GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Klebsiella michiganensis M5al

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate BWI76_RS23445 BWI76_RS23445 acetyl-CoA acetyltransferase

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



>FitnessBrowser__Koxy:BWI76_RS23445
          Length = 391

 Score =  242 bits (618), Expect = 1e-68
 Identities = 143/398 (35%), Positives = 222/398 (55%), Gaps = 22/398 (5%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           M + VIV   RTPIG  ++G L+      L    ++  V+R+G+DP+ +++V++G  +  
Sbjct: 1   MKDVVIVGALRTPIG-CFQGTLSRHSAVELGSVVVKALVERSGVDPQSIDEVILGQVLTA 59

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G TG N AR++ +R GLP T +  TI+  C SGL+A+ LA +++     ++ + GG E++
Sbjct: 60  G-TGQNPARQSAIRGGLPNTVSAITINDVCGSGLKALHLATQAIQCGEADVVIAGGQENM 118

Query: 121 SLVQN--------DKMNTFHAVDPALEAIKGDVY--MAMLDTAETVAKRYGISRERQDEY 170
           S   +         ++     +D  +     D +    M  TAE +A+ YGISRE QD +
Sbjct: 119 SRAPHVLTDSRTGAQLGNSQLIDSLVHDGLWDAFNDYHMGVTAENLAREYGISRELQDAW 178

Query: 171 SLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGL 230
           +L SQ +   A   G+F DEI P+++++  + +           +  DE PR + +AE L
Sbjct: 179 ALSSQHKARRAIDSGRFRDEIVPVTSELNGIPRL----------VDTDEQPRVDPSAEAL 228

Query: 231 AGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEM 290
           A L     +  ++TAGNAS ++DGA+A ++MS+  A A GL  L   R   S G +P  M
Sbjct: 229 ASLLPTFDQQGSVTAGNASSINDGAAAVMMMSETKAEALGLPILARIRAFASVGVDPALM 288

Query: 291 GIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGH 350
           GI PV A  R L+R G  +D++ L E NEAFA Q +     L  D  ++NVNGGAI++GH
Sbjct: 289 GIAPVHATRRCLERAGWKLDEVDLIEANEAFAAQAISVGRVLEWDERRVNVNGGAIALGH 348

Query: 351 PYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388
           P G SG R+    + E  +R A+  + T+C+GGG G A
Sbjct: 349 PIGASGCRILVSLVHEMIKRDARKGLATLCIGGGQGVA 386


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: 393
Number of extensions: 18
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: 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 ( 7.3 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