GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Shewanella loihica PV-4

Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate 5209189 Shew_1667 acetyl-CoA acetyltransferase (RefSeq)

Query= reanno::pseudo3_N2E3:AO353_25685
         (397 letters)



>lcl|FitnessBrowser__PV4:5209189 Shew_1667 acetyl-CoA
           acetyltransferase (RefSeq)
          Length = 396

 Score =  476 bits (1226), Expect = e-139
 Identities = 242/391 (61%), Positives = 298/391 (76%), Gaps = 1/391 (0%)

Query: 4   SHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSA 63
           ++  IVIV+A RTPMGGFQG L S+ +P L A AI+  ++ AGV    V EVL GCVL A
Sbjct: 6   TNQEIVIVAAKRTPMGGFQGSLSSVPSPTLAATAIKGLMDAAGVQGGDVNEVLMGCVLPA 65

Query: 64  GLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMS 123
           GLGQAPARQA LGA L  S   TT+NK+CGSGM+  +LAHD++ AGSADVV+AGGMESMS
Sbjct: 66  GLGQAPARQATLGADLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSADVVIAGGMESMS 125

Query: 124 NAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEF 183
            APYLLD+AR G RMGHGKVLDHMFLDGLEDAY  G  MGTFA+  A+  G TREA D F
Sbjct: 126 QAPYLLDKARGGMRMGHGKVLDHMFLDGLEDAYTGGA-MGTFAQKTADDFGITREAMDNF 184

Query: 184 AIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGG 243
           A++S  +A  AI+ G+F AEIVP+ V   K   ++  DEQP  A+ +KI +L+PAF   G
Sbjct: 185 ALSSLQKANAAIESGAFKAEIVPVTVASRKGDLVVDTDEQPGNARPEKIPTLRPAFAKDG 244

Query: 244 TVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKL 303
           T+TAANSSSISDGAA L++M   EA KRGL+ LA I GH   +  P +F  APVGA+ KL
Sbjct: 245 TITAANSSSISDGAAVLMMMSADEASKRGLEVLATIKGHTTHSQEPSMFTTAPVGAMNKL 304

Query: 304 LKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILV 363
           L K  WS DEV+LFE+NEAFA+V+++ +++L +  +KVNV+GGACALGHPIG SGAR+LV
Sbjct: 305 LDKVNWSKDEVDLFEINEAFAMVTMLAISELGLDEAKVNVNGGACALGHPIGCSGARVLV 364

Query: 364 TLLSALRQKGLKRGVAAICIGGGEATAMAVE 394
           TL+ AL+ +GLKRGVA++CIGGGEATAMA+E
Sbjct: 365 TLIHALKARGLKRGVASLCIGGGEATAMAIE 395


Lambda     K      H
   0.318    0.133    0.378 

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: 509
Number of extensions: 16
Number of successful extensions: 2
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: 397
Length of database: 396
Length adjustment: 31
Effective length of query: 366
Effective length of database: 365
Effective search space:   133590
Effective search space used:   133590
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: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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