNAPTAQKMRDTLAILQERAPELQVDGEMHGDVA 694

Query: 246 VDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGY---KTAQRTGHALAVGPILQGLNKPV 302
           +D  + R+ +PDS + G AN+ + P+++A NI Y   KTA   G+ +A+GP+L G  KPV
Sbjct: 695 LDANLRREVLPDSTLEGDANLLVLPNIDAANISYNLLKTA--AGNNIAIGPMLLGAAKPV 752

Query: 303 NDLSRGATVPDIVNTVAI 320
           + L+  ATV  IVN  A+
Sbjct: 753 HVLTASATVRRIVNMTAL 770


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: 30
Number of successful extensions: 4
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: 329
Length of database: 779
Length adjustment: 34
Effective length of query: 295
Effective length of database: 745
Effective search space:   219775
Effective search space used:   219775
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