GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Burkholderia phytofirmans PsJN

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate BPHYT_RS09150 BPHYT_RS09150 acetyl-CoA acetyltransferase

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



>FitnessBrowser__BFirm:BPHYT_RS09150
          Length = 393

 Score =  267 bits (683), Expect = 3e-76
 Identities = 161/398 (40%), Positives = 233/398 (58%), Gaps = 21/398 (5%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           MT+ VIVS ART +GK + G+L       L    I   ++RAG+ P++V +V++G  +  
Sbjct: 1   MTDVVIVSAARTAVGK-FGGSLAKIAAPELGATVIRAVLERAGLKPEQVSEVILGQVLTA 59

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G+ G N AR+A+++AGLP    G TI+  C SGL+A+ LAA +++    +I V GG E++
Sbjct: 60  GS-GQNPARQAVIKAGLPTAVPGMTINVVCGSGLKAVMLAANAIIAGDADIVVAGGQENM 118

Query: 121 SLVQND--------KMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEY 170
           S   +         +M     +D  +     DVY    M  TAE VAK YGI+RE+QD +
Sbjct: 119 SAAPHVLPGSRDGFRMGDAKLIDSMIVDGLWDVYNQYHMGVTAENVAKEYGITREQQDAF 178

Query: 171 SLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGL 230
           +  SQ +  AAQ+ G+F+DEI P+      + +  G    + +  + DE  R   TAE L
Sbjct: 179 AALSQNKAEAAQKAGRFDDEIVPVE-----IPQRKG----EPLRFATDEFVRHGVTAESL 229

Query: 231 AGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEM 290
           AGLK    +  ++TA NAS L+DGA+A ++MS K A A GLKPL   +   + G +P  M
Sbjct: 230 AGLKPAFSKEGSVTAANASGLNDGAAAVLVMSAKKAEALGLKPLARIKAYATSGLDPKVM 289

Query: 291 GIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGH 350
           G+GPV A  R L+R G +  D+ L E+NEAFA Q      ++G D  K+NVNGGAI++GH
Sbjct: 290 GMGPVPASRRCLERAGWTPADLDLMEINEAFAAQACAVNQQMGWDTSKINVNGGAIAIGH 349

Query: 351 PYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388
           P G SG R+    L E ++R AK  + ++C+GGGMG A
Sbjct: 350 PIGASGCRILVTLLHEMQKRDAKKGLASLCIGGGMGVA 387


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: 429
Number of extensions: 16
Number of successful extensions: 5
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 ( 7.3 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