GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Klebsiella michiganensis M5al

Align Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate BWI76_RS23710 BWI76_RS23710 acetyl-CoA acetyltransferase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2411
         (393 letters)



>FitnessBrowser__Koxy:BWI76_RS23710
          Length = 396

 Score =  362 bits (929), Expect = e-104
 Identities = 196/389 (50%), Positives = 254/389 (65%), Gaps = 2/389 (0%)

Query: 5   EIYVVSAARTAIGTFGGSLKDVPLADLATTAVKAALERAAVDPALVGHLVMGNVIPTETR 64
           +I VVS  RTAIGTF GSLK     DL    ++ A+ RA + P  +   ++GNV      
Sbjct: 6   DIVVVSGVRTAIGTFNGSLKHTHQHDLGAAVIREAVNRAGLAPQDIDETIVGNVGQI-AE 64

Query: 65  DAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAESMSRG 124
             +I+R+  + AGIP+E+ AY+VNR CGSGLQA+ +    L  G A++VV  G E+M++ 
Sbjct: 65  SGFIARICQLRAGIPQESTAYSVNRQCGSGLQALADGMMQLQSGQAEVVVACGTENMTQL 124

Query: 125 PYLMPAARWGSRMGNAQVIDYMLGILHDPFHGIHMGITAENVAARNGITREMQDALAFED 184
           PY +  AR G RMG+ ++ D ++ IL  P    H GITAENVA R GITRE  D  A+  
Sbjct: 125 PYYLRKARDGYRMGHGELEDGLISILTWPEGPYHNGITAENVAQRFGITREAMDDFAWSS 184

Query: 185 QQRAAHAIANGYFSEQIATVEIQD-RKGVKLFSVDEHPRATSLEQLAAMKPAFKKDGSVT 243
           QQ+A  AIA   F EQI  +E+ D +K  +LF+ DEHPR T  E+LAA++PAFK DG VT
Sbjct: 185 QQKALKAIAEERFREQILALEVPDGKKATRLFATDEHPRDTPREKLAALRPAFKADGVVT 244

Query: 244 AGNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIPATRLALKR 303
           A N+SG+NDGAAALVM +    +   L P  R+  +A AG   E MG GP PATR  + R
Sbjct: 245 AANSSGINDGAAALVMMTRQQAEKRGLTPRMRIRGWAVAGCGAEIMGFGPSPATRRLMDR 304

Query: 304 AGLTVADLDVIEANIAFAAQACAVSQELDLDPAKVNPNGSGIALGHPVGATGAIIATKAI 363
             + V  +D+IE N AFAAQA AV  +L LDPA+VN NG  IALGHPVGA+GAI+  K +
Sbjct: 305 LNMDVHAIDLIELNEAFAAQALAVMNDLRLDPARVNVNGGAIALGHPVGASGAILPVKLM 364

Query: 364 HELHRTGGRYALVTMCIGGGQGIAAIFER 392
           +E+ R+G R  LVTMCIGGGQGI+ +FER
Sbjct: 365 YEMARSGARTGLVTMCIGGGQGISMLFER 393


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: 414
Number of extensions: 17
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: 393
Length of database: 396
Length adjustment: 31
Effective length of query: 362
Effective length of database: 365
Effective search space:   132130
Effective search space used:   132130
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