GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Bacteroides clarus YIT 12056

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_009123269.1 BUB52_RS02120 NADP-dependent malic enzyme

Query= curated2:Q59330
         (328 letters)



>NCBI__GCF_900129655.1:WP_009123269.1
          Length = 762

 Score =  166 bits (420), Expect = 2e-45
 Identities = 106/332 (31%), Positives = 175/332 (52%), Gaps = 14/332 (4%)

Query: 3   IIQSIIEKAKSNKKKIVLPEGAEPRTLKAADIVLKEGIADLVLLGNADEIRNAAEGLDIS 62
           + + + + A+ N +++V  EG  P  LKAA     EGI   ++LGN + I   A+ LD+S
Sbjct: 429 LTRQLYDTARRNPQRVVFAEGIHPNMLKAAVEAKAEGICHPIILGNDEAIEKLAKELDLS 488

Query: 63  KA--EIID---PLKSEKFDKYATDFYELRKNKGITLEKAKETIKDNIYFGCMMVKEGYAD 117
               EI++   P +SE+ ++YA    E R  +G+T E+A + + +  YFG MMV+ G AD
Sbjct: 489 LEGIEIVNLRHPDESERRERYARILSEKRAREGVTYEEANDKMFERNYFGMMMVETGEAD 548

Query: 118 GLVSGAIHATADLLRPAFQIVKTAPGAKIVSSFFIMEVPNCEFGENGVFLFADCAVNPSP 177
             ++G     ++ ++ A +++   P  K   +  I+        + G +  AD  +N  P
Sbjct: 549 AFITGLYTKYSNTIKVAKEVIGIRPEYKHFGTMHILN------SKKGTYFLADTLINRHP 602

Query: 178 NAEELASIAVQSANTAKTLLGMEPRVAMLSFSTKGSASHELVDKVRTATEIAKNLIPDVA 237
           NAE L  IA  S  T +      P +AMLS+S  G+        V  A +  +   PD+A
Sbjct: 603 NAETLIDIAKLSEYTVR-FFNHTPVMAMLSYSNFGTDKEGSPVSVHEAVDYMQQNYPDLA 661

Query: 238 IDGELQLDAALVKEVAELKAPGSPVAGR-ANVLIFPDLQAGNIGYKLVQRL-AKANAIGP 295
           IDGE+Q++ A+ +E+ + K P + + G+  N LIFP+L + N  YKL+Q +   +  IGP
Sbjct: 662 IDGEMQVNFAMNRELRDAKYPFTRLKGKDVNTLIFPNLSSANSAYKLLQTMDMDSELIGP 721

Query: 296 ITQGMGAPVNDLSRGCSYKDIVDVIATTAVQA 327
           I  G+  P++      S +DIV++ A   + A
Sbjct: 722 IQMGLNKPIHFTDFESSVRDIVNITAVAVIDA 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: 520
Number of extensions: 24
Number of successful extensions: 5
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: 762
Length adjustment: 34
Effective length of query: 294
Effective length of database: 728
Effective search space:   214032
Effective search space used:   214032
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 24 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