GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Marinobacter adhaerens HP15

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate GFF3052 HP15_2996 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>FitnessBrowser__Marino:GFF3052
          Length = 398

 Score =  243 bits (619), Expect = 9e-69
 Identities = 145/398 (36%), Positives = 220/398 (55%), Gaps = 21/398 (5%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           M + VIV+  RT IG  + G L++     L    I+  ++  G+   ++ +VV+G  +  
Sbjct: 7   MRDVVIVAARRTAIG-TFGGGLSSLSADQLGTAVIKAILEETGVAGDQINEVVLGQVLTA 65

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G  G N AR++ + AG+P +    TI++ C SGL+A+ +A +++     E+ + GG ES+
Sbjct: 66  GC-GQNPARQSAINAGIPASVPAMTINKVCGSGLKAVHMAVQAIRCGDAEMMIAGGQESM 124

Query: 121 SLVQN--------DKMNTFHAVDPALEAIKGDVY--MAMLDTAETVAKRYGISRERQDEY 170
           S   +         +M  +  VD  ++    D +    M  TAE + ++YGISR+ QDE+
Sbjct: 125 SQAPHVLPNSRNGQRMGNWSMVDTMIKDGLWDAFNDYHMGITAENIVEKYGISRDEQDEF 184

Query: 171 SLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGL 230
           +  SQ++ AAA++ G F+ +I P+S      D          I + +DEGPR   TAEGL
Sbjct: 185 AAASQQKAAAAREAGYFDGQIVPVSIPQRKGDP---------IVVDRDEGPRDGVTAEGL 235

Query: 231 AGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEM 290
             L+A   +  T+TAGNAS L+DGA+A ++ S + A   GL P+   +   + G +P  M
Sbjct: 236 GKLRAAFKKDGTVTAGNASSLNDGAAAVMVCSAEKAEELGLTPIATIKAYANAGVDPTIM 295

Query: 291 GIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGH 350
           G GP+ A  R LK  G S +D+ L E NEAFA Q +     +G D  K+NVNGGAI++GH
Sbjct: 296 GTGPIPASQRCLKLAGWSTEDLDLVEANEAFAAQAISVNRDMGWDTGKVNVNGGAIALGH 355

Query: 351 PYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388
           P G SG R+    L E  RR     + T+C+GGGMG A
Sbjct: 356 PIGASGCRILVSLLHEMVRRDVHKGLATLCIGGGMGVA 393


Lambda     K      H
   0.316    0.134    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: 418
Number of extensions: 21
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: 398
Length adjustment: 31
Effective length of query: 364
Effective length of database: 367
Effective search space:   133588
Effective search space used:   133588
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 (21.6 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