GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Marinobacter adhaerens HP15

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 GFF1030 HP15_1009 acyl-CoA thiolase

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



>FitnessBrowser__Marino:GFF1030
          Length = 397

 Score =  461 bits (1185), Expect = e-134
 Identities = 230/395 (58%), Positives = 303/395 (76%), Gaps = 1/395 (0%)

Query: 2   TMSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVL 61
           TMS++ +VI  + RTPMGG  G L S+ +P LGA +I+AA+ER+G+    V+EV+ GCVL
Sbjct: 4   TMSNNDVVIAGSARTPMGGMMGSLSSVRSPDLGAISIKAAIERSGLQPADVQEVIMGCVL 63

Query: 62  SAGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMES 121
            AGLGQAPARQA+  +G+  S+ CTT+NKMCGSGM+A I+AHD + AG+ ++++AGGME+
Sbjct: 64  PAGLGQAPARQASRASGIPDSSGCTTINKMCGSGMQAVIMAHDQIKAGTNNIMIAGGMEN 123

Query: 122 MSNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQD 181
           MS APYLL +AR G RMGHG+V+D MFLDGLEDAY+ G LMG FA+  A+    +R+A D
Sbjct: 124 MSQAPYLLPKARGGMRMGHGQVMDSMFLDGLEDAYEGG-LMGVFAQRTADKYDISRQAMD 182

Query: 182 EFAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRD 241
           EFAI S  ++  AI++G F  EIVP+ V        +  DEQP  AK +KI  LKPAF  
Sbjct: 183 EFAIGSLQKSLAAIENGWFRDEIVPVTVSGRGGDTEVDTDEQPGNAKPEKIPHLKPAFAK 242

Query: 242 GGTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIK 301
            G+VTAANSSSISDGA+AL+L   +EA+ RGL P A I  HA  A  P  F +AP+G+I+
Sbjct: 243 DGSVTAANSSSISDGASALVLASAAEADARGLTPQARIVAHATHARLPAEFTLAPIGSIE 302

Query: 302 KLLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARI 361
           K+LKK GWS+D+V+LFE+NEAFAVV+L  + +L++P  KVNVHGGACALGHPIG+SG+RI
Sbjct: 303 KVLKKAGWSVDDVDLFEINEAFAVVTLAAINELKLPADKVNVHGGACALGHPIGSSGSRI 362

Query: 362 LVTLLSALRQKGLKRGVAAICIGGGEATAMAVECL 396
           +VTL++AL+Q+GLKRGVA++CIGGGE TA+A+E +
Sbjct: 363 IVTLINALKQRGLKRGVASLCIGGGEGTAVAIELI 397


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: 479
Number of extensions: 17
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: 397
Length adjustment: 31
Effective length of query: 366
Effective length of database: 366
Effective search space:   133956
Effective search space used:   133956
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:

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