GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Acidovorax sp. GW101-3H11

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate Ac3H11_4331 NADP-dependent malic enzyme (EC 1.1.1.40)

Query= curated2:P39197
         (318 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4331
          Length = 781

 Score =  163 bits (412), Expect = 1e-44
 Identities = 126/334 (37%), Positives = 176/334 (52%), Gaps = 26/334 (7%)

Query: 1   MKPL-DRIHEAAKALDRHIILPEGEDPRVAEAARRLLAAGLARVTLMGGPEIPGAGRIDP 59
           MKP+ D    AAK   + +   EGE+ RV  AA+ ++   +AR TL+G P I  A RI+ 
Sbjct: 445 MKPIFDAARNAAK---KRVAYAEGEEERVLRAAQIVVDEKVARPTLIGRPAII-AQRIEK 500

Query: 60  AG-----GPDLAELA--------DHW---HRMRAARGMTAERALTEMRDPIRQ-AAMRVR 102
            G     G D   +         D W   HRM   +G+T + A  EMR  +    +M + 
Sbjct: 501 FGLRLKEGVDYDVVNTDFDHRYNDFWQTYHRMTERKGITQQVAKIEMRRRLTLIGSMMLH 560

Query: 103 LGQADGTVGGAVATTADTVRAALQIIGK-APGAGIVSSFFLMLSCGPGAPVRGGMIF-AD 160
            G+ DG + G   TTA+ +    Q+IGK A GA   +    + +C  G  + G  +F  D
Sbjct: 561 KGEVDGLICGTWGTTANHLLYIDQVIGKHAGGADSTAQDVPVYACMNGLMLPGRQVFLVD 620

Query: 161 CGLVIQPDARELAAIALSAADSCRRILAEEPRVALLSFSTAGSAEHPSLGRIREALALIR 220
             +   P  +ELA I   AA+   R    +P+ ALLS S  G++ HPS  ++R+ L L+R
Sbjct: 621 THVNYDPTPQELAEITALAAEEMMRF-GIKPKAALLSHSNFGTSNHPSAVKMRQTLELLR 679

Query: 221 AAAPGLEVDGEMQFDAALDEAIRARKAPESPLTGRPNVFVFPDLADGNIGYKIAERLA-G 279
             AP LEVDGEM  D ALD   RA   P S LTG  N+ VFP++   NI Y + +  A G
Sbjct: 680 QQAPWLEVDGEMHGDVALDGKARAALMPSSELTGDANLLVFPNIDAANIAYNLLKTAAGG 739

Query: 280 LTAIGPILQGLAKPANDLSRACSVKDIVNATAIT 313
             AIGP+L G AKP + L+ + +V+ IVN TA+T
Sbjct: 740 GIAIGPVLLGAAKPVHILTPSATVRRIVNMTALT 773


Lambda     K      H
   0.320    0.136    0.391 

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: 454
Number of extensions: 18
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: 318
Length of database: 781
Length adjustment: 34
Effective length of query: 284
Effective length of database: 747
Effective search space:   212148
Effective search space used:   212148
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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