GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Echinicola vietnamensis KMM 6221, DSM 17526

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized)
to candidate Echvi_3705 Echvi_3705 acetyl-CoA acetyltransferases

Query= SwissProt::Q9UQW6
         (395 letters)



>FitnessBrowser__Cola:Echvi_3705
          Length = 393

 Score =  461 bits (1186), Expect = e-134
 Identities = 233/391 (59%), Positives = 298/391 (76%), Gaps = 1/391 (0%)

Query: 5   EVYIVSAVRTPMGSFGGSFASLPATKLGSIAIKGALERVNIKPSDVDEVFMGNVVSANLG 64
           EVYI+SAVRTP+GSFGG  + L A +LG+ AIKGAL R  + P  VDEV MGNV+SANLG
Sbjct: 3   EVYIISAVRTPLGSFGGKLSGLTAVELGAQAIKGALGRAQVTPEQVDEVIMGNVLSANLG 62

Query: 65  QNPARQCALGAGLPRSIVCTTVNKVCASGMKATILGAQTIMTGNAEIVVAGGTESMSNAP 124
           Q PARQ A+GAG+   + CTTVNKVCASGMK+ +  AQ+IMTG ++I+VAGG ESMSN P
Sbjct: 63  QAPARQAAIGAGIGYHVPCTTVNKVCASGMKSVMFAAQSIMTGQSDIIVAGGMESMSNVP 122

Query: 125 YYAPKNRFGAKYGNVELVDGLLRDGLSDAYDGLPMGNAAELCAEEHSIDRASQDAFAISS 184
           YY PK RFG K+GN E VDGL +DGL + Y   PMGN A+  A+E +I R +QD +AI S
Sbjct: 123 YYIPKARFGYKFGNGEFVDGLAKDGLHEVYYNFPMGNCADNTAKEKNISREAQDEYAIQS 182

Query: 185 YKRAQNAQATKAFEQEIVPVEVPVGRGKPNKLVTEDEEPKNLNEDKLKSVRAVFKSNGTV 244
           Y+RA  A   +AF+ E++PV     +G+ +  V EDEE +N+  +K+ S+R VF   GTV
Sbjct: 183 YRRAAEAWKAQAFQDEVIPVTFKSRKGE-SITVDEDEEYQNVLFEKIPSLRPVFDKEGTV 241

Query: 245 TAANASTLNDGASALVLMSAAKVKELGLKPLAKIIGWGEAAQDPERFTTSPSLAIPKALK 304
           TAANAST+NDGA+ALVLMS  K + LGL+P+AKI+G+ +AA DP  FTT+P+LAIPKALK
Sbjct: 242 TAANASTMNDGAAALVLMSKEKAEALGLQPVAKILGFADAATDPIWFTTAPALAIPKALK 301

Query: 305 HAGIEASQVDYYEINEAFSVVAVANTKILGLDPERVNINGGGVAMGHPLGSSGSRIICTL 364
           +AGI+A  VDYYEINEAFS VA+AN + L +  +R+N+ GG V++GHPLG+SG+RI+ TL
Sbjct: 302 NAGIQAEAVDYYEINEAFSAVALANQQELNIPNDRLNVFGGAVSLGHPLGASGARIMATL 361

Query: 365 AYILAQKDAKIGVAAVCNGGGGASSIVIERV 395
             +L QK  KIGVA +CNGGGGAS++VIE +
Sbjct: 362 HSVLRQKGGKIGVAGICNGGGGASAMVIENL 392


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: 459
Number of extensions: 12
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: 395
Length of database: 393
Length adjustment: 31
Effective length of query: 364
Effective length of database: 362
Effective search space:   131768
Effective search space used:   131768
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