GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Brevibacterium jeotgali SJ5-8

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_101588593.1 BJEO58_RS06055 thiolase family protein

Query= BRENDA::Q0K368
         (391 letters)



>NCBI__GCF_900169175.1:WP_101588593.1
          Length = 379

 Score =  407 bits (1047), Expect = e-118
 Identities = 222/392 (56%), Positives = 283/392 (72%), Gaps = 14/392 (3%)

Query: 1   MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60
           M +A IVAA RT  G++ G LSG HPADL+A VL+ LV+  G DPALVEDVI GCV+Q G
Sbjct: 1   MTDAVIVAARRTPTGKREGVLSGVHPADLSAHVLEDLVQTAGVDPALVEDVIWGCVTQAG 60

Query: 61  EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120
           EQ G++AR A L++  PE+V G +VDRQCGSSQQA+HFAA  ++SG  DIVIA GVESM+
Sbjct: 61  EQTGDIARTAALSAGFPETVTGVTVDRQCGSSQQAVHFAAAGIVSGQYDIVIAGGVESMS 120

Query: 121 RVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180
           R PMG SS    KN +G         RY GV+ +Q  GAEMIA K+ LSR Q+D  AL+S
Sbjct: 121 RNPMGSSSM--GKNPYG----DRFMERY-GVKPNQGVGAEMIAEKWGLSRSQVDDLALES 173

Query: 181 HQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVKLI-AEGGR 239
           H RA AAT SG F ++I PV+  T DG    + + DEG+R   T E +G +K +  E G 
Sbjct: 174 HARAAAATDSGAFESQITPVQ--TEDG----LVSADEGIRRGGTPEGLGKLKTVFKEDGI 227

Query: 240 VTAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVAL 299
           VTA ++SQI DG++ L++++    K+LG+KP+ARVH   + G DPV+ML AP+PAT+ AL
Sbjct: 228 VTAGNSSQISDGSSALLMMSSDRAKELGLKPIARVHTAVLAGTDPVIMLTAPIPATQKAL 287

Query: 300 KKAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMTT 359
           KK+GL + DI +FEVNEAFA VPLAW +  GAD A++N +GGAIA+GHPLGGSG++LMTT
Sbjct: 288 KKSGLSVDDIGVFEVNEAFATVPLAWQRELGADFAKVNPNGGAIAMGHPLGGSGSRLMTT 347

Query: 360 LVHALHTHGKRYGLQTMCEGGGLANVTIVERL 391
           +VH +  +G  YGLQTMCEGGG AN TI+E L
Sbjct: 348 MVHHMQNNGITYGLQTMCEGGGQANATILELL 379


Lambda     K      H
   0.317    0.132    0.379 

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: 458
Number of extensions: 14
Number of successful extensions: 4
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: 391
Length of database: 379
Length adjustment: 30
Effective length of query: 361
Effective length of database: 349
Effective search space:   125989
Effective search space used:   125989
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 24 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