GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pedobacter sp. GW460-11-11-14-LB5

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized)
to candidate CA265_RS06590 CA265_RS06590 acetyl-CoA acetyltransferase

Query= SwissProt::Q9UQW6
         (395 letters)



>FitnessBrowser__Pedo557:CA265_RS06590
          Length = 391

 Score =  446 bits (1147), Expect = e-130
 Identities = 232/391 (59%), Positives = 294/391 (75%), Gaps = 2/391 (0%)

Query: 5   EVYIVSAVRTPMGSFGGSFASLPATKLGSIAIKGALERVNIKPSDVDEVFMGNVVSANLG 64
           EV IVSAVRTP+GSFGGS A   AT+LG  AIK A+E+  +KP  + EV+MGNV+SANLG
Sbjct: 3   EVVIVSAVRTPIGSFGGSLAQFSATQLGGFAIKAAIEKAGLKPEQIQEVYMGNVLSANLG 62

Query: 65  QNPARQCALGAGLPRSIVCTTVNKVCASGMKATILGAQTIMTGNAEIVVAGGTESMSNAP 124
           Q PA Q A  AGLP  +  TT+NKVCASG KA +L AQ+I  G+ EI+VAGG ESMSN P
Sbjct: 63  QAPATQAAKFAGLP-DLPATTINKVCASGTKAIMLAAQSIANGDNEIIVAGGMESMSNVP 121

Query: 125 YYAPKNRFGAKYGNVELVDGLLRDGLSDAYDGLPMGNAAELCAEEHSIDRASQDAFAISS 184
           YY  K R G + G+ ++ DGL++DGL D Y+   MG+AAELCA E +I+R +QD FAISS
Sbjct: 122 YYLDKARNGYRLGHGQITDGLVKDGLWDVYNDYHMGSAAELCATECNINREAQDNFAISS 181

Query: 185 YKRAQNAQATKAFEQEIVPVEVPVGRGKPNKLVTEDEEPKNLNEDKLKSVRAVFKSNGTV 244
           YKRAQ AQ +  F  EIV +EV   +G    LV  D+EP  +  DK+ S++ VFK +GTV
Sbjct: 182 YKRAQAAQTSGKFANEIVAIEVKDRKGDIT-LVDTDDEPTAVKFDKIPSLKPVFKKDGTV 240

Query: 245 TAANASTLNDGASALVLMSAAKVKELGLKPLAKIIGWGEAAQDPERFTTSPSLAIPKALK 304
           TAANASTLNDGA+ALVLMSA K KELGL PLAKI+G+ +A Q PE FTT+PS AIP AL 
Sbjct: 241 TAANASTLNDGAAALVLMSADKAKELGLTPLAKILGYADAQQAPEWFTTAPSKAIPLALH 300

Query: 305 HAGIEASQVDYYEINEAFSVVAVANTKILGLDPERVNINGGGVAMGHPLGSSGSRIICTL 364
            A +  + VD++EINEAF+VV++AN ++L L+  +VN+NGG V++GHPLG+SG+RI+ TL
Sbjct: 301 KANVNINDVDFFEINEAFAVVSIANNQLLALNDNQVNVNGGAVSLGHPLGASGARIVVTL 360

Query: 365 AYILAQKDAKIGVAAVCNGGGGASSIVIERV 395
             +LAQ D KIGVA +CNGGGGAS++VI ++
Sbjct: 361 LSVLAQNDGKIGVAGICNGGGGASALVIGKL 391


Lambda     K      H
   0.313    0.130    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: 469
Number of extensions: 14
Number of successful extensions: 3
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: 395
Length of database: 391
Length adjustment: 31
Effective length of query: 364
Effective length of database: 360
Effective search space:   131040
Effective search space used:   131040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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:

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