GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Azospirillum brasilense Sp245

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate AZOBR_RS21145 AZOBR_RS21145 NADP-dependent malic enzyme

Query= curated2:Q59330
         (328 letters)



>FitnessBrowser__azobra:AZOBR_RS21145
          Length = 772

 Score =  172 bits (437), Expect = 2e-47
 Identities = 109/332 (32%), Positives = 171/332 (51%), Gaps = 13/332 (3%)

Query: 3   IIQSIIEKAKSNKKKIVLPEGAEPRTLKAADIVLKEGIADLVLLGNADEIRN--AAEGLD 60
           +++ +I KAK+  K+IV  EG EPR L+ A +V+ +GIA  VLLG AD I    A  GL 
Sbjct: 429 VMKPVITKAKAAPKRIVYAEGEEPRVLRCAQVVVDDGIAHPVLLGRADVIERTIADMGLR 488

Query: 61  I---SKAEIIDPLKSEKFDKYATDFYELRKNKGITLEKAKETIKDN-IYFGCMMVKEGYA 116
           I      E+I+  +  +   YA  + +L   +G++   A   ++     FG +MV+ G A
Sbjct: 489 IRIGKDVEVIEAARDLRCHNYAEVYRQLMGRRGVSPANALNVVRTQPSVFGALMVRRGEA 548

Query: 117 DGLVSGAIHATADLLRPAFQIVKTAPGAKIVSSFFIMEVPNCEFGENGVFLFADCAVNPS 176
           DG+V G      D       ++    G K+  +       N    + G     D  VNP 
Sbjct: 549 DGMVCGTSGRYGDHFNHVMDVIGLRKGVKVAGAM------NGLISQKGTHFICDTYVNPD 602

Query: 177 PNAEELASIAVQSANTAKTLLGMEPRVAMLSFSTKGSASHELVDKVRTATEIAKNLIPDV 236
           P AE++A IA  +A   K   G+EP+VA+LS S  GSA      K+R A ++     PD+
Sbjct: 603 PTAEQVAEIARLAAEEVKRF-GIEPKVALLSHSNFGSADTPSARKMRLAYQLIAEENPDL 661

Query: 237 AIDGELQLDAALVKEVAELKAPGSPVAGRANVLIFPDLQAGNIGYKLVQRLAKANAIGPI 296
            +DGE+  DAAL + + +   P S + G AN+L+ P L A NI + +++ +A A  +GP+
Sbjct: 662 EVDGEMHADAALSEVLRKGVLPDSRLKGEANLLVMPTLDAANIAFNMLKIMADAQNVGPM 721

Query: 297 TQGMGAPVNDLSRGCSYKDIVDVIATTAVQAQ 328
             G   PV+ ++   + + +V++ A   V AQ
Sbjct: 722 LLGAARPVHIVTPSVTTRGLVNMTAVAVVDAQ 753


Lambda     K      H
   0.315    0.133    0.365 

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: 548
Number of extensions: 33
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: 328
Length of database: 772
Length adjustment: 34
Effective length of query: 294
Effective length of database: 738
Effective search space:   216972
Effective search space used:   216972
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 (21.6 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